STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0004 DIPHTHERIA TOX REPRESSOR (C102D B DOUBLE HELIX OVERHANGING BASES N N N MUTANT)/TOX DNA OPERATOR COMPLEX PD0007 ANTENNAPEDIA HOMEODOMAIN (MUTANT B DOUBLE HELIX OVERHANGING BASES N N N C39S)/DNA COMPLEX PD0008 REVERBA ORPHAN NUCLEAR B DOUBLE HELIX n.a. Y N N RECEPTOR/DNA COMPLEX PD0016 ENGRAILED HOMEODOMAIN/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0020 SAP-1 ETS DOMAIN/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0022 CRO REPRESSOR/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0024 EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0025 ARC FV10 REPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0027 ERUM RESPONSE FACTOR ACCESSORY B DOUBLE HELIX n.a. N N N PROTEIN 1A (SAP-1)/DNA COMPLEX PD0028 TRANSCRIPTION FACTOR STAT3B/DNA B DOUBLE HELIX OVERHANGING BASES N N Y COMPLEX PD0035 WILD TYPE GENE-REGULATING PROTEIN B DOUBLE HELIX OVERHANGING BASES N N N ARC/DNA COMPLEX PD0042 ULTRABITHORAX HOMEOTIC PROTEIN B DOUBLE HELIX OVERHANGING BASE N N N IV/HOMEOBOX PROTEIN EXTRADENTICLE/DNA COMPLEX PD0045 TRANSCRIPTION FACTOR E2F-4 DP- B DOUBLE HELIX n.a. N N N 2/DNA TERNARY COMPLEX PD0046 ORPHAN NUCLEAR RECEPTOR NGFI-B/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0050 HOMEOBOX PROTEIN PAX-6/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0051 HIGH MOBILITY GROUP PROTEIN B DOUBLE HELIX n.a. N N N HMG1/DNA COMPLEX PD0056 PURINE NUCLEOTIDE SYNTHESIS B DOUBLE HELIX OVERHANGING BASES N N N REPRESSOR/DNA COMPLEX PD0057 PURINE NUCLEOTIDE SYNTHESIS B DOUBLE HELIX OVERHANGING BASES N N N REPRESSOR/DNA COMPLEX PD0058 PURINE NUCLEOTIDE SYNTHESIS B DOUBLE HELIX OVERHANGING BASES N N N REPRESSOR/DNA COMPLEX, HYPOXANTHINE PD0059 PURINE REPRESSOR/DNA COMPLEX, B DOUBLE HELIX OVERHANGING BASES N N N HYPOXANTHINE ----------------------------------------------------------------------------------------------------------------------------- Page 1 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0060 PURINE NUCLEOTIDE SYNTHESIS B DOUBLE HELIX OVERHANGING BASES N N N REPRESSOR/DNA COMPLEX PD0061 PURINE NUCLEOTIDE SYNTHESIS n.a. n.a. n.a. N N N REPRESSOR/DNA COMPLEX PD0069 DIPHTHERIA TOXIN REPRESSOR/DNA B DOUBLE HELIX n.a. N N Y COMPLEX PD0070 TATA-BINDING PROTEIN/TRANSCRIPTION B DOUBLE HELIX n.a. N N N INITIATION FACTOR IIB/DNA COMPLEX PD0071 PROTEIN RETINOIC ACID RECEPTOR RXR- B DOUBLE HELIX n.a. N N N ALPHA/DNA COMPLEX PD0073 HEAT SHOCK TRANSCRIPTION B DOUBLE HELIX n.a. N N N FACTOR/DNA COMPLEX PD0075 PBX1, HOMEOBOX PROTEIN HOX-B1/DNA B DOUBLE HELIX OVERHANGING BASES N N N TERNARY COMPLEX PD0076 INTERFERON REGULATORY FACTOR 2/DNA B DOUBLE HELIX FLIPPED-OUT BASES, Y N N COMPLEX OVERHANGING BASES PD0078 ROB TRANSCRIPTION FACTOR/DNA B DOUBLE HELIX OVERHANGING BASES N N N COMPLEX PD0088 PROTEIN (CHROMOSOMAL PROTEIN B DOUBLE HELIX n.a. N N N SSO7D)/DNA COMPLEX PD0089 PROTEIN (HEME ACTIVATOR B DOUBLE HELIX n.a. N N N PROTEIN)/DNA COMPLEX PD0090 HEME ACTIVATOR PROTEIN HAP1-18/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0091 TRANSCRIPTIONAL REPRESSOR COPG/DNA B DOUBLE HELIX OVERHANGING BASES N N N COMPLEX PD0092 POU DOMAIN, CLASS 2, TRANSCRIPTION B DOUBLE HELIX OVERHANGING BASES N N N FACTOR 1/POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1/DNA COMPLEX PD0102 TRANSCRIPTION FACTOR CREB/DNA B DOUBLE HELIX OVERHANGING BASES N N N COMPLEX PD0107 REPLICATION INITIATION PROTEIN/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0109 PURINE REPRESSOR/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0110 HIGH MOBILITY GROUP PROTEIN D/DNA RH DOUBLE HELIX FLIPPED-OUT BASES N N N COMPLEX PD0111 MHC CLASS II TRANSCRIPTION FACTOR B DOUBLE HELIX n.a. Y N N HRFX1/DNA COMPLEX PD0112 TATA-BOX BINDING PROTEIN, GENERAL B DOUBLE HELIX OVERHANGING BASES N N N TRANSCRIPTION FACTOR IIB/DNA COMPLEX ----------------------------------------------------------------------------------------------------------------------------- Page 2 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0114 ENGRAILED HOMEODOMAIN (MUTANT B DOUBLE HELIX OVERHANGING BASES N N N Q50A)/DNA COMPLEX PD0115 RETINOIC ACID RECEPTOR RXR ALPHA B DOUBLE HELIX n.a. N N N AND RAR ALPHA/DNA COMPLEX PD0116 ETS-DOMAIN PROTEIN ELK-1/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0118 LAC REPRESSOR/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0121 MADS BOX TRANSCRIPTION ENHANCER B DOUBLE HELIX OVERHANGING BASES N N N FACTOR 2, POLYPEPTIDE A/DNA COMPLEX PD0122 TETRACYCLINE REPRESSOR/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0142 DNA MISMATCH REPAIR PROTEIN B DOUBLE HELIX n.a. N N N MUTS/DNA COMPLEX PD0144 SINGLE-STRAND DNA-BINDING U SINGLE STRAND n.a. N N N PROTEIN/DNA COMPLEX PD0145 MULTIDRUG-EFFLUX TRANSPORTER B DOUBLE HELIX n.a. N N N REGULATOR/DNA COMPLEX PD0146 MULTIDRUG-EFFLUX TRANSPORTER B DOUBLE HELIX n.a. N N N REGULATOR/DNA COMPLEX PD0148 CYP1(HAP1-PC7) ACTIVATORY B DOUBLE HELIX OVERHANGING BASES N N N PROTEIN/DNA COMPLEX PD0154 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0155 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0156 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0157 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0158 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0159 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0160 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0161 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0162 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX ----------------------------------------------------------------------------------------------------------------------------- Page 3 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0163 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0164 TRANSCRIPTION INITIATION FACTOR B DOUBLE HELIX n.a. N N N TFIID-1/DNA COMPLEX PD0165 FUSION OF N-TERMINAL 17-MER B DOUBLE HELIX n.a. N N N PEPTIDE EXTENSION TO ZIF12/DNA COMPLEX PD0167 REPLICATION TERMINATION B DOUBLE HELIX n.a. N N N PROTEIN/DNA COMPLEX PD0170 DIPHTHERIA TOXIN REPRESSOR/DNA B DOUBLE HELIX OVERHANGING BASES N N N COMPLEX PD0173 METHIONINE REPRESSOR MUTANT B DOUBLE HELIX OVERHANGING BASES N N N (Q44K)/ DNA COMPLEX PD0180 TRANSCRIPTION FACTOR PAP1/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0181 DNA MISMATCH REPAIR PROTEIN B DOUBLE HELIX n.a. N N N MUTS/DNA COMPLEX PD0182 HEAT SHOCK FACTOR PROTEIN/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0183 HEAT SHOCK FACTOR PROTEIN/DNA B DOUBLE HELIX n.a. Y N N COMPLEX PD0184 HEAT SHOCK FACTOR PROTEIN/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0185 STAPHYLOCOCCAL ACCESSORY REGULATOR B DOUBLE HELIX n.a. N N Y A, 5'-D(P*AP*TP*AP*TP*AP*TP*A)-3' PD0186 TATA BOX ZINC FINGER PROTEIN/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0187 TATA BOX ZINC FINGER PROTEIN/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0191 ORPHAN NUCLEAR RECEPTOR REV- B DOUBLE HELIX n.a. N N N ERB(ALPHA)/DNA COMPLEX PD0193 ORPHAN NUCLEAR RECEPTOR REV- B DOUBLE HELIX n.a. N N N ERB(ALPHA)/DNA COMPLEX PD0198 CAAT/ENHANCER BINDING PROTEIN B DOUBLE HELIX n.a. N N N BETA/DNA COMPLEX PD0199 FATTY ACID METABOLISM REGULATOR B DOUBLE HELIX FLIPPED-OUT BASE N N N PROTEIN/DNA COMPLEX PD0201 DNA MISMATCH REPAIR PROTEIN B DOUBLE HELIX n.a. N N Y MUTS/DNA Complex PD0204 CAAT/ENHANCER BINDING PROTEIN B DOUBLE HELIX n.a. N N N BETA/DNA COMPLEX ----------------------------------------------------------------------------------------------------------------------------- Page 4 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0205 RUNT-RELATED TRANSCRIPTION FACTOR B DOUBLE HELIX n.a. N N N 1/DNA Complex PD0208 HEPATOCYTE NUCLEAR FACTOR 1- B DOUBLE HELIX n.a. N N N ALPHA/DNA Complex PD0210 CORE-BINDING FACTOR ALPHA B DOUBLE HELIX n.a. N N N SUBUNIT1, CORE-BINDING FACTOR CBF- BETA/DNA Complex PD0211 HOMEOTIC PROTEIN MSX-1/DNA Complex B DOUBLE HELIX OVERHANGING BASES N N N PD0214 TonEBP/DNA Complex B DOUBLE HELIX OVERHANGING BASES N N N PD0219 NARL/DNA Complex B DOUBLE HELIX n.a. N N N PD0221 NC2/TBP/DNA Complex B DOUBLE HELIX n.a. N N N PD0222 C-REL PROTO-ONCOGENE PROTEIN/DNA B DOUBLE HELIX n.a. N N N Complex PD0223 PURINE NUCLEOTIDE SYNTHESIS B DOUBLE HELIX n.a. N N N REPRESSOR/DNA Complex PD0224 PURINE NUCLEOTIDE SYNTHESIS B DOUBLE HELIX n.a. N N N REPRESSOR/DNA Complex PD0225 OCTAMER-BINDING TRANSCRIPTION B DOUBLE HELIX n.a. N N N FACTOR 1/DNA Complex PD0226 PURINE NUCLEOTIDE SYNTHESIS B DOUBLE HELIX n.a. N N N REPRESSOR/DNA Complex PD0227 REGULATORY PROTEIN E2/DNA Complex B DOUBLE HELIX n.a. N N N PD0230 ZIF268/DNA Complex B DOUBLE HELIX OVERHANGING BASES N N N PD0231 ZIF268/DNA Complex B DOUBLE HELIX OVERHANGING BASES N N N PD0232 FATTY ACID METABOLISM REGULATOR B DOUBLE HELIX n.a. N N N PROTEIN/DNA Complex PD0233 SERUM RESPONSE FACTOR, ETS-DOMAIN B DOUBLE HELIX OVERHANGING BASES N N N PROTEIN ELK-4/DNA Complex PD0241 PROTO-ONCOGENE C-JUN/DNA Complex B DOUBLE HELIX n.a. N N N PD0243 SMAD3/DNA Complex B DOUBLE HELIX n.a. N N N PD0245 METHIONINE REPRESSOR/DNA Complex B DOUBLE HELIX n.a. N N N ----------------------------------------------------------------------------------------------------------------------------- Page 5 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0246 METHIONINE REPRESSOR/DNA Complex B DOUBLE HELIX n.a. N N N PD0247 METHIONINE REPRESSOR/DNA Complex B DOUBLE HELIX n.a. N N N PD0248 METHIONINE REPRESSOR/DNA Complex B DOUBLE HELIX n.a. N N N PD0249 HYPOTHETICAL TRANSCRIPTIONAL B DOUBLE HELIX n.a. N N N REGULATOR IN QACA 5'REGION/DNA Complex PD0250 LACTOSE OPERON REPRESSOR/DNA B DOUBLE HELIX n.a. N N N Complex PD0257 MATING-TYPE PROTEIN ALPHA-2/DNA B DOUBLE HELIX n.a. Y N N Complex PD0258 ETS-domain protein ELK-4/Serum B DOUBLE HELIX n.a. N N N response factor/DNA Complex PD0259 PAIRED BOX PROTEIN PAX5/C-ETS-1 B DOUBLE HELIX n.a. N N N PROTEIN/DNA COMPLEX PD0260 C-ETS-1 PROTEIN/DNA Complex B DOUBLE HELIX n.a. N N Y PD0261 C-ETS-1 PROTEIN/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0268 VITAMIN D3 RECEPTOR/DNA Complex B DOUBLE HELIX n.a. N N N PD0269 VITAMIN D3 RECEPTOR/DNA Complex B DOUBLE HELIX n.a. N N N PD0270 VITAMIN D3 RECEPTOR/DNA Complex B DOUBLE HELIX n.a. N N N PD0274 OCTAMER-BINDING TRANSCRIPTION B DOUBLE HELIX n.a. N N N FACTOR 1/DNA Complex PD0282 REPLICATION PROTEIN E1/DNA Complex B DOUBLE HELIX n.a. N N N PD0283 REPLICATION PROTEIN E1/DNA Complex B DOUBLE HELIX n.a. N N N PD0284 SIGMA FACTOR SIGA/DNA Complex B DOUBLE HELIX n.a. N N N PD0288 CAAT/ENHANCER BINDING PROTEIN B DOUBLE HELIX n.a. N N N BETA/MYB PROTO-ONCOGENE PROTEIN/DNA COMPLEX PD0289 CAAT/ENHANCER BINDING PROTEIN B DOUBLE HELIX n.a. N N N BETA/MYB PROTO-ONCOGENE PROTEIN/DNA Complex PD0290 CAAT/ENHANCER BINDING PROTEIN n.a. n.a. n.a. N N N BETA/MYB TRANSFORMING PROTEIN/DNA Complex ----------------------------------------------------------------------------------------------------------------------------- Page 6 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0297 SEQA PROTEIN/DNA Complex B DOUBLE HELIX n.a. N N N PD0298 Transcriptional activator protein B DOUBLE HELIX n.a. N N N traR/DNA Complex PD0299 CATABOLITE GENE ACTIVATOR PROTEIN B DOUBLE HELIX OVERHANGING BASE, N N Y (CAP)/DNA Complex, ADENOSINE-3',5'- KINKED CYCLIC-MONOPHOSPHATE PD0305 RNA polymerase Holoenzyme/DNA B DOUBLE HELIX n.a. N N N PD0306 CATABOLITE GENE ACTIVATOR B DOUBLE HELIX OVERHANGING BASES N N N PROTEIN/DNA-directed RNA polymerase alpha chain (E.C.2.7.7.6)/DNA Complex, ADENOSINE-3',5'-CYCLIC- MONOPHOSPHATE PD0307 Nuclear factor NF-kappa-B p65 B DOUBLE HELIX OVERHANGING BASE N N Y subunit/Nuclear factor NF-kappa-B p50 subunit/DNA Complex PD0308 MATING-TYPE PROTEIN A-1, Mating- B DOUBLE HELIX OVERHANGING BASES N N N type protein alpha-2/DNA Complex PD0309 NUCLEAR FACTOR NF-KAPPA-B P65 B DOUBLE HELIX OVERHANGING BASE N N Y SUBUNIT/NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT/DNA Complex PD0310 NUCLEAR FACTOR NF-KAPPA-B P65 B DOUBLE HELIX OVERHANGING BASE N N N SUBUNIT/NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT/DNA Complex PD0311 T-BOX TRANSCRIPTION FACTOR B DOUBLE HELIX OVERHANGING BASES N N N TBX3/DNA Complex PD0312 Zif23-GCN4 Chimera/DNA Complex B DOUBLE HELIX n.a. N N N PD0314 Stage 0 sporulation protein A/DNA B DOUBLE HELIX n.a. N N N PD0315 SeqA protein/DNA Complex B DOUBLE HELIX n.a. Y N N PD0338 PAIRED BOX PROTEIN PAX-5, C-ETS-1 B DOUBLE HELIX n.a. N N N PROTEIN/DNA Complex PD0339 DELETED IN SPLIT HAND/SPLIT FOOT U SINGLE STRAND n.a. N N N PROTEIN 1/BREAST CANCER TYPE 2 SUSCEPTIBILITY PROTEIN/DNA Complex PD0341 Ndt80 protein/DNA Complex B DOUBLE HELIX n.a. N N N PD0363 Myocyte-specific enhancer factor B DOUBLE HELIX n.a. N N N 2B/Calcineurin-binding protein Cabin 1/DNA complex PD0368 Transcription initiation factor B DOUBLE HELIX n.a. N N Y TFIID/Transcription factor IIIB 70 kDa subunit/DNA PD0369 Transcription initiation factor B DOUBLE HELIX n.a. N N Y TFIID, Transcription initiation factor IIA large chain, Transcription initiation factor IIA small chain/DNA Complex PD0371 Chromosomal replication initiator B DOUBLE HELIX n.a. N N N protein dnaA/DNA ----------------------------------------------------------------------------------------------------------------------------- Page 7 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0386 Myc proto-oncogene protein/Max B DOUBLE HELIX OVERHANGING BASE N N N protein/DNA PD0387 MAD PROTEIN/MAX PROTEIN/DNA B DOUBLE HELIX n.a. N N N PD0388 DNA Mismatch Repair protein B DOUBLE HELIX n.a. N N Y MutS/DNA PD0393 TATA box binding protein, B DOUBLE HELIX n.a. N N N Transcription initiation factor IIA alpha and beta chains, Transcription initiation factor IIA gamma chain/DNA Complex PD0395 CCAAT/enhancer binding protein B DOUBLE HELIX OVERHANGING BASES N N N alpha/DNA PD0398 CATABOLITE GENE ACTIVATOR B DOUBLE HELIX OVERHANGING BASES N N N PROTEIN/DNA COMPLEX PD0399 CATABOLITE GENE ACTIVATOR B DOUBLE HELIX OVERHANGING BASES N N N PROTEIN/DNA COMPLEX PD0400 CATABOLITE GENE ACTIVATOR B DOUBLE HELIX OVERHANGING BASES N N N PROTEIN/DNA COMPLEX PD0401 CATABOLITE GENE ACTIVATOR B DOUBLE HELIX OVERHANGING BASES N N Y PROTEIN/DNA COMPLEX PD0405 Integration Host Factor Alpha- B DOUBLE HELIX OVERHANGING BASES, N N N subunit/Integration Host Factor DNA BENDING Beta-subunit/DNA (35-MER)/5'- D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP *CP*AP*TP*T)-3'/5'- D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP *TP*GP*TP*AP*GP*CP*AP*CP*C)-3' PD0406 Integration Host Factor Alpha- B DOUBLE HELIX OVERHANGING BASES, N N N subunit/Integration Host Factor DNA BENDING Beta-subunit/Phage lambda H' site/5'- D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP *CP*AP*TP*T)-3'/5'- D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP *TP*GP*TP*TP*GP*CP*AP*CP*C)-3' PD0407 Integration Host Factor Alpha- B DOUBLE HELIX OVERHANGING BASES, N N N subunit/Integration Host Factor DNA BENDING Beta-subunit/DNA (35-MER)/5'- D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP *CP*AP*TP*T)-3'/5'- D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP *TP*GP*TP*AP*GP*CP*AP*CP*C)-3' PD0408 Nuclear factor of activated T- B DOUBLE HELIX OVERHANGING BASES N N N cells, cytoplasmic 2/DNA PD0409 SMAD 3/Smad binding element B DOUBLE HELIX n.a. N N N PD0424 Early growth response protein B DOUBLE HELIX OVERHANGING BASES N N N 1/DNA Complex PD0429 NUCLEAR FACTOR OF ACTIVATED T- B DOUBLE HELIX OVERHANGING BASES N N N CELLS, CYTOPLASMIC 2/DNA Complex PD0452 39 kDa initiator binding B DOUBLE HELIX OVERHANGING BASES N N N protein/FERREDOXIN INR Complex PD0453 39 kDa initiator binding B DOUBLE HELIX OVERHANGING BASES N N N protein/ALPHA-SCS INR Complex PD0455 Homeobox protein Hox-A9, Pre-B- B DOUBLE HELIX OVERHANGING BASES N N N cell leukemia transcription factor- 1/DNA Complex PD0456 Transcription termination factor U SINGLE STRAND n.a. N N N rho/DNA Complex ----------------------------------------------------------------------------------------------------------------------------- Page 8 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PD0464 Nuclear factor of activated T- B DOUBLE HELIX OVERHANGING BASES N N N cells, cytoplasmic 2/DNA Complex PD0470 Retinoic acid receptor RXR- B DOUBLE HELIX OVERHANGING BASES N N N alpha/Ecdysone receptor/DNA Complex PD0471 Ultraspiracle protein/Ecdysone B DOUBLE HELIX OVERHANGING BASES N N N receptor/DNA Complex PD0475 Glucocorticoid receptor/DNA Complex B DOUBLE HELIX OVERHANGING BASES N N N PD0476 Glucocorticoid receptor/DNA Complex B DOUBLE HELIX OVERHANGING BASES N N Y PD0480 Transcriptional repressor protein B DOUBLE HELIX n.a. N N N korB/DNA Complex PD0492 sigma factor SigA/Repressor B DOUBLE HELIX n.a. N N N protein CI/DNA Complex PD0495 5'- B DOUBLE HELIX INTERNAL LOOP, N N N D(AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP FLIPPED-OUT BASE, *C)-3'/5'- OVERHANGING BASE D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T) -3'/MutY PD0496 5'- B DOUBLE HELIX INTERNAL LOOP, N N N D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*A OVERHANGING BASE P*C)-3'/5'- D(*TP*GP*TP*CP*CP*AP*(HPD)P*GP*TP*C P*T)-3'/MutY PD0497 5'- B DOUBLE HELIX INTERNAL LOOP, N N N D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*A OVERHANGING BASE P*C)-3'/5'- D(*TP*GP*TP*CP*CP*AP*(HPD)P*GP*TP*C P*T)-3'/MutY PD0506 Rep PROTEIN/DNA Complex B DOUBLE HELIX n.a. N N N PDE025 SEGMENTATION PROTEIN PAIRED/DNA B DOUBLE HELIX OVERHANGING BASES N N N COMPLEX PDO001 REPLICATION PROTEIN A/DNA COMPLEX U SINGLE STRAND n.a. N N N PDR001 434 CRO/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR002 434 CRO/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDR003 LAMBDA CRO/DNA COMPLEX B DOUBLE HELIX KINKED N N N PDR004 434 REPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR005 434 CRO/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDR006 CATABOLITE GENE ACTIVATOR PROTEIN B DOUBLE HELIX OVERHANGING BASE N N N (CAP)/DNA COMPLEX + ADENOSINE- 3',5'-CYCLIC-MONOPHOSPHATE PDR008 MET REPRESSOR/DNA COMPLEX + S- B DOUBLE HELIX OVERHANGING BASE N N N ADENOSYL-METHIONINE ----------------------------------------------------------------------------------------------------------------------------- Page 9 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PDR009 TRP REPRESSOR/DNA COMPLEX + B DOUBLE HELIX OVERHANGING BASES N N Y TRYPTOPHAN PDR010 LAMBDA REPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR011 434 REPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR012 ARC REPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR013 TRP REPRESSOR/DNA COMPLEX + B DOUBLE HELIX OVERHANGING BASES N N N TRYPTOPHAN PDR015 434 REPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR016 LAMBDA REPRESSOR (TRIPLE B DOUBLE HELIX OVERHANGING BASE N N N MUTANT)/DNA COMPLEX PDR018 PRD PAIRED/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR020 PURINE REPRESSOR/DNA COMPLEX + B DOUBLE HELIX OVERHANGING BASE N N N HYPOXANTHINE 1 PDR021 RETINOIC ACID RECEPTOR, THYROID B DOUBLE HELIX n.a. Y N N HORMONE RECEPTOR/DNA COMPLEX PDR022 P53 TUMOR SUPPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR024 CATABOLITE GENE ACTIVATOR PROTEIN B DOUBLE HELIX OVERHANGING BASE, N N N (CAP)/DNA COMPLEX + ADENOSINE- KINKED 3',5'-CYCLIC-MONOPHOSPHATE PDR025 CATABOLITE GENE ACTIVATOR PROTEIN B DOUBLE HELIX OVERHANGING BASE, N N N (CAP) MUTANT/DNA COMPLEX + KINKED ADENOSINE-3',5'-CYCLIC- MONOPHOSPHATE PDR026 LACTOSE OPERON REPRESSOR/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDR027 P53 TUMOR SUPPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDR028 PURINE REPRESSOR MUTANT/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX + HYPOXANTHINE 1 PDR029 PURINE REPRESSOR/DNA COMPLEX + B DOUBLE HELIX OVERHANGING BASE N N N HYPOXANTHINE 1 PDR030 PURINE REPRESSOR/DNA COMPLEX + RH DOUBLE HELIX OVERHANGING BASE N N N GUANINE PDR031 TATA-BINDING PROTEIN, RH DOUBLE HELIX n.a. Y N N TRANSCRIPTION INITIATION FACTOR IIB/DNA COMPLEX PDR032 HUMAN NF-KAPPA-B P52 BOUND TO DNA B DOUBLE HELIX n.a. N N N ----------------------------------------------------------------------------------------------------------------------------- Page 10 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PDR033 NF-KAPPA B P65 AND P50 B DOUBLE HELIX OVERHANGING BASES N N N SUBUNITS/DNA COMPLEX PDR034 PIT-1 MUTANT/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDR035 INTERFERON REGULATORY FACTOR 1/DNA B DOUBLE HELIX n.a. N N N COMPLEX PDR036 MCM1 TRANSCRIPTIONAL REGULATOR, B DOUBLE HELIX OVERHANGING BASE N N N MAT ALPHA-2 TRANSCRIPTIONAL REPRESSOR/DNA COMPLEX PDR040 PURINE REPRESSOR/CO-REPRESSOR/DNA B DOUBLE HELIX DNA KINKED 45 N N N COMPLEX DEGREES. PDR041 PURINE REPRESSOR/CO-REPRESSOR/DNA B DOUBLE HELIX THE DNA IS KINKED N N N COMPELX 45 DEGREES AT THE CENTER PDR042 PURINE REPRESSOR/DNA COMPLEX, B DOUBLE HELIX DNA IS KINKED 45 N N N GUANINE DEGREE AT THE CENTER PDR043 PURINE REPRESSOR/DNA COMPLEX, B DOUBLE HELIX THE DNA IS KINKED N N N ADENINE 45 DEGREES AT THE CENTER PDR044 PURINE REPRESSOR/DNA COMPLEX, B DOUBLE HELIX THE DNA IS KINKED N N N GUANINE 45 DEGREES AT THE CENTER PDR045 PURINE REPRESSOR/DNA COMPLEX, B DOUBLE HELIX THE DNA IS KINKED N N N HYPOXANTHINE 45 DEGREES AT THE CENTER PDR046 PURINE REPRESSOR/DNA COMPLEX, B DOUBLE HELIX THE DNA IS KINKED N N N HYPOXANTHINE 45 DEGREES AT THE CENTER PDR049 MAT A1/ALPHA2/DNA TERNARY COMPLEX B DOUBLE HELIX DNA IS BENT N N N PDR050 TRANSCRIPTION FACTOR NF-KB P65/DNA B DOUBLE HELIX THE DNA IS BENT 25 N N N COMPLEX DEGREES PDR051 TRANSCRIPTION FACTOR NF-KB P65/DNA B DOUBLE HELIX n.a. Y N N COMPLEX PDR052 TYROSINE PHOSPHORYLATED STAT-1/DNA B DOUBLE HELIX n.a. N N N COMPLEX PDR053 LAMBDA-CRO REPRESSOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PDR056 MULTIPLE ANTIBIOTIC RESISTANCE B DOUBLE HELIX OVERHANGING BASES N N N PROTEIN/DNA COMPLEX PDRC01 GLUCOCORTICOID RECEPTOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDRC03 ESTROGEN RECEPTOR/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT002 GCN4/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N ----------------------------------------------------------------------------------------------------------------------------- Page 11 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PDT003 GAL4/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDT004 ENGRAILED HOMEODOMAIN/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT005 MAT-ALPHA2 HOMEODOMAIN/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT006 ZIF268/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT007 GCN4/DNA COMPLEX RH DOUBLE HELIX OVERHANGING BASE N N N PDT008 FIVE-FINGER GLI/DNA COMPLEX RH DOUBLE HELIX OVERHANGING BASE N N N PDT009 TATA BINDING PROTEIN (TBP)/DNA RH DOUBLE HELIX KINKED N N N COMPLEX PDT011 TRAMTRACK DNA-BINDING DOMAIN/DNA RH DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDT012 TATA BINDING PROTEIN (TBP)/DNA RH DOUBLE HELIX KINKED, BUCKLED, N N N COMPLEX HAIRPIN LOOP PDT013 HNF-3/FORK HEAD DNA-RECOGNITION B DOUBLE HELIX n.a. N N N MOTIF/DNA COMPLEX PDT014 C-FOS:C-JUN PROTO-ONCOGENE B DOUBLE HELIX OVERHANGING BASE N N N PROTEIN/DNA COMPLEX PDT015 NUCLEAR FACTOR KAPPA-B (NF-KB)/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDT016 MYOD BHLH DOMAIN/DNA COMPLEX B DOUBLE HELIX BUCKLED N N N PDT017 PYRIMIDINE PATHWAY REGULATOR 1/DNA B DOUBLE HELIX n.a. N N N COMPLEX PDT019 OCT-1 POU DOMAIN/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT020 TRANSCRIPTION FACTOR E47 (TF E47) B DOUBLE HELIX OVERHANGING BASE N N N PDT021 SERUM RESPONSE FACTOR (SRF)/DNA B DOUBLE HELIX OVERHANGING BASE Y N N COMPLEX PDT022 NUCLEAR FACTOR KAPPA-B (NF-KB) B DOUBLE HELIX OVERHANGING BASE N N Y MUTANT/DNA COMPLEX PDT023 TRANSCRIPTION FACTOR MAX (TF B DOUBLE HELIX n.a. N N N MAX)/DNA COMPLEX PDT024 TATA BINDING PROTEIN (TBP)/DNA RH DOUBLE HELIX n.a. N N N COMPLEX ----------------------------------------------------------------------------------------------------------------------------- Page 12 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PDT025 TATA BINDING PROTEIN (TBP)/DNA RH DOUBLE HELIX KINKED N N N COMPLEX PDT027 UPSTREAM STIMULATORY FACTOR/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDT028 MAT A1 HOMEODOMAIN, MAT ALPHA2 B DOUBLE HELIX OVERHANGING BASE N N N HOMEODOMAIN/DNA COMPLEX PDT029 GCN4/DNA COMPLEX RH DOUBLE HELIX OVERHANGING BASE N N N PDT030 GLUCOCORTICOID RECEPTOR MUTANT/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDT031 EVEN-SKIPPED HOMEODOMAIN/DNA B DOUBLE HELIX n.a. N N N Complex PDT032 TRANSCRIPTION FACTOR IIB (TFIIB), B DOUBLE HELIX n.a. N N N TATA BINDING PROTEIN (TBP)/DNA COMPLEX PDT033 TRANSCRIPTION FACTOR PU.1 (TF B DOUBLE HELIX OVERHANGING BASE N N N PU.1)/DNA COMPLEX PDT034 TATA BINDING PROTEIN (TBP)/DNA RH DOUBLE HELIX KINKED N N N COMPLEX PDT035 RAP1/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT036 TATA BINDING PROTEIN (TBP), RH DOUBLE HELIX n.a. N N N TRANSCRIPTION FACTOR IIA (TFIIA)/DNA COMPLEX PDT037 TATA BINDING PROTEIN (TBP), RH DOUBLE HELIX n.a. N N N TRANSCRIPTION FACTOR IIA (TFIIA) PDT038 YY1 ZINC FINGER DOMAIN MUTANT/DNA B DOUBLE HELIX n.a. N N N COMPLEX PDT039 ZIF268 ZINC FINGER PEPTIDE/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDT040 INTEGRATION HOST FACTOR/DNA COMPLEX RH DOUBLE HELIX OVERHANGING BASE, N N N KINKED PDT042 MAX/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDT043 ENGRAILED HOMEODOMAIN Q50K B DOUBLE HELIX OVERHANGING BASE N N N VARIANT/DNA COMPLEX PDT044 PROLINE UTILIZATION TRANSCRIPTION B DOUBLE HELIX OVERHANGING BASES Y N N ACTIVATOR (PUT3)/DNA COMPLEX PDT045 T DOMAIN/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDT046 PHOSPHATE SYSTEM POSITIVE B DOUBLE HELIX n.a. N N N REGULATORY PROTEIN PHO4/DNA COMPLEX ----------------------------------------------------------------------------------------------------------------------------- Page 13 created by the NDB Project on Wed May 26 14:33:25 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (REGULATORY) ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- PDT048 GA BINDING PROTEIN ALPHA, GA B DOUBLE HELIX OVERHANGING BASE Y N N BINDING PROTEIN BETA 1/DNA COMPLEX PDT049 CATABOLITE GENE ACTIVATOR B DOUBLE HELIX THE DNA IS KINKED N N N PROTEIN/DNA COMPLEX, ADENOSINE- 90 DEGREES, 3',5'-CYCLIC-MONOPHOSPHATE OVERHANGING BASE PDT050 TERNARY PROTEIN-DNA COMPLEX (NFAT- B DOUBLE HELIX OVERHANGING BASES N N N FOS-JUN/DNA) PDT055 THREE-FINGER ZIF268 PEPTIDE/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDT056 THREE-FINGER ZIF268 PEPTIDE/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDT057 QGSR (THREE-FINGER ZIF268 B DOUBLE HELIX OVERHANGING BASE N N N VARIANT)/DNA COMPLEX PDT058 RADR (ZIF268 VARIANT)/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT059 ZINC FINGER/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT060 ZINC FINGER/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT061 ZINC FINGER/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDT062 STEROL REGULATORY ELEMENT B DOUBLE HELIX n.a. N N N BINDING(STRE)/DNA COMPLEX PDT063 PURINE REPRESSOR MUTANT L54M/PURF B DOUBLE HELIX OVERHANGING BASES N N N OPERATOR/DNA COMPLEX PDT064 BINDING DOMAIN OF SKN-1/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PDT065 SIX-FINGER TRANSCRIPTION FACTOR B DOUBLE HELIX OVERHANGING BASE N N N IIIA/DNA COMPLEX PDTB41 CONSENSUS ZINC FINGER/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE Y N N PDTE01 REPLICATION-TERMINATOR PROTEIN RH DOUBLE HELIX OVERHANGING BASE N N N (TUS)/DNA COMPLEX PDV001 E2/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE, N N N KINKED PDV004 CORE GP32/DNA COMPLEX n.a. n.a. n.a. N N N PH0008 T7 RNA B DOUBLE HELIX n.a. N N N polymerase(E.C.2.7.7.6)/DNA/RNA Complex ----------------------------------------------------------------------------------------------------------------------------- Page 14 created by the NDB Project on Wed May 26 14:33:25 2004