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As of 3-Mar-2021 number of released structures: 11234
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 7607  Download results as an excel file       Gallery view

NDB ID:

 6LER

PDB ID:

6LER 

Release:

2021-03-03

Title:

169 bp nucleosome harboring non-identical cohesive DNA termini.

Classification:

DNA BINDING PROTEIN

Authors:

Sharma, D., Davey, C.A., Adhireksan, Z.

Citation:

169 bp nucleosome harboring non-palindromic DNA with cohesive ends.
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.208R free:0.26

NDB ID:

 7B1Y

PDB ID:

7B1Y 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR complexed with cobalt and its consensus DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.12Å R work:0.224R free:0.248

NDB ID:

 7B20

PDB ID:

7B20 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR complexed with iron and its consensus DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.18Å R work:0.209R free:0.242

NDB ID:

 7B23

PDB ID:

7B23 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR complexed with cobalt and the SACE_2689 promoter DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.15Å R work:0.222R free:0.248

NDB ID:

 7B24

PDB ID:

7B24 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR (P39G variant) complexed with cobalt and its consensus DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.05Å R work:0.22R free:0.253

NDB ID:

 7B25

PDB ID:

7B25 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR (Q43A variant) complexed with cobalt and its consensus DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.34Å R work:0.255R free:0.295

NDB ID:

 7BPV

PDB ID:

7BPV 

Release:

2021-03-03

Title:

r(GUGGGCCGAC)/d(GTCGGCCCAC) hybrid duplex structure

Classification:

DNA-RNA HYBRID

Authors:

Wang, S.C., Satange, R.B., Hou, M.H.

Citation:

r(GUGGGCCGAC)/d(GTCGGCCCAC) hybrid structure
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.781Å R work:0.217R free:0.237

NDB ID:

 7K5O

PDB ID:

7K5O 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 1 min post dATP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.16Å R work:0.186R free:0.226

NDB ID:

 7K5P

PDB ID:

7K5P 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 4 min post dATP addition

Classification:

TRANSFERASE

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.97Å R work:0.219R free:0.257

NDB ID:

 7K5Q

PDB ID:

7K5Q 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 8 min post dATP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.193R free:0.246

NDB ID:

 7K5R

PDB ID:

7K5R 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 120 min post dATP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.3Å R work:0.188R free:0.238

NDB ID:

 7K5S

PDB ID:

7K5S 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 4 hr post dATP and dCTP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.67Å R work:0.186R free:0.209

NDB ID:

 7K5T

PDB ID:

7K5T 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 25.5 hr post dATP and dCTP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.3Å R work:0.19R free:0.236

NDB ID:

 7K5U

PDB ID:

7K5U 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 48 hr post dATP and dCTP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.189R free:0.229

NDB ID:

 7LFQ

PDB ID:

7LFQ 

Release:

2021-03-03

Title:

Pyrococcus RNA ligase

Classification:

LIGASE/DNA

Authors:

Banerjee, A., Goldgur, Y., Shuman, S.

Citation:

Structure of 3'-PO4/5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide
Rna pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.191R free:0.216

NDB ID:

 6WJK

PDB ID:

6WJK 

Release:

2021-02-24

Title:

Crystal Structure of a Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry

Classification:

DNA

Authors:

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

Citation:

A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.
Angew.Chem.Int.Ed.Engl. pp. - 2020

Experiment:

 X-RAY DIFFRACTION Resolution:4.514Å R work:0.197R free:0.242

NDB ID:

 6L9Z

PDB ID:

6L9Z 

Release:

2021-02-17

Title:

338 bp di-nucleosome assembled with linker histone H1.X

Classification:

DNA BINDING PROTEIN

Authors:

Sharma, D., Davey, C.A., Adhireksan, Z.

Citation:

Dinucleosome 338 bp with linker histone H1.X
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.203R free:0.256

NDB ID:

 6LA2

PDB ID:

6LA2 

Release:

2021-02-17

Title:

343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0

Classification:

DNA BINDING PROTEIN

Authors:

Sharma, D., Davey, C.A., Adhireksan, Z.

Citation:

Dinucleosome 338 bp with linker histone H1.X
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.89Å R work:0.199R free:0.266

NDB ID:

 6LAB

PDB ID:

6LAB 

Release:

2021-02-17

Title:

169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0

Classification:

DNA BINDING PROTEIN

Authors:

Sharma, D., Davey, C.A., Adhireksan, Z.

Citation:

Nucleosome 169 bp with linker histone H1.0
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.2Å R work:0.208R free:0.263

NDB ID:

 6VUG

PDB ID:

6VUG 

Release:

2021-02-17

Title:

Diabody bound to a Reverse Transcriptase Aptamer Complex

Classification:

PROTEIN BINDING

Authors:

Chesterman, C., Arnold, E.

Citation:

Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.202R free:0.254

NDB ID:

 6ZIX

PDB ID:

6ZIX 

Release:

2021-02-17

Title:

Structure of RcsB from Salmonella enterica serovar Typhimurium bound to promoter P1flhDC in the presence of phosphomimetic BeF3-

Classification:

DNA BINDING PROTEIN

Authors:

Huesa, J., Giner-Lamia, J., Pucciarelli, M.G., Paredes-Martinez, F., Garcia-Del Portillo, F., Marina, A., Casino, P.

Citation:

Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.4Å R work:0.238R free:0.273

NDB ID:

 6ZJ2

PDB ID:

6ZJ2 

Release:

2021-02-17

Title:

Structure of RcsB from Salmonella enterica serovar Typhimurium bound to promoter rprA in the presence of phosphomimetic BeF3-

Classification:

DNA BINDING PROTEIN

Authors:

Huesa, J., Giner-Lamia, J., Pucciarelli, M.G., Paredes-Martinez, F., Garcia-Del Portillo, F., Marina, A., Casino, P.

Citation:

Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.38Å R work:0.265R free:0.318

NDB ID:

 7LH9

PDB ID:

7LH9 

Release:

2021-02-17

Title:

Crystal structure of BRPF2 PWWP domain in complex with DNA

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Zhang, M., Lei, M., Qin, S., Dong, A., Yang, A., Li, Y., Loppnau, P., Hughes, T.R., Min, J., Liu, Y.

Citation:

Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than the HDGF family of PWWP domains.
Biochim Biophys Acta Gene Regul Mech 1864 pp.194688 - 194688 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.224R free:0.278

NDB ID:

 6LBI

PDB ID:

6LBI 

Release:

2021-02-10

Title:

Crystal Structure of FOXO1-DBD homodimer bound to a palindromic DNA sequence

Classification:

DNA BINDING PROTEIN

Authors:

Li, J., Dai, S.Y., Chen, X.J., Liang, X.J., Qu, L.Z., Jiang, L.Y., Guo, M., Zhou, Z., Wei, H.D., Chen, Z.C., Chen, L., Chen, Y.H.

Citation:

Structural basis for the cooperative DNA recognition by FOXO1 homodimer
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.067Å R work:0.226R free:0.264

NDB ID:

 6LBM

PDB ID:

6LBM 

Release:

2021-02-10

Title:

Crystal Structure of FOXC2-DBD bound to a palindromic DNA sequence

Classification:

TRANSCRIPTION

Authors:

Li, J., Dai, S.Y., Chen, X.J., Liang, X.J., Qu, L.Z., Jiang, L.Y., Guo, M., Zhou, Z., Wei, H.D., Chen, Z.C., Chen, L., Chen, Y.H.

Citation:

Structural basis for the cooperative DNA recognition by FOXO1 homodimer
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.841Å R work:0.232R free:0.262

NDB ID:

 7D5D

PDB ID:

7D5D 

Release:

2021-02-10

Title:

Left-handed G-quadruplex containing one bulge

Classification:

DNA

Authors:

Das, P., Ngo, K.H., Winnerdy, F.R., Maity, A., Bakalar, B., Mechulam, Y., Schmitt, E., Phan, A.T.

Citation:

Bulges in left-handed G-quadruplexes.
Nucleic Acids Res. 49 pp.1724 - 1736 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.18Å R work:0.119R free:0.167

NDB ID:

 7D5E

PDB ID:

7D5E 

Release:

2021-02-10

Title:

Left-handed G-quadruplex containing two bulges

Classification:

DNA

Authors:

Das, P., Ngo, K.H., Winnerdy, F.R., Maity, A., Bakalar, B., Mechulam, Y., Schmitt, E., Phan, A.T.

Citation:

Bulges in left-handed G-quadruplexes.
Nucleic Acids Res. 49 pp.1724 - 1736 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.296Å R work:0.183R free:0.214

NDB ID:

 7D5F

PDB ID:

7D5F 

Release:

2021-02-10

Title:

Left-handed G-quadruplex containing 3 bulges

Classification:

DNA

Authors:

Das, P., Ngo, K.H., Winnerdy, F.R., Maity, A., Bakalar, B., Mechulam, Y., Schmitt, E., Phan, A.T.

Citation:

Bulges in left-handed G-quadruplexes.
Nucleic Acids Res. 49 pp.1724 - 1736 2021

Experiment:

 SOLUTION NMR

NDB ID:

 6LUI

PDB ID:

6LUI 

Release:

2021-02-03

Title:

Crystal structure of the SAMD1 WH domain and DNA complex

Classification:

DNA BINDING PROTEIN

Authors:

Zhou, Y., Cao, Y., Wang, Z.

Citation:

Structure of the SAMD1 WH domain and a CpG-containing double stranded DNA complex
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.781Å R work:0.202R free:0.241

NDB ID:

 6R8E

PDB ID:

6R8E 

Release:

2021-02-03

Title:

SC14 G-hairpin

Classification:

DNA

Authors:

Lenarcic Zivkovic, M., Gajarsky, M., Bekova, K., Plavec, J., Trantirek, L.

Citation:

G-hairpin formation propensity
To Be Published pp. - 0

Experiment:

 SOLUTION NMR

NDB ID:

 6VNP

PDB ID:

6VNP 

Release:

2021-02-03

Title:

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT

Classification:

TRANSFERASE/DNA

Authors:

Jung, H., Lee, S.

Citation:

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.42Å R work:0.199R free:0.241

NDB ID:

 6W7A

PDB ID:

6W7A 

Release:

2021-02-03

Title:

The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D bound to DNA oligomer TAGCAT (uncleaved, 5mM overnight DNA soak)

Classification:

VIRAL PROTEIN/DNA

Authors:

Kumar, G., Cuypers, M., Webby, R.R., Webb, T.R., White, S.W.

Citation:

Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Nucleic Acids Res. 49 pp.1609 - 1618 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.09Å R work:0.174R free:0.204

NDB ID:

 6WHM

PDB ID:

6WHM 

Release:

2021-02-03

Title:

The crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA oligomer TAGC (cleaved TTAGCATT, 5mM overnight DNA soak)

Classification:

VIRAL PROTEIN/DNA

Authors:

Kumar, G., Cuypers, M., Webby, R.R., Webb, T.R., White, S.W.

Citation:

Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Nucleic Acids Res. 49 pp.1609 - 1618 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.92Å R work:0.177R free:0.216

NDB ID:

 6WS3

PDB ID:

6WS3 

Release:

2021-02-03

Title:

The crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA oligomers TG and AGCA (from cleaved GTGAGCAGTG)

Classification:

VIRAL PROTEIN/DNA

Authors:

Kumar, G., Cuypers, M., Webby, R.R., Webb, T.R., White, S.W.

Citation:

Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Nucleic Acids Res. 49 pp.1609 - 1618 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.2Å R work:0.19R free:0.215

NDB ID:

 6XUP

PDB ID:

6XUP 

Release:

2021-02-03

Title:

Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT

Classification:

DNA BINDING PROTEIN

Authors:

Golovinas, E., Manakova, E., Sasnauskas, G., Zaremba, M.

Citation:

Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.181R free:0.224

NDB ID:

 7BZG

PDB ID:

7BZG 

Release:

2021-02-03

Title:

Structure of Bacillus subtilis HxlR, wild type in complex with formaldehyde and DNA

Classification:

DNA BINDING PROTEIN

Authors:

Zhu, R., Zhang, G., Jing, M., Han, Y., Li, J., Zhao, J., Li, Y., Chen, P.R.

Citation:

Genetically encoded formaldehyde sensors inspired by a protein intra-helical crosslinking reaction.
Nat Commun 12 pp.581 - 581 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.9Å R work:0.179R free:0.223

NDB ID:

 7CSZ

PDB ID:

7CSZ 

Release:

2021-02-03

Title:

Crystal structure of the N-terminal tandem RRM domains of RBM45 in complex with single-stranded DNA

Classification:

RNA BINDING PROTEIN/DNA

Authors:

Chen, X., Yang, Z., Wang, W., Qian, K., Liu, M., Wang, J., Wang, M.

Citation:

Structural basis for RNA recognition by the N-terminal tandem RRM domains of human RBM45.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.8Å R work:0.185R free:0.233

NDB ID:

 7D0X

PDB ID:

7D0X 

Release:

2021-02-03

Title:

NMR solution structures of the DNA minidumbbell formed by 5'-mCTTGXmCTTG-3'

Classification:

DNA

Authors:

Wan, L., Yi, J., Lam, S.L., Lee, H.K., Guo, P.

Citation:

5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbell.
Chemistry pp. - 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7D0Y

PDB ID:

7D0Y 

Release:

2021-02-03

Title:

NMR solution structures of the DNA minidumbbell formed by two CmCTG repeats at pH 5

Classification:

DNA

Authors:

Wan, L., Yi, J., Lam, S.L., Lee, H.K., Guo, P.

Citation:

5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbell.
Chemistry pp. - 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7D0Z

PDB ID:

7D0Z 

Release:

2021-02-03

Title:

NMR solution structures of the DNA minidumbbell formed by two CCTG repeats at pH 5

Classification:

DNA

Authors:

Wan, L., Yi, J., Lam, S.L., Lee, H.K., Guo, P.

Citation:

5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbell.
Chemistry pp. - 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7K96

PDB ID:

7K96 

Release:

2021-02-03

Title:

Human DNA polymerase beta ternary complex with templating cytosine and incoming deoxyguanosine diphosphate

Classification:

TRANSFERASE/DNA

Authors:

Varela, F.A., Freudenthal, B.D.

Citation:

Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta.
Biochemistry 60 pp.373 - 380 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.183R free:0.245

NDB ID:

 7K97

PDB ID:

7K97 

Release:

2021-02-03

Title:

Human DNA polymerase beta dGDP product complex with Mn2+

Classification:

TRANSFERASE/DNA

Authors:

Varela, F.A., Freudenthal, B.D.

Citation:

Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta.
Biochemistry 60 pp.373 - 380 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.4Å R work:0.185R free:0.239

NDB ID:

 7KR3

PDB ID:

7KR3 

Release:

2021-02-03

Title:

Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate

Classification:

LIGASE/DNA

Authors:

Williams, J.S., Tumbale, P.P., Arana, M.E., Rana, J.A., Williams, R.S., Kunkel, T.A.

Citation:

High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication.
Nat Commun 12 pp.482 - 482 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.778Å R work:0.193R free:0.239

NDB ID:

 7KR4

PDB ID:

7KR4 

Release:

2021-02-03

Title:

Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex

Classification:

LIGASE/DNA

Authors:

Williams, J.S., Tumbale, P.P., Arana, M.E., Rana, J.A., Williams, R.S., Kunkel, T.A.

Citation:

High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication.
Nat Commun 12 pp.482 - 482 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.2Å R work:0.162R free:0.215

NDB ID:

 6TUO

PDB ID:

6TUO 

Release:

2021-01-27

Title:

Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT

Classification:

DNA BINDING PROTEIN

Authors:

Golovinas, E., Manakova, E., Sasnauskas, G., Zaremba, M.

Citation:

Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.8Å R work:0.184R free:0.226

NDB ID:

 6VJW

PDB ID:

6VJW 

Release:

2021-01-27

Title:

Crystal structure of WT hMBD4 complexed with T:G mismatch DNA

Classification:

TRANSFERASE

Authors:

Ouzon-Shubeita, H., Jung, H., Lee, M.H., Koag, M.C., Lee, S.

Citation:

Catalytic mechanism of the mismatch-specific DNA glycosylase methyl-CpG-binding domain 4.
Biochem.J. 477 pp.1601 - 1612 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.02Å R work:0.218R free:0.263

NDB ID:

 6VKP

PDB ID:

6VKP 

Release:

2021-01-27

Title:

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dG

Classification:

TRANSFERASE/DNA

Authors:

Jung, H., Lee, S.

Citation:

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dG
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.54Å R work:0.21R free:0.26

NDB ID:

 6XU0

PDB ID:

6XU0 

Release:

2021-01-27

Title:

Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT

Classification:

DNA BINDING PROTEIN

Authors:

Golovinas, E., Manakova, E., Sasnauskas, G., Zaremba, M.

Citation:

Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.18R free:0.225

NDB ID:

 6Z8V

PDB ID:

6Z8V 

Release:

2021-01-27

Title:

X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3L), which contains 1-beta-D-lactopyranosyl residue in the side chain of Thy3 at N3.

Classification:

HYDROLASE

Authors:

Smirnov, I., Kolganova, N., Troisi, R., Sica, F., Timofeev, E.

Citation:

Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12.
Mol Ther Nucleic Acids 23 pp.863 - 871 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.58Å R work:0.179R free:0.205

NDB ID:

 6Z8W

PDB ID:

6Z8W 

Release:

2021-01-27

Title:

X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3G), which contains 1-beta-D-glucopyranosyl residue in the side chain of Thy3 at N3.

Classification:

HYDROLASE

Authors:

Smirnov, I., Kolganova, N., Troisi, R., Sica, F., Timofeev, E.

Citation:

Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12.
Mol Ther Nucleic Acids 23 pp.863 - 871 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.73Å R work:0.178R free:0.207

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