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As of 21-Jun-2017 number of released structures: 8945
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 6041  Download results as an excel file       Gallery view

NDB ID:

 5IU5

PDB ID:

5IU5 

Release:

2017-06-21

Title:

Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCICCGA)2

Classification:

DNA

Authors:

Keane, P.M., Hall, J.P., Poynton, F.E., Gurung, S.P., Clark, I.P., Sazanovich, I.V., Towrie, M., Gunnlaugsson, T., Brazier, J.A., Quinn, S.J., Cardin, C.J., Kelly, J.M.

Citation:

Unexpected enhancement of sensitised photo-oxidation by a Ru(II) complex on replacement of guanine with inosine in DNA
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.198R free:0.209

NDB ID:

 5J70

PDB ID:

5J70 

Release:

2017-06-21

Title:

The Chd1 DNA-binding domain in complex with 17mer DNA duplex

Classification:

chromatin-binding protein/DNA

Authors:

Nodelman, I.M., Jenkins, K.R., Ren, R., Horvath, K.C., Hauk, G., Bowman, G.D.

Citation:

Chd1 domains communicate across the DNA gyres of the nucleosome
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.956Å R work:0.23R free:0.251

NDB ID:

 5MGA

PDB ID:

5MGA 

Release:

2017-06-21

Title:

Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage

Classification:

HYDROLASE

Authors:

Stella, S., Alcon, P., Montoya, G.

Citation:

Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage.
Nature pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.241R free:0.265

NDB ID:

 5TJG

PDB ID:

5TJG 

Release:

2017-06-21

Title:

Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp

Classification:

Transferase/DNA

Authors:

Feklistov, A., Bae, B., Hauver, J., Lass-Napiorkowska, A., Kalesse, M., Glaus, F., Altmann, K.H., Heyduk, T., Landick, R., Darst, S.A.

Citation:

RNA polymerase motions during promoter melting.
Science 356 pp.863 - 866 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.224R free:0.261

NDB ID:

 5XEW

PDB ID:

5XEW 

Release:

2017-06-21

Title:

Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex

Classification:

DNA/ANTIBIOTIC

Authors:

Tseng, W.H., Chang, C.K., Wu, P.C., Hu, N.J., Lee, G.H., Tzeng, C.C., Neidle, S., Hou, M.H.

Citation:

Induced-fit recognition of CCG trinucleotide repeats by a nickel chromomycin complex results in large-scale DNA deformation
Angew. Chem. Int. Ed. Engl. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.751Å R work:0.207R free:0.237

NDB ID:

 5J4P

PDB ID:

5J4P 

Release:

2017-06-14

Title:

DIY G-Quadruplexes: Solution structure of d(GGTTTGGTTTTGGTTTGG) in sodium

Classification:

DNA

Authors:

Dvorkin, S.A., Webba da Silva, M.

Citation:

DIY G-Quadruplexes: Solution structure of d(GGTTTGGTTTTGGTTTGG) in sodium
To Be Published pp. - 0

Experiment:

 SOLUTION NMR

NDB ID:

 5LIT

PDB ID:

5LIT 

Release:

2017-06-14

Title:

Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast

Classification:

DNA

Authors:

Acosta-Reyes, F., Campos, J.L., Dardonville, C., Ebiloma, G., Lagartera, L., Lemgruber, L., Millan, C.R., Nue Martinez, J.J., Saperas, N., de Koning, H.P.

Citation:

Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.25Å R work:0.12R free:0.166

NDB ID:

 5N9G

PDB ID:

5N9G 

Release:

2017-06-14

Title:

TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-

Classification:

TRANSCRIPTION

Authors:

Gouge, J., Vannini, A., Guthertz, N.

Citation:

Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA Polymerase III transcription initiation
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.194R free:0.233

NDB ID:

 5NFV

PDB ID:

5NFV 

Release:

2017-06-14

Title:

Crystal structure of catalytically inactive FnCas12 mutant bound to an R-loop structure containing a pre-crRNA mimic and full-length DNA target

Classification:

HYDROLASE

Authors:

Swarts, D.C., van der Oost, J., Jinek, M.

Citation:

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.
Mol. Cell 66 pp.221 - 233.e4 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.501Å R work:0.205R free:0.237

NDB ID:

 5NW5

PDB ID:

5NW5 

Release:

2017-06-14

Title:

Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae in complex with DNA

Classification:

DNA BINDING PROTEIN

Authors:

Mattarocci, M., Reinert, J.K., Bunker, R.D., Fontana, G.A., Shi, T., Klein, D., Cavadini, S., Faty, M., Shyian, M., Hafner, L., Shore, D., Thoma, N.H., Rass, U.

Citation:

Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends
Nat.Struct.Mol.Biol. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:6.502Å R work:0.252R free:0.276

NDB ID:

 5XH6

PDB ID:

5XH6 

Release:

2017-06-14

Title:

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM)

Classification:

HYDROLASE/RNA/DNA

Authors:

Nishimasu, H., Yamano, T., Gao, L., Zhang, F., Ishitani, R., Nureki, O.

Citation:

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1
Mol.Cell 67 pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.174R free:0.209

NDB ID:

 5XH7

PDB ID:

5XH7 

Release:

2017-06-14

Title:

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RR variant in complex with crRNA and target DNA (TCCA PAM)

Classification:

HYDROLASE/RNA/DNA

Authors:

Nishimasu, H., Yamano, T., Gao, L., Zhang, F., Ishitani, R., Nureki, O.

Citation:

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1
Mol.Cell 67 pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.182R free:0.214

NDB ID:

 5LTY

PDB ID:

5LTY 

Release:

2017-05-31

Title:

Homeobox transcription factor CDX2 bound to methylated DNA

Classification:

TRANSCRIPTION

Authors:

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P.K., Kivioja, T., Dave, K., Zhong, F., Nitta, K.R., Taipale, M., Popov, A., Ginno, P.A., Domcke, S., Yan, J., Schubeler, D., Vinson, C., Taipale, J.

Citation:

Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Science 356 pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.66Å R work:0.202R free:0.242

NDB ID:

 5M1L

PDB ID:

5M1L 

Release:

2017-05-31

Title:

Structure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

Classification:

DNA

Authors:

Kocman, V., Plavec, J.

Citation:

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions.
Nat Commun 8 pp.15355 - 15355 2017

Experiment:

 SOLUTION NMR

NDB ID:

 5M2L

PDB ID:

5M2L 

Release:

2017-05-31

Title:

Structure of DNA tetrameric AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

Classification:

DNA

Authors:

Kocman, V., Plavec, J.

Citation:

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions.
Nat Commun 8 pp.15355 - 15355 2017

Experiment:

 SOLUTION NMR

NDB ID:

 5M4W

PDB ID:

5M4W 

Release:

2017-05-31

Title:

Structure of DNA AGCGA-quadruplex adopted by 15-mer oligonucleotide found in regulatory region of the PLEKHG3 human gene with G11 to I11 mutation, d(GCGAGGGAGCIAGGG),VK34_I11

Classification:

DNA

Authors:

Kocman, V., Plavec, J.

Citation:

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions.
Nat Commun 8 pp.15355 - 15355 2017

Experiment:

 SOLUTION NMR

NDB ID:

 5MVB

PDB ID:

5MVB 

Release:

2017-05-31

Title:

Solution structure of a human G-Quadruplex hybrid-2 form in complex with a Gold-ligand

Classification:

DNA

Authors:

Wirmer-Bartoschek, J., Bendel, L.E., Jonker, H.R.A., Grun, J.T., Papi, F., Bazzicalupi, C., Messori, L., Gratteri, P., Schwalbe, H.

Citation:

Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding.
Angew. Chem. Int. Ed. Engl. 56 pp.7102 - 7106 2017

Experiment:

 SOLUTION NMR

NDB ID:

 5UZ1

PDB ID:

5UZ1 

Release:

2017-05-31

Title:

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd position and 8-oxoguanine at the 10th position

Classification:

DNA

Authors:

Gruber, D.R., Hoppins, J.J., Miears, H.L., Endutkin, A.V., Zharkov, D.O., Smirnov, S.L.

Citation:

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd position 8-oxoguanine at the 10th position
To Be Published pp. - 0

Experiment:

 SOLUTION NMR

NDB ID:

 5UZ3

PDB ID:

5UZ3 

Release:

2017-05-31

Title:

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 10th position

Classification:

DNA

Authors:

Gruber, D.R., Hoppins, J.J., Miears, H.L., Kasymov, R.D., Zharkov, D.O., Smirnov, S.L.

Citation:

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 10th position
To Be Published pp. - 0

Experiment:

 SOLUTION NMR

NDB ID:

 5K07

PDB ID:

5K07 

Release:

2017-05-24

Title:

Crystal structure of CREN7-DSDNA (GTAATTGC) complex

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Tian, L., Zhang, Z.F., Wang, H., Zhao, M., Dong, Y., Gong, Y.

Citation:

Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea
PLoS ONE 11 pp.e0163361 - e0163361 2016

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.197R free:0.229

NDB ID:

 5K17

PDB ID:

5K17 

Release:

2017-05-24

Title:

Crystal structure of CREN7-DSDNA (GTGATCGC) complex

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Tian, L., Zhang, Z.F., Wang, H., Zhao, M., Dong, Y., Gong, Y.

Citation:

Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea
PLoS ONE 11 pp.e0163361 - e0163361 2016

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.195R free:0.209

NDB ID:

 5K5H

PDB ID:

5K5H 

Release:

2017-05-24

Title:

Homo sapiens CCCTC-binding factor (CTCF) ZnF4-7 and DNA complex structure

Classification:

TRANSCRIPTION/DNA

Authors:

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

Citation:

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Mol. Cell 66 pp.711 - 720.e3 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.108Å R work:0.236R free:0.263

NDB ID:

 5K5I

PDB ID:

5K5I 

Release:

2017-05-24

Title:

Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P65

Classification:

TRANSCRIPTION/DNA

Authors:

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

Citation:

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Mol. Cell 66 pp.711 - 720.e3 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.19Å R work:0.218R free:0.244

NDB ID:

 5K5J

PDB ID:

5K5J 

Release:

2017-05-24

Title:

Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P41212

Classification:

TRANSCRIPTION/DNA

Authors:

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

Citation:

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Mol. Cell 66 pp.711 - 720.e3 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.287Å R work:0.207R free:0.253

NDB ID:

 5K5L

PDB ID:

5K5L 

Release:

2017-05-24

Title:

Homo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence DNA complex structure

Classification:

TRANSCRIPTION/DNA

Authors:

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

Citation:

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Mol. Cell 66 pp.711 - 720.e3 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.125Å R work:0.236R free:0.27

NDB ID:

 5KKQ

PDB ID:

5KKQ 

Release:

2017-05-24

Title:

Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure

Classification:

TRANSCRIPTION/DNA

Authors:

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

Citation:

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Mol. Cell 66 pp.711 - 720.e3 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.744Å R work:0.17R free:0.199

NDB ID:

 5MHJ

PDB ID:

5MHJ 

Release:

2017-05-24

Title:

ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12mer DNA duplex from its own promoter

Classification:

TRANSCRIPTION

Authors:

Tunnicliffe, R.B., Lockhart-Cairns, M.P., Levy, C., Mould, A.P., Jowitt, T.A., Sito, H., Baldock, C., Sandri-Goldin, R.M., Golovanov, A.P.

Citation:

The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.117Å R work:0.196R free:0.235

NDB ID:

 5MHK

PDB ID:

5MHK 

Release:

2017-05-24

Title:

ICP4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter

Classification:

TRANSCRIPTION

Authors:

Tunnicliffe, R.B., Lockhart-Cairns, M.P., Levy, C., Mould, A.P., Jowitt, T.A., Sito, H., Baldock, C., Sandri-Goldin, R.M., Golovanov, A.P.

Citation:

The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.28Å R work:0.211R free:0.242

NDB ID:

 5T00

PDB ID:

5T00 

Release:

2017-05-24

Title:

Human CTCF ZnF3-7 and methylated DNA complex

Classification:

TRANSCRIPTION REGULATOR/DNA

Authors:

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

Citation:

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Mol. Cell 66 pp.711 - 720.e3 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.19Å R work:0.218R free:0.242

NDB ID:

 5T0U

PDB ID:

5T0U 

Release:

2017-05-24

Title:

CTCF ZnF2-7 and DNA complex structure

Classification:

TRANSCRIPTION REGULATOR/DNA

Authors:

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

Citation:

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Mol. Cell 66 pp.711 - 720.e3 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.199Å R work:0.229R free:0.266

NDB ID:

 5U2R

PDB ID:

5U2R 

Release:

2017-05-24

Title:

PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTARTE, INCOMING L-DCTP AND CA2+

Classification:

TRANSFERASE/DNA

Authors:

Vyas, R., Reed, A.J., Raper, A.T., Zahurancik, W.J., Wallenmeyer, P.C., Suo, Z.

Citation:

Structural basis for the D-stereoselectivity of human DNA polymerase beta.
Nucleic Acids Res. 45 pp.6228 - 6237 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.8Å R work:0.19R free:0.229

NDB ID:

 5U2S

PDB ID:

5U2S 

Release:

2017-05-24

Title:

Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)3TC-TP and Ca2+.

Classification:

TRANSFERASE/DNA

Authors:

Vyas, R., Reed, A.J., Raper, A.T., Zahurancik, W.J., Wallenmeyer, P.C., Suo, Z.

Citation:

Structural basis for the D-stereoselectivity of human DNA polymerase beta.
Nucleic Acids Res. 45 pp.6228 - 6237 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.3Å R work:0.23R free:0.284

NDB ID:

 5U2T

PDB ID:

5U2T 

Release:

2017-05-24

Title:

Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)FTC-TP and Ca2+.

Classification:

TRANSFERASE/DNA

Authors:

Vyas, R., Reed, A.J., Raper, A.T., Zahurancik, W.J., Wallenmeyer, P.C., Suo, Z.

Citation:

Structural basis for the D-stereoselectivity of human DNA polymerase beta.
Nucleic Acids Res. 45 pp.6228 - 6237 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.79Å R work:0.2R free:0.246

NDB ID:

 5UND

PDB ID:

5UND 

Release:

2017-05-24

Title:

Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA

Classification:

transcription/dna

Authors:

Hashimoto, H., Wang, D., Horton, J.R., Zhang, X., Corces, V.G., Cheng, X.

Citation:

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Mol. Cell 66 pp.711 - 720.e3 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.549Å R work:0.211R free:0.236

NDB ID:

 5UZV

PDB ID:

5UZV 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rI)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.45Å R work:0.213R free:0.253

NDB ID:

 5V04

PDB ID:

5V04 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rII)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.65Å R work:0.229R free:0.255

NDB ID:

 5V05

PDB ID:

5V05 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rIII)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.902Å R work:0.199R free:0.248

NDB ID:

 5V06

PDB ID:

5V06 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rIV)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.75Å R work:0.218R free:0.265

NDB ID:

 5V07

PDB ID:

5V07 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with 5' recessed-end DNA (rV)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.15Å R work:0.175R free:0.219

NDB ID:

 5V08

PDB ID:

5V08 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with 5' recessed-end DNA (rVI)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.812Å R work:0.214R free:0.262

NDB ID:

 5V09

PDB ID:

5V09 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (D225A) in complex with 5' recessed-end DNA (rVII)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.75Å R work:0.218R free:0.254

NDB ID:

 5V0A

PDB ID:

5V0A 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (D225A) in complex with 5' recessed-end DNA (rVIII)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.38Å R work:0.21R free:0.246

NDB ID:

 5V0B

PDB ID:

5V0B 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rIX)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.63Å R work:0.207R free:0.25

NDB ID:

 5V0C

PDB ID:

5V0C 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA (f2I)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.58Å R work:0.229R free:0.272

NDB ID:

 5V0D

PDB ID:

5V0D 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA (f2II)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.63Å R work:0.204R free:0.237

NDB ID:

 5V0E

PDB ID:

5V0E 

Release:

2017-05-24

Title:

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA (f5I)

Classification:

HYDROLASE/DNA

Authors:

Shi, Y., Hellinga, H.W., Beese, L.S.

Citation:

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.6010 - 6015 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.744Å R work:0.203R free:0.246

NDB ID:

 5VO8

PDB ID:

5VO8 

Release:

2017-05-24

Title:

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter

Classification:

transcription/DNA/RNA

Authors:

Murakami, K.S., Shin, Y., Turnbough Jr., C.L., Molodtsov, V.

Citation:

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.3Å R work:0.185R free:0.246

NDB ID:

 5VOI

PDB ID:

5VOI 

Release:

2017-05-24

Title:

X-ray crystal structure of bacterial RNA polymerase and pyrG promoter complex

Classification:

transcription/dna/rna

Authors:

Murakami, K.S., Shin, Y., Turnbough Jr., C.L., Molodtsov, V.

Citation:

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.8Å R work:0.192R free:0.235

NDB ID:

 5WV7

PDB ID:

5WV7 

Release:

2017-05-24

Title:

Crystal structure of d(CCGGGGTACCCCGG)2 at 1.4A resolution

Classification:

DNA

Authors:

Karthik, S., Thirugnanasambandam, A., Mandal, P.K., Gautham, N.

Citation:

Crystal structure of d(CCGGGGTACCCCGG)2 at 1.4 angstrom resolution.
Acta Crystallogr F Struct Biol Commun 73 pp.259 - 265 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.406Å R work:0.221R free:0.242

NDB ID:

 5LUX

PDB ID:

5LUX 

Release:

2017-05-17

Title:

Homeobox transcription factor CDX1 bound to methylated DNA

Classification:

TRANSCRIPTION

Authors:

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P.K., Kivioja, T., Dave, K., Zhong, F., Nitta, K.R., Taipale, M., Popov, A., Ginno, P.A., Domcke, S., Yan, J., Schubeler, D., Vinson, C., Taipale, J.

Citation:

Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Science 356 pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.23Å R work:0.241R free:0.299

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