A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 10-Aug-2017 number of released structures: 9059
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 6110  Download results as an excel file       Gallery view

NDB ID:

 5EOS

PDB ID:

5EOS 

Release:

2017-08-09

Title:

Crystallizing Strained DNA: Self-Assembly of 3D Crystals Containing a Torsionally-Stressed Component

Classification:

DNA

Authors:

Hernandez, C., Birktoft, J.J., Seeman, N.C., Ohayon, Y.P., Chandrasekaran, A.R.

Citation:

Crystallizing Strained DNA: Self-Assembly of 3D Crystals Containing a Torsionally-Stressed Component
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:4.7Å R work:0.189R free:0.21

NDB ID:

 5GQ9

PDB ID:

5GQ9 

Release:

2017-08-09

Title:

Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Zhao, H., Sheng, G., Wang, Y.

Citation:

Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.189R free:0.236

NDB ID:

 5TGG

PDB ID:

5TGG 

Release:

2017-08-09

Title:

Solution structure of parallel stranded adenosine duplex

Classification:

RNA,DNA

Authors:

Copp, W., Denisov, A., Xie, J., Noronha, A., Liczner, C., Safaee, N., Wilds, C., Gehring, K.

Citation:

Influence of Nucleotide Modifications at the C2' Position on the Hoogsteen Base-Paired Parallel-Stranded Duplex of Poly(A) RNA
Nucleic Acids Res. pp. - 2017

Experiment:

 SOLUTION NMR

NDB ID:

 5VA0

PDB ID:

5VA0 

Release:

2017-08-09

Title:

Glucocorticoid Receptor DNA Binding Domain in complex with AP-1 response element from VCAM-1 Promoter

Classification:

transcription/dna

Authors:

Weikum, E.R., de Vera, I.M.S., Nwachukwu, J.C., Hudson, W.H., Nettles, K.W., Kojetin, .J., Ortlund, E.A.

Citation:

Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.295Å R work:0.197R free:0.231

NDB ID:

 5VA7

PDB ID:

5VA7 

Release:

2017-08-09

Title:

Glucocorticoid Receptor DNA Binding Domain - IL11 AP-1 recognition element Complex

Classification:

transcription/dna

Authors:

Weikum, E.R., de Vera, I.M.S., Nwachukwu, J.C., Hudson, W.H., Nettles, K.W., Kojetin, .J., Ortlund, E.A.

Citation:

Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.153Å R work:0.2R free:0.226

NDB ID:

 5VBJ

PDB ID:

5VBJ 

Release:

2017-08-09

Title:

Sulfur as a bromine biomolecular halogen-bond acceptor

Classification:

DNA

Authors:

Ford, M.C., Ho, P.S.

Citation:

Structure-energy relationships of sulfur as a bromine halogen-bond acceptor
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.944Å R work:0.218R free:0.276

NDB ID:

 5VY7

PDB ID:

5VY7 

Release:

2017-08-09

Title:

A self-assembling L-form DNA crystal lattice

Classification:

DNA

Authors:

Simmons, C.R., Zhang, F., MacCulloch, T., Fahmi, N.E., Stephanopoulos, N., Liu, Y., Seeman, N.C., Yan, H.

Citation:

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.
J. Am. Chem. Soc. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.238R free:0.246

NDB ID:

 5WJR

PDB ID:

5WJR 

Release:

2017-08-09

Title:

2-Se-T2/4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant

Classification:

HYDROLASE

Authors:

Fang, Z., Huang, Z.

Citation:

RNase H catalytic domain D132N mutant in complex with native DNA/RNA at 1.70 angstroms
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.7Å R work:0.188R free:0.233

NDB ID:

 5XUS

PDB ID:

5XUS 

Release:

2017-08-09

Title:

Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TTTA PAM)

Classification:

HYDROLASE/RNA/DNA

Authors:

Yamano, T., Zetsche, B., Ishitani, R., Zhang, F., Nishimasu, H., Nureki, O.

Citation:

Structural basis for the canonical and non-canonical PAM recognition by CRISPR-Cpf1
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.178R free:0.227

NDB ID:

 5XUT

PDB ID:

5XUT 

Release:

2017-08-09

Title:

Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TCTA PAM)

Classification:

HYDROLASE/RNA/DNA

Authors:

Yamano, T., Zetsche, B., Ishitani, R., Zhang, F., Nishimasu, H., Nureki, O.

Citation:

Structural basis for the canonical and non-canonical PAM recognition by CRISPR-Cpf1
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.4Å R work:0.192R free:0.237

NDB ID:

 5XUU

PDB ID:

5XUU 

Release:

2017-08-09

Title:

Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TCCA PAM)

Classification:

HYDROLASE/RNA/DNA

Authors:

Yamano, T., Zetsche, B., Ishitani, R., Zhang, F., Nishimasu, H., Nureki, O.

Citation:

Structural basis for the canonical and non-canonical PAM recognition by CRISPR-Cpf1
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.192R free:0.244

NDB ID:

 5XUZ

PDB ID:

5XUZ 

Release:

2017-08-09

Title:

Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (CCCA PAM)

Classification:

HYDROLASE/RNA/DNA

Authors:

Yamano, T., Zetsche, B., Ishitani, R., Zhang, F., Nishimasu, H., Nureki, O.

Citation:

Structural basis for the canonical and non-canonical PAM recognition by CRISPR-Cpf1
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.4Å R work:0.177R free:0.229

NDB ID:

 5XZB

PDB ID:

5XZB 

Release:

2017-08-09

Title:

Mouse cGAS bound to the inhibitor RU365

Classification:

IMMUNE SYSTEM/INHIBITOR

Authors:

Vincent, J., Adura, C., Gao, P., Luz, A., Lama, L., Asano, Y., Okamoto, R., Imaeda, T., Aida, J., Rothamel, K., Gogakos, T., Steinberg, J., Reasoner, S., Aso, K., Tuschl, T., Patel, D.J., Glickman, J.F., Ascano, M.

Citation:

Novel inhibition of the DNA sensor cyclic GMP-AMP synthase reduces interferon expression in primary macrophages from an autoimmune mouse model
To be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.13Å R work:0.213R free:0.247

NDB ID:

 5H3R

PDB ID:

5H3R 

Release:

2017-08-02

Title:

Crystal Structure of mutant MarR C80S from E.coli complexed with operator DNA

Classification:

TRANSCRIPTION/DNA

Authors:

Zhu, R., Hao, Z., Lou, H., Song, Y., Zhao, J., Chen, Y., Zhu, J., Chen, P.R.

Citation:

Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator.
J. Biol. Inorg. Chem. 22 pp.685 - 693 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.67Å R work:0.199R free:0.241

NDB ID:

 5MMA

PDB ID:

5MMA 

Release:

2017-08-02

Title:

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ379 (compound 5'g)

Classification:

VIRAL PROTEIN

Authors:

Zhao, X.Z., Smith, S.J., Maskell, D.P., Metifiot, M., Pye, V.E., Fesen, K., Marchand, C., Pommier, Y., Cherepanov, P., Hughes, S.H., Burke, T.R.

Citation:

Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors.
J. Med. Chem. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.55Å R work:0.178R free:0.207

NDB ID:

 5MMB

PDB ID:

5MMB 

Release:

2017-08-02

Title:

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ434 (compound 6p)

Classification:

VIRAL PROTEIN

Authors:

Zhao, X.Z., Smith, S.J., Maskell, D.P., Metifiot, M., Pye, V.E., Fesen, K., Marchand, C., Pommier, Y., Cherepanov, P., Hughes, S.H., Burke, T.R.

Citation:

Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors.
J. Med. Chem. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.77Å R work:0.183R free:0.203

NDB ID:

 5NO1

PDB ID:

5NO1 

Release:

2017-08-02

Title:

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ407 (compound 5g)

Classification:

VIRAL PROTEIN

Authors:

Zhao, X.Z., Smith, S.J., Maskell, D.P., Metifiot, M., Pye, V.E., Fesen, K., Marchand, C., Pommier, Y., Cherepanov, P., Hughes, S.H., Burke, T.R.

Citation:

Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors.
J. Med. Chem. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.176R free:0.203

NDB ID:

 5O63

PDB ID:

5O63 

Release:

2017-08-02

Title:

Crystal structure of UbaLAI restriction endonuclease B3 domain domain (mutant L24M L53M L95M) with cognate DNA

Classification:

HYDROLASE

Authors:

Laime, M., Lubys, A., Rimseliene, R., Sasnauskas, G., Siksnys, V., Tamulaitiene, G., Tamulaitis, G., Calyseva, J.

Citation:

UbaLAI is a monomeric Type IIE restriction enzyme
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.6Å R work:0.159R free:0.19

NDB ID:

 5VVJ

PDB ID:

5VVJ 

Release:

2017-08-02

Title:

Cas1-Cas2 bound to half-site intermediate

Classification:

HYDROLASE/DNA

Authors:

Wright, A.V., Liu, J.J., Knott, G.J., Doxzen, K.W., Nogales, E., Doudna, J.A.

Citation:

Structures of the CRISPR genome integration complex.
Science pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.89Å R work:0.288R free:0.328

NDB ID:

 5VVK

PDB ID:

5VVK 

Release:

2017-08-02

Title:

Cas1-Cas2 bound to full-site mimic

Classification:

HYDROLASE/DNA

Authors:

Wright, A.V., Liu, J.J., Knott, G.J., Doxzen, K.W., Nogales, E., Doudna, J.A.

Citation:

Structures of the CRISPR genome integration complex.
Science pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.9Å R work:0.216R free:0.253

NDB ID:

 5VVL

PDB ID:

5VVL 

Release:

2017-08-02

Title:

Cas1-Cas2 bound to full-site mimic with Ni

Classification:

HYDROLASE/DNA

Authors:

Wright, A.V., Liu, J.J., Knott, G.J., Doxzen, K.W., Nogales, E., Doudna, J.A.

Citation:

Structures of the CRISPR genome integration complex.
Science pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.31Å R work:0.224R free:0.262

NDB ID:

 5VY6

PDB ID:

5VY6 

Release:

2017-08-02

Title:

A self-assembling D-form DNA crystal lattice

Classification:

DNA

Authors:

Simmons, C.R., Zhang, F., MacCulloch, T., Fahmi, N.E., Stephanopoulos, N., Liu, Y., Seeman, N.C., Yan, H.

Citation:

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.
J. Am. Chem. Soc. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.064Å R work:0.211R free:0.236

NDB ID:

 5GNQ

PDB ID:

5GNQ 

Release:

2017-07-26

Title:

Crystal structure of replisomal dimer of DNA polymerase from bacteriophage RB69 with DNA duplexes

Classification:

TRANSFERASE/DNA

Authors:

Youn, H.-S., Lee, Y., Kang, J.Y., An, J.Y., Lee, J.-G., Park, K.R., Lim, J.J., Wang, J., Eom, S.H.

Citation:

Crystal structure of a eukaryotic replisomal dimer at 2.1 Angstrom resolution.
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.18R free:0.238

NDB ID:

 5J5P

PDB ID:

5J5P 

Release:

2017-07-26

Title:

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type I

Classification:

ISOMERASE/DNA

Authors:

Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R.

Citation:

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type I
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.97Å R work:0.15R free:0.173

NDB ID:

 5J5Q

PDB ID:

5J5Q 

Release:

2017-07-26

Title:

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II

Classification:

ISOMERASE/DNA

Authors:

Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R.

Citation:

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.83Å R work:0.183R free:0.263

NDB ID:

 5U91

PDB ID:

5U91 

Release:

2017-07-26

Title:

Crystal structure of Tre/loxLTR complex

Classification:

ISOMERASE/DNA

Authors:

Meinke, G., Karpinski, J., Buchholz, F., Bohm, A.

Citation:

Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.104Å R work:0.209R free:0.252

NDB ID:

 5UGN

PDB ID:

5UGN 

Release:

2017-07-26

Title:

DNA polymerase beta imidodiphosphate reactant complex

Classification:

Transferase/DNA

Authors:

Shock, D.D., Freudenthal, B.D., Beard, W.A., Wilson, S.H.

Citation:

Modulating the DNA polymerase reaction equilibrium through chemical biology
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.997Å R work:0.18R free:0.243

NDB ID:

 5UGO

PDB ID:

5UGO 

Release:

2017-07-26

Title:

DNA polymerase beta nick complex with imidodiphosphate

Classification:

Transferase/DNA

Authors:

Shock, D.D., Freudenthal, B.D., Beard, W.A., Wilson, S.H.

Citation:

Modulating the DNA polymerase reaction equilibrium through chemical biology
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.897Å R work:0.179R free:0.235

NDB ID:

 5UGP

PDB ID:

5UGP 

Release:

2017-07-26

Title:

DNA polymerase beta complex with a 1nt gap and dCMPPNP

Classification:

Transferase/DNA

Authors:

Shock, D.D., Freudenthal, B.D., Beard, W.A., Wilson, S.H.

Citation:

Modulating the DNA polymerase reaction equilibrium through chemical biology
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.955Å R work:0.182R free:0.233

NDB ID:

 5VI5

PDB ID:

5VI5 

Release:

2017-07-26

Title:

Structure of Mycobacterium smegmatis transcription initiation complex with a full transcription bubble

Classification:

TRANSCRIPTION

Authors:

Hubin, E.A., Lilic, M., Darst, S.A., Campbell, E.A.

Citation:

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures.
Nat Commun 8 pp.16072 - 16072 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.196Å R work:0.253R free:0.279

NDB ID:

 5T7X

PDB ID:

5T7X 

Release:

2017-07-19

Title:

Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Dheekollu, J., Malecka, K., Wiedmer, A., Delecluse, H.J., Chiang, A.K., Altieri, D.C., Messick, T.E., Lieberman, P.M.

Citation:

Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency.
Oncotarget 8 pp.7248 - 7264 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.35Å R work:0.185R free:0.232

NDB ID:

 5UUF

PDB ID:

5UUF 

Release:

2017-07-19

Title:

Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (12-mer product complex)

Classification:

HYDROLASE/DNA/ANTIBIOTIC

Authors:

Mullins, E.A., Shi, R., Eichman, B.F.

Citation:

Toxicity and repair of DNA adducts produced by the natural product yatakemycin
Nat.Chem.Biol. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.612Å R work:0.153R free:0.19

NDB ID:

 5UUG

PDB ID:

5UUG 

Release:

2017-07-19

Title:

Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (9-mer product complex)

Classification:

HYDROLASE/DNA/ANTIBIOTIC

Authors:

Mullins, E.A., Shi, R., Eichman, B.F.

Citation:

Toxicity and repair of DNA adducts produced by the natural product yatakemycin
Nat.Chem.Biol. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.712Å R work:0.136R free:0.176

NDB ID:

 5UUH

PDB ID:

5UUH 

Release:

2017-07-19

Title:

Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing a fluorinated abasic site (9-mer product complex)

Classification:

HYDROLASE/DNA/ANTIBIOTIC

Authors:

Mullins, E.A., Shi, R., Eichman, B.F.

Citation:

Toxicity and repair of DNA adducts produced by the natural product yatakemycin
Nat.Chem.Biol. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.569Å R work:0.14R free:0.173

NDB ID:

 5VRW

PDB ID:

5VRW 

Release:

2017-07-19

Title:

Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in non-planar conformation

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.58Å R work:0.234R free:0.305

NDB ID:

 5VRX

PDB ID:

5VRX 

Release:

2017-07-19

Title:

Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in Watson-Crick conformation

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.2Å R work:0.186R free:0.259

NDB ID:

 5VRY

PDB ID:

5VRY 

Release:

2017-07-19

Title:

Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 20 s

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.202R free:0.243

NDB ID:

 5VRZ

PDB ID:

5VRZ 

Release:

2017-07-19

Title:

Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 60 s

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.05Å R work:0.196R free:0.241

NDB ID:

 5VS0

PDB ID:

5VS0 

Release:

2017-07-19

Title:

Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 80 s

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.201R free:0.262

NDB ID:

 5VS1

PDB ID:

5VS1 

Release:

2017-07-19

Title:

Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension complex with dTTP bound in non-planar conformation

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.21R free:0.272

NDB ID:

 5VS2

PDB ID:

5VS2 

Release:

2017-07-19

Title:

Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension complex with dTTP bound in Watson-Crick conformation

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.33Å R work:0.187R free:0.249

NDB ID:

 5VS3

PDB ID:

5VS3 

Release:

2017-07-19

Title:

Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 90 s

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.7Å R work:0.206R free:0.248

NDB ID:

 5VS4

PDB ID:

5VS4 

Release:

2017-07-19

Title:

Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 120 s

Classification:

transferase, lyase/dna

Authors:

Reed, A.J., Suo, Z.

Citation:

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc. 139 pp.9684 - 9690 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.87Å R work:0.198R free:0.256

NDB ID:

 5NPK

PDB ID:

5NPK 

Release:

2017-07-12

Title:

1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA

Classification:

ISOMERASE

Authors:

Chan, P.F., Germe, T., Bax, B.D., Huang, J., Thalji, R.K., Bacque, E., Checchia, A., Chen, D., Cui, H., Ding, X., Ingraham, K., McCloskey, L., Raha, K., Srikannathasan, V., Maxwell, A., Stavenger, R.A.

Citation:

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.E4492 - E4500 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.98Å R work:0.153R free:0.183

NDB ID:

 5NPP

PDB ID:

5NPP 

Release:

2017-07-12

Title:

2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYRASE AND DNA

Classification:

ISOMERASE

Authors:

Chan, P.F., Germe, T., Bax, B.D., Huang, J., Thalji, R.K., Bacque, E., Checchia, A., Chen, D., Cui, H., Ding, X., Ingraham, K., McCloskey, L., Raha, K., Srikannathasan, V., Maxwell, A., Stavenger, R.A.

Citation:

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.E4492 - E4500 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.22Å R work:0.181R free:0.226

NDB ID:

 5GKR

PDB ID:

5GKR 

Release:

2017-07-05

Title:

Crystal structure of SLE patient-derived anti-DNA antibody in complex with oligonucleotide

Classification:

IMMUNE SYSTEM/DNA

Authors:

Sakakibara, S., Arimori, T., Yamashita, K., Jinzai, H., Motooka, D., Nakamura, S., Li, S., Takeda, K., Yasui, T., Narazaki, M., Tanaka, T., Standley, D.M., Takagi, J., Kikutani, H.

Citation:

Clonal evolution and antigen-recognition of anti-nuclear antibodies in acute systemic lupus erythematosus
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.162R free:0.185

NDB ID:

 5IX7

PDB ID:

5IX7 

Release:

2017-07-05

Title:

Crystal structure of metallo-DNA nanowire with infinite one-dimensional silver array

Classification:

DNA

Authors:

Kondo, J., Tada, Y., Dairaku, T., Hattori, Y., Saneyoshi, H., Ono, A., Tanaka, Y.

Citation:

A metallo-DNA nanowire with uninterrupted one-dimensional silver array
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.398Å R work:0.165R free:0.188

NDB ID:

 5TWP

PDB ID:

5TWP 

Release:

2017-07-05

Title:

Pre-catalytic ternary complex of human Polymerase Mu with incoming nonhydrolyzable UMPNPP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.001Å R work:0.185R free:0.237

NDB ID:

 5TWQ

PDB ID:

5TWQ 

Release:

2017-07-05

Title:

Post-catalytic nicked complex of human Polymerase Mu with newly incorporated UTP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.8Å R work:0.167R free:0.204

NDB ID:

 5TWR

PDB ID:

5TWR 

Release:

2017-07-05

Title:

Pre-catalytic ternary complex of human Polymerase Mu (H329A) mutant with incoming nonhydrolyzable UMPNPP

Classification:

TRANSFERASE/DNA

Authors:

Moon, A.F., Pryor, J.M., Ramsden, D.A., Kunkel, T.A., Bebenek, K., Pedersen, L.C.

Citation:

Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme Polymerase Mu
Nucleic Acids Res. pp. - 2017

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.162R free:0.194

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