Loading
PDBj
English日本語简体中文繁體中文한국어
✖
ﾒﾆｭｰPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
PDB: 258 件
6W2M
DownloadVisualize
BU of 6w2m by Molmil
Abortive ternary complex crystal structure of DNA polymerase Beta with 8OG-dC base pair at the primer terminus and flipped out dA
分子名称: CHLORIDE ION, DNA polymerase beta, Downstream Primer Strand, ...
著者Batra, V.K, Wilson, S.H.
登録日2020-03-06
公開日2020-07-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.998 Å)
主引用文献Structure of a DNA polymerase abortive complex with the 8OG:dA base pair at the primer terminus.
Commun Biol, 3, 2020
6NKR
DownloadVisualize
BU of 6nkr by Molmil
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with dGTP
分子名称: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.45 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6NKU
DownloadVisualize
BU of 6nku by Molmil
Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with dGTP
分子名称: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6NKX
DownloadVisualize
BU of 6nkx by Molmil
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with dGTP
分子名称: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (1.98 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6NKS
DownloadVisualize
BU of 6nks by Molmil
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with beta-gamma CHF analog of dGTP
分子名称: 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.349 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6NKW
DownloadVisualize
BU of 6nkw by Molmil
Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma-methylene dGTP
分子名称: 2'-DEOXY-5'-O-(HYDROXY{[HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]OXY}PHOSPHORYL)GUANOSINE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (1.98 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6NL0
DownloadVisualize
BU of 6nl0 by Molmil
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CF2 analogue of dGTP
分子名称: 2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL}OXY)(HYDROXY)PHOSPHORYL]GUANOSINE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (1.97 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6PH6
DownloadVisualize
BU of 6ph6 by Molmil
Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream
分子名称: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*G)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-06-25
公開日2019-12-11
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context.
J.Biol.Chem., 295, 2020
6PH5
DownloadVisualize
BU of 6ph5 by Molmil
Binary product complex crystal structure of DNA polymerase Beta with an extra-helical template base
分子名称: DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-06-25
公開日2019-12-11
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.602 Å)
主引用文献DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context.
J.Biol.Chem., 295, 2020
6MR8
DownloadVisualize
BU of 6mr8 by Molmil
D276G DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog
分子名称: 1,2-ETHANEDIOL, 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol, CALCIUM ION, ...
著者Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A.
登録日2018-10-11
公開日2019-01-30
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (1.897 Å)
主引用文献A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition.
Nucleic Acids Res., 47, 2019
6N2R
DownloadVisualize
BU of 6n2r by Molmil
Binary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) at the templating position
分子名称: DNA (5'-D(*CP*CP*GP*AP*CP*(1CC)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2018-11-14
公開日2019-04-03
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta.
J.Biol.Chem., 294, 2019
6N2T
DownloadVisualize
BU of 6n2t by Molmil
Ternary complex crystal structure of DNA polymerase Beta with 5-hydroxymethyl-dC (5-hmC) at the templating position
分子名称: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine, DNA (5'-D(*CP*CP*GP*AP*CP*(5HC)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2018-11-14
公開日2019-03-27
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta.
J.Biol.Chem., 294, 2019
6N2S
DownloadVisualize
BU of 6n2s by Molmil
Ternary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) at the templating position
分子名称: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine, DNA (5'-D(*CP*CP*GP*AP*CP*(1CC)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2018-11-14
公開日2019-03-27
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.457 Å)
主引用文献Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta.
J.Biol.Chem., 294, 2019
6NKZ
DownloadVisualize
BU of 6nkz by Molmil
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma methylene dGTP
分子名称: 2'-DEOXY-5'-O-(HYDROXY{[HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]OXY}PHOSPHORYL)GUANOSINE, DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.01 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6MR7
DownloadVisualize
BU of 6mr7 by Molmil
DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog
分子名称: 1,2-ETHANEDIOL, 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol, CALCIUM ION, ...
著者Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A.
登録日2018-10-11
公開日2019-01-30
最終更新日2023-10-11
実験手法X-RAY DIFFRACTION (2.144 Å)
主引用文献A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition.
Nucleic Acids Res., 47, 2019
6NKT
DownloadVisualize
BU of 6nkt by Molmil
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with beta-gamma difluoro analogue of dGTP
分子名称: 2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL}OXY)(HYDROXY)PHOSPHORYL]GUANOSINE, DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6NKY
DownloadVisualize
BU of 6nky by Molmil
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP
分子名称: 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.094 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
6NKV
DownloadVisualize
BU of 6nkv by Molmil
Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP
分子名称: 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ...
著者Batra, V.K, Wilson, S.H.
登録日2019-01-07
公開日2020-01-08
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
3C2K
DownloadVisualize
BU of 3c2k by Molmil
DNA POLYMERASE BETA with a gapped DNA substrate and DUMPNPP with Manganese in the active site
分子名称: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3'), ...
著者Batra, V.K, Beard, W.A, Shock, D.D, Pedersen, L.C, Wilson, S.H.
登録日2008-01-25
公開日2008-05-20
最終更新日2023-08-30
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
Mol.Cell, 30, 2008
3C2M
DownloadVisualize
BU of 3c2m by Molmil
Ternary complex of DNA POLYMERASE BETA with a G:dAPCPP mismatch in the active site
分子名称: 1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DGP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3'), ...
著者Batra, V.K, Beard, W.A, Shock, D.D, Pedersen, L.C, Wilson, S.H.
登録日2008-01-25
公開日2008-05-20
最終更新日2023-08-30
実験手法X-RAY DIFFRACTION (2.15 Å)
主引用文献Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
Mol.Cell, 30, 2008
3C2L
DownloadVisualize
BU of 3c2l by Molmil
Ternary complex of DNA POLYMERASE BETA with a C:DAPCPP mismatch in the active site
分子名称: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DCP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3'), DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DTP*DGP*DCP*DGP*DC)-3'), ...
著者Batra, V.K, Beard, W.A, Shock, D.D, Pedersen, L.C, Wilson, S.H.
登録日2008-01-25
公開日2008-05-20
最終更新日2023-08-30
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
Mol.Cell, 30, 2008
4LVS
DownloadVisualize
BU of 4lvs by Molmil
DNA polymerase beta mismatched substrate complex with Mn2+, 2.5 min
分子名称: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ...
著者Freudenthal, B.D, Beard, W.A, Shock, D.D, Wilson, S.H.
登録日2013-07-26
公開日2013-09-04
最終更新日2023-09-20
実験手法X-RAY DIFFRACTION (2.002 Å)
主引用文献Observing a DNA polymerase choose right from wrong.
Cell(Cambridge,Mass.), 154, 2013
1BPZ
DownloadVisualize
BU of 1bpz by Molmil
HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA
分子名称: DNA (5'-D(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3'), DNA (5'-D(*GP*TP*CP*GP*G)-3'), ...
著者Sawaya, M.R, Prasad, R, Wilson, S.H, Kraut, J, Pelletier, H.
登録日1997-04-14
公開日1997-06-16
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
Biochemistry, 36, 1997
1BPY
DownloadVisualize
BU of 1bpy by Molmil
HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP
分子名称: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*DOC)-3'), ...
著者Sawaya, M.R, Pelletier, H, Prasad, R, Wilson, S.H, Kraut, J.
登録日1997-04-15
公開日1997-06-16
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
Biochemistry, 36, 1997
1BPX
DownloadVisualize
BU of 1bpx by Molmil
DNA POLYMERASE BETA/DNA COMPLEX
分子名称: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*TP*CP*GP*G)-3'), ...
著者Sawaya, M.R, Prasad, R, Wilson, S.H, Kraut, J, Pelletier, H.
登録日1997-04-11
公開日1997-06-16
最終更新日2023-08-02
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
Biochemistry, 36, 1997

226262

件を2024-10-16に公開中

PDB statisticsPDBj update infoContact PDBjnumon