A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 4-Mar-2015 number of released structures: 7399
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 5007  Download results as an excel file       Gallery view

NDB ID:

4U29

PDB ID:

4U29 

Release:

2015-03-04

Title:

Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Chen, X., Velmurugu, Y., Zheng, G., Park, B., Shim, Y., Kim, Y., Liu, L., Van Houten, B., He, C., Ansari, A., Min, J.H.

Citation:

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.
Nat Commun 6 pp.5849 - 5849 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.05Å R work:0.204R free:0.256

NDB ID:

NA3121

PDB ID:

4R22 

Release:

2015-03-04

Title:

TnrA-DNA complex

Classification:

transcription/DNA

Authors:

Schumacher, M.A., Chinnam, N.B., Cuthbert, B., Tonthat, N.K., Whitfill, T.

Citation:

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Genes Dev. 29 pp.451 - 464 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.26R free:0.278

NDB ID:

NA3122

PDB ID:

4R24 

Release:

2015-03-04

Title:

Complete dissection of B. subtilis nitrogen homeostatic circuitry

Classification:

transcrption/DNA

Authors:

Schumacher, M.A., Chinnam, N.B., Cuthbert, B., Tonthat, N.K., Whitfill, T.

Citation:

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Genes Dev. 29 pp.451 - 464 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.25Å R work:0.217R free:0.242

NDB ID:

NA3141

PDB ID:

4R15 

Release:

2015-03-04

Title:

High-resolution crystal structure of Z-DNA in complex with Cr3+ cations

Classification:

DNA

Authors:

Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L., Jaskolski, M.

Citation:

High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations.
J.Biol.Inorg.Chem. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:0.97Å R work:0.143R free:0.184

NDB ID:

NA3142

PDB ID:

4R4E 

Release:

2015-03-04

Title:

Structure of GlnR-DNA complex

Classification:

Transcription regulator/DNA

Authors:

Schumacher, M.A., Chinnam, N.B., Cuthbert, B., Tonthat, N.K., Whitfill, T.

Citation:

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Genes Dev. 29 pp.451 - 464 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.57Å R work:0.254R free:0.274

NDB ID:

2MMF

PDB ID:

2MMF 

Release:

2015-02-25

Title:

Solution structure of AGA modified

Classification:

DNA

Authors:

Li, L., Brown, K.L., Ma, R., Stone, M.P.

Citation:

DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct.
Chem.Res.Toxicol. pp. - 2015

Experiment:

SOLUTION NMR

NDB ID:

2MMQ

PDB ID:

2MMQ 

Release:

2015-02-25

Title:

Solution structure of AGT FAPY Modified duplex

Classification:

DNA

Authors:

Li, L., Brown, K.L., Ma, R., Stone, M.P.

Citation:

DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct.
Chem.Res.Toxicol. pp. - 2015

Experiment:

SOLUTION NMR

NDB ID:

2MMR

PDB ID:

2MMR 

Release:

2015-02-25

Title:

AGC FAPY modified duplex Major isomer

Classification:

DNA

Authors:

Li, L., Brown, K.L., Ma, R., Stone, M.P.

Citation:

DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct.
Chem.Res.Toxicol. pp. - 2015

Experiment:

SOLUTION NMR

NDB ID:

2MMS

PDB ID:

2MMS 

Release:

2015-02-25

Title:

AG(7-deaza)G FAPY modified duplex

Classification:

DNA

Authors:

Li, L., Brown, K.L., Ma, R., Stone, M.P.

Citation:

DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct.
Chem.Res.Toxicol. pp. - 2015

Experiment:

SOLUTION NMR

NDB ID:

4U5M

PDB ID:

4U5M 

Release:

2015-02-25

Title:

Structure of a left-handed DNA G-quadruplex

Classification:

DNA

Authors:

Chung, W.J., Heddi, B., Schmitt, E., Lim, K.W., Mechulam, Y., Phan, A.T.

Citation:

Structure of a left-handed DNA G-quadruplex.
Proc.Natl.Acad.Sci.USA pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.5Å R work:0.141R free:0.18

NDB ID:

2MS9

PDB ID:

2MS9 

Release:

2015-02-18

Title:

Solution structure of a G-quadruplex

Classification:

DNA

Authors:

Chung, W.J., Heddi, B., Schmitt, E., Lim, K.W., Mechulam, Y., Phan, A.T.

Citation:

Structure of a left-handed DNA G-quadruplex
Proc.Natl.Acad.Sci.USA pp. - 2015

Experiment:

SOLUTION NMR

NDB ID:

4WQS

PDB ID:

4WQS 

Release:

2015-02-18

Title:

Thermus thermophilus RNA polymerase backtracked complex

Classification:

TRANSFERASE/DNA/RNA

Authors:

Sekine, S.I., Murayama, Y., Svetlov, V., Nudler, E., Yokoyama, S.

Citation:

The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions.
Mol.Cell 57 pp.408 - 421 2015

Experiment:

X-RAY DIFFRACTION Resolution:4.306Å R work:0.28R free:0.311

NDB ID:

NA3257

PDB ID:

4RNM 

Release:

2015-02-18

Title:

Crystal structure of human polymerase eta inserting dAMPnPP opposite DNA template containing an abasic site

Classification:

TRANSFERASE/DNA

Authors:

Patra, A., Zhang, Q., Lei, L., Su, Y., Egli, M., Guengerich, F.P.

Citation:

Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase Eta
J.Biol.Chem. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.144Å R work:0.166R free:0.218

NDB ID:

NA3258

PDB ID:

4RNN 

Release:

2015-02-18

Title:

Crystal structure of human polymerase eta inserting dGMPnPP opposite DNA template containing an abasic site

Classification:

TRANSFERASE/DNA

Authors:

Patra, A., Zhang, Q., Lei, L., Su, Y., Egli, M., Guengerich, F.P.

Citation:

Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase Eta
J.Biol.Chem. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.808Å R work:0.167R free:0.202

NDB ID:

NA3259

PDB ID:

4RNO 

Release:

2015-02-18

Title:

Crystal structure of human polymerase eta extending an abasic site-dA pair by inserting dCTP opposite template G

Classification:

TRANSFERASE/DNA

Authors:

Patra, A., Zhang, Q., Lei, L., Su, Y., Egli, M., Guengerich, F.P.

Citation:

Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase Eta
J.Biol.Chem. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.82Å R work:0.241R free:0.281

NDB ID:

NA3356

PDB ID:

4CN2 

Release:

2015-02-18

Title:

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Ramp2 Response Element

Classification:

TRANSCRIPTION/DNA

Authors:

Osz, J., Mcewen, A.G., Poussin-Courmontagne, P., Moutier, E., Birck, C., Davidson, I., Moras, D., Rochel, N.

Citation:

Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor.
Sci.Rep. 5 pp.8216 - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.069Å R work:0.164R free:0.214

NDB ID:

NA3357

PDB ID:

4CN3 

Release:

2015-02-18

Title:

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Gde1SpA Response Element

Classification:

TRANSCRIPTION/DNA

Authors:

Osz, J., Mcewen, A.G., Poussin-Courmontagne, P., Moutier, E., Birck, C., Davidson, I., Moras, D., Rochel, N.

Citation:

Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor.
Sci.Rep. 5 pp.8216 - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.35Å R work:0.179R free:0.249

NDB ID:

NA3358

PDB ID:

4CN5 

Release:

2015-02-18

Title:

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Nr1d1 Response Element

Classification:

TRANSCRIPTION/DNA

Authors:

Osz, J., Mcewen, A.G., Poussin-Courmontagne, P., Moutier, E., Birck, C., Davidson, I., Moras, D., Rochel, N.

Citation:

Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor.
Sci.Rep. 5 pp.8216 - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.167R free:0.226

NDB ID:

NA3359

PDB ID:

4CN7 

Release:

2015-02-18

Title:

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to an idealized DR1 Response Element

Classification:

TRANSCRIPTION/DNA

Authors:

Osz, J., Mcewen, A.G., Poussin-Courmontagne, P., Moutier, E., Birck, C., Davidson, I., Moras, D., Rochel, N.

Citation:

Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor.
Sci.Rep. 5 pp.8216 - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.34Å R work:0.173R free:0.209

NDB ID:

NA3360

PDB ID:

4CYC 

Release:

2015-02-18

Title:

CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPTIDE AND UBDA MOTIFS

Classification:

TRANSCRIPTION

Authors:

Foos, N., Maurel-Zaffran, C., Mate, M.J., Vincentelli, R., Hainaut, M., Berenger, H., Pradel, J., Saurin, A.J., Ortiz-Lombardia, M., Graba, Y.

Citation:

A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/Pbc Interaction Mode.
Structure 23 pp.270 - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.36Å R work:0.212R free:0.226

NDB ID:

NA3361

PDB ID:

4UUS 

Release:

2015-02-18

Title:

CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF

Classification:

TRANSCRIPTION

Authors:

Foos, N., Maurel-Zaffran, C., Mate, M.J., Vincentelli, R., Hainaut, M., Berenger, H., Pradel, J., Saurin, A.J., Ortiz-Lombardia, M., Graba, Y.

Citation:

A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/Pbc Interaction Mode.
Structure 23 pp.270 - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.55Å R work:0.187R free:0.239

NDB ID:

4U7B

PDB ID:

4U7B 

Release:

2015-02-11

Title:

Crystal structure of a pre-cleavage Mos1 transpososome

Classification:

Hydrolase/DNA

Authors:

Dornan, J., Grey, H., Richardson, J.M.

Citation:

Structural role of the flanking DNA in mariner transposon excision.
Nucleic Acids Res. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.09Å R work:0.228R free:0.261

NDB ID:

NA2877

PDB ID:

3WPC 

Release:

2015-02-11

Title:

Crystal structure of horse TLR9 in complex with agonistic DNA1668_12mer

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Ohto, U., Shibata, T., Tanji, H., Ishida, H., Krayukhina, E., Uchiyama, S., Miyake, K., Shimizu, T.

Citation:

Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
Nature pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.6Å R work:0.183R free:0.22

NDB ID:

NA2878

PDB ID:

3WPD 

Release:

2015-02-11

Title:

Crystal structure of horse TLR9 in complex with inhibitory DNA4084

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Ohto, U., Shibata, T., Tanji, H., Ishida, H., Krayukhina, E., Uchiyama, S., Miyake, K., Shimizu, T.

Citation:

Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
Nature pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.2R free:0.258

NDB ID:

NA2879

PDB ID:

3WPE 

Release:

2015-02-11

Title:

Crystal structure of bovine TLR9 in complex with agonistic DNA1668_12mer

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Ohto, U., Shibata, T., Tanji, H., Ishida, H., Krayukhina, E., Uchiyama, S., Miyake, K., Shimizu, T.

Citation:

Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
Nature pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.38Å R work:0.217R free:0.273

NDB ID:

NA2880

PDB ID:

3WPG 

Release:

2015-02-11

Title:

Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 1)

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Ohto, U., Shibata, T., Tanji, H., Ishida, H., Krayukhina, E., Uchiyama, S., Miyake, K., Shimizu, T.

Citation:

Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
Nature pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.246Å R work:0.235R free:0.28

NDB ID:

NA2881

PDB ID:

3WPH 

Release:

2015-02-11

Title:

Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 2)

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Ohto, U., Shibata, T., Tanji, H., Ishida, H., Krayukhina, E., Uchiyama, S., Miyake, K., Shimizu, T.

Citation:

Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
Nature pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.327Å R work:0.213R free:0.247

NDB ID:

NA2882

PDB ID:

3WPI 

Release:

2015-02-11

Title:

Crystal structure of mouse TLR9 in complex with inhibitory DNA_super

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Ohto, U., Shibata, T., Tanji, H., Ishida, H., Krayukhina, E., Uchiyama, S., Miyake, K., Shimizu, T.

Citation:

Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
Nature pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.246Å R work:0.221R free:0.254

NDB ID:

NA2907

PDB ID:

4OPJ 

Release:

2015-02-11

Title:

Bh-RNaseH:tcdA-DNA complex

Classification:

HYDROLASE/DNA

Authors:

Egli, M., Pallan, P.S.

Citation:

Generating Crystallographic Models of DNA Dodecamers From Structures Of RNase H:DNA Complexes
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.541Å R work:0.162R free:0.22

NDB ID:

NA2908

PDB ID:

4OPK 

Release:

2015-02-11

Title:

Bh-RNaseH:2'-SMe-DNA complex

Classification:

HYDROLASE/DNA

Authors:

Egli, M., Pallan, P.S.

Citation:

Generating Crystallographic Models of DNA Dodecamers From Structures Of RNase H:DNA Complexes
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.539Å R work:0.193R free:0.258

NDB ID:

NA2939

PDB ID:

4ORJ 

Release:

2015-02-11

Title:

Metal Ion Binding at the Catalytic Site Induces Widespread Changes in a Sequence-specific Protein-DNA Complex

Classification:

HYDROLASE/DNA

Authors:

Sinha, K., Kurpiewski, M.R., Sangani, S.S., Kehr, A.D., Rule, G.S., Jen-Jacobson, L.

Citation:

Metal Ion Binding at the Catalytic Site Induces Widespread Changes in a Sequence-specific Protein-DNA Complex
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.16R free:0.219

NDB ID:

NA2964

PDB ID:

4PWM 

Release:

2015-02-11

Title:

Crystal structure of Dickerson Drew Dodecamer with 5-carboxycytosine

Classification:

DNA

Authors:

Szulik, M.W., Pallan, P.S., Nocek, B., Voehler, M., Banerjee, S., Brooks, S., Joachimiak, A., Egli, M., Eichman, B.F., Stone, M.P.

Citation:

Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.
Biochemistry 54 pp.1294 - 1305 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.95Å R work:0.221R free:0.267

NDB ID:

NA2993

PDB ID:

4QC7 

Release:

2015-02-11

Title:

Dodecamer structure of 5-formylcytosine containing DNA

Classification:

DNA

Authors:

Szulik, M.W., Pallan, P.S., Nocek, B., Voehler, M., Banerjee, S., Brooks, S., Joachimiak, A., Egli, M., Eichman, B.F., Stone, M.P.

Citation:

Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.
Biochemistry 54 pp.1294 - 1305 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.226R free:0.245

NDB ID:

NA3216

PDB ID:

4RIM 

Release:

2015-02-11

Title:

Native structure of intercalation-locked DNA tetraplex

Classification:

DNA

Authors:

Tripathi, S., Zhang, D., Paukstelis, P.J.

Citation:

An intercalation-locked parallel-stranded DNA tetraplex.
Nucleic Acids Res. 43 pp.1937 - 1944 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.299R free:0.301

NDB ID:

NA3217

PDB ID:

4RIP 

Release:

2015-02-11

Title:

BromoUracil substituted structure of intercalation-locked DNA tetraplex

Classification:

DNA

Authors:

Tripathi, S., Zhang, D., Paukstelis, P.J.

Citation:

An intercalation-locked parallel-stranded DNA tetraplex.
Nucleic Acids Res. 43 pp.1937 - 1944 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.232R free:0.238

NDB ID:

2MAY

PDB ID:

2MAY 

Release:

2015-02-04

Title:

Structure of a G-quadruplex containing a single LNA modification

Classification:

DNA

Authors:

Li, Z., Lech, C., Adrian, M., Heddi, B., Phan, A.T.

Citation:

Engineering G4: Towards effective incorporation of locked nucleic acid into G-quadruplexes
To be Published pp. - 0

Experiment:

SOLUTION NMR

NDB ID:

2MRU

PDB ID:

2MRU 

Release:

2015-02-04

Title:

Structure of truncated EcMazE-DNA complex

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Zorzini, V., Buts, L., Schrank, E., Sterckx, Y.G., Respondek, M., Engelberg-Kulka, H., Loris, R., Zangger, K., van Nuland, N.A.

Citation:

Escherichia coli antitoxin MazE as transcription factor: insights into MazE-DNA binding.
Nucleic Acids Res. 43 pp.1241 - 1256 2015

Experiment:

SOLUTION NMR

NDB ID:

4P9U

PDB ID:

4P9U 

Release:

2015-02-04

Title:

FadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in Complex with DNA

Classification:

Transcription Regulator/DNA

Authors:

Shi, W., Kovacikova, G., Lin, W., Taylor, R.K., Skorupski, K., Kull, F.J.

Citation:

The 40-residue insertion in Vibrio cholerae FadR facilitates binding of an additional fatty acyl-CoA ligand.
Nat Commun 6 pp.6032 - 6032 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.208Å R work:0.217R free:0.252

NDB ID:

4U8A

PDB ID:

4U8A 

Release:

2015-02-04

Title:

Crystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1503

Classification:

DNA/ANTIBIOTIC

Authors:

Zhu, W., Wang, Y., Li, K., Gao, J., Huang, C.H., Chen, C.C., Ko, T.P., Zhang, Y., Guo, R.T., Oldfield, E.

Citation:

Antibacterial drug leads: DNA and enzyme multitargeting.
J.Med.Chem. 58 pp.1215 - 1227 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.48Å R work:0.266R free:0.322

NDB ID:

4U8B

PDB ID:

4U8B 

Release:

2015-02-04

Title:

Crystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1358

Classification:

DNA/ANTIBIOTIC

Authors:

Zhu, W., Wang, Y., Li, K., Gao, J., Huang, C.H., Chen, C.C., Ko, T.P., Zhang, Y., Guo, R.T., Oldfield, E.

Citation:

Antibacterial drug leads: DNA and enzyme multitargeting.
J.Med.Chem. 58 pp.1215 - 1227 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.31Å R work:0.241R free:0.246

NDB ID:

4U8C

PDB ID:

4U8C 

Release:

2015-02-04

Title:

Crystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1409

Classification:

DNA/ANTIBIOTIC

Authors:

Zhu, W., Wang, Y., Li, K., Gao, J., Huang, C.H., Chen, C.C., Ko, T.P., Zhang, Y., Guo, R.T., Oldfield, E.

Citation:

Antibacterial drug leads: DNA and enzyme multitargeting.
J.Med.Chem. 58 pp.1215 - 1227 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.24Å R work:0.276R free:0.332

NDB ID:

4X67

PDB ID:

4X67 

Release:

2015-02-04

Title:

Crystal structure of elongating yeast RNA polymerase II stalled at oxidative Cyclopurine DNA lesions.

Classification:

TRANSCRIPTION/DNA

Authors:

Walmacq, C., Wang, L., Chong, J., Scibelli, K., Lubkowska, L., Gnatt, A., Brooks, P.J., Wang, D., Kashlev, M.

Citation:

Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions.
Proc.Natl.Acad.Sci.USA 112 pp.E410 - E419 2015

Experiment:

X-RAY DIFFRACTION Resolution:4.1Å R work:0.242R free:0.289

NDB ID:

4X6A

PDB ID:

4X6A 

Release:

2015-02-04

Title:

Crystal structure of yeast RNA polymerase II encountering oxidative Cyclopurine DNA lesions

Classification:

TRANSCRIPTION/DNA

Authors:

Walmacq, C., Wang, L., Chong, J., Scibelli, K., Lubkowska, L., Gnatt, A., Brooks, P.J., Wang, D., Kashlev, M.

Citation:

Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions.
Proc.Natl.Acad.Sci.USA 112 pp.E410 - E419 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.96Å R work:0.248R free:0.296

NDB ID:

NA3351

PDB ID:

4S20 

Release:

2015-02-04

Title:

Structural basis for transcription reactivation by RapA

Classification:

TRANSFERASE/DNA/RNA

Authors:

Liu, B., Zuo, Y., Steitz, T.A.

Citation:

Structural basis for transcription reactivation by RapA.
Proc.Natl.Acad.Sci.USA 112 pp.2006 - 2010 2015

Experiment:

X-RAY DIFFRACTION Resolution:4.7Å R work:0.273R free:0.369

NDB ID:

2MS6

PDB ID:

2MS6 

Release:

2015-01-28

Title:

Human Telomeric G-quadruplex DNA sequence (TTAGGGT)4 complexed with Flavonoid Quercetin

Classification:

DNA

Authors:

Kumar, A., Tawani, A.

Citation:

Structural Insight Reveals Flavonoids as Anticancer Agents
To be Published pp. - 0

Experiment:

SOLUTION NMR

NDB ID:

4U7D

PDB ID:

4U7D 

Release:

2015-01-21

Title:

Structure of human RECQ-like helicase in complex with an oligonucleotide

Classification:

HYDROLASE/DNA

Authors:

Pike, A.C.W., Zhang, Y., Schnecke, C., Cooper, C.D.O., Von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

Citation:

Structure of human RECQ-like helicase in complex with an oligonucleotide
TO BE PUBLISHED pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.4Å R work:0.205R free:0.248

NDB ID:

4WK8

PDB ID:

4WK8 

Release:

2015-01-21

Title:

FOXP3 forms a domain-swapped dimer to bridge DNA

Classification:

TRANSCRIPTION/DNA

Authors:

Chen, Y., Chen, C., Zhang, Z., Liu, C.C., Johnson, M.E., Espinoza, C.A., Edsall, L.E., Ren, B., Zhou, X.J., Grant, S.F., Wells, A.D., Chen, L.

Citation:

DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.
Nucleic Acids Res. 43 pp.1268 - 1282 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.4006Å R work:0.19R free:0.252

NDB ID:

4X0G

PDB ID:

4X0G 

Release:

2015-01-21

Title:

Structure of Bsg25A binding with DNA

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Dai, Q., Ren, A., Westholm, J.O., Duan, H., Patel, D.J., Lai, E.C.

Citation:

Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family.
Genes Dev. 29 pp.48 - 62 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.2065Å R work:0.228R free:0.276

NDB ID:

4XIU

PDB ID:

4XIU 

Release:

2015-01-21

Title:

Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant with DNA containing TTT overhang

Classification:

TRANSFERASE/DNA

Authors:

Wu, E.Y., Walsh, A.R., Materne, E.C., Hiltner, E.P., Zielinski, B., Miller, B.R., Mawby, L., Modeste, E., Parish, C.A., Barnes, W.M., Kermekchiev, M.B.

Citation:

A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase.
Biochemistry 54 pp.881 - 889 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.223R free:0.286

NDB ID:

NA2737

PDB ID:

4N56 

Release:

2015-01-21

Title:

Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA

Classification:

TRANSFERASE/DNA

Authors:

Wu, E.Y., Walsh, A.R., Materne, E.C., Hiltner, E.P., Zielinski, B., Miller, B.R., Mawby, L., Modeste, E., Parish, C.A., Barnes, W.M., Kermekchiev, M.B.

Citation:

A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase.
Biochemistry 54 pp.881 - 889 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.2Å R work:0.222R free:0.273