PDB: 8880 resultsInfo pagesStatus searchChemie searchBIRD

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4P36	Crystal structure of DJ-1 With Zn(II) bound (crystal 2) Descriptor: 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL, Protein DJ-1, ZINC ION Authors: Tashiro, S, Wu, C.-X, Hoang, Q.Q, Caaveiro, J.M.M, Tsumoto, K. Deposit date: 2014-03-05 Release date: 2014-04-09 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (1.182 Å) Cite: Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1. Biochemistry, 53, 2014
4P35	Crystal structure of DJ-1 with Zinc(II) bound (crystal I) Descriptor: CHLORIDE ION, GLYCEROL, Protein DJ-1, ... Authors: Tashiro, S, Wu, C.-X, Hoang, Q.Q, Caaveiro, J.M.M, Tsumoto, K. Deposit date: 2014-03-05 Release date: 2014-04-09 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.75 Å) Cite: Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1. Biochemistry, 53, 2014
4GXJ	R283K DNA polymerase beta ternary complex with a templating 8OG and incoming dCTP analog Descriptor: 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... Authors: Freudenthal, B.D, Beard, W.A, Wilson, S.H. Deposit date: 2012-09-04 Release date: 2013-01-16 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.2 Å) Cite: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion. Nucleic Acids Res., 41, 2013
4GXK	R283K DNA polymerase beta ternary complex with a templating 8OG and incoming dATP analog Descriptor: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... Authors: Freudenthal, B.D, Beard, W.A, Wilson, S.H. Deposit date: 2012-09-04 Release date: 2013-01-16 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.998 Å) Cite: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion. Nucleic Acids Res., 41, 2013
1HAV	HEPATITIS A VIRUS 3C PROTEINASE Descriptor: CHLORIDE ION, HEPATITIS A VIRUS 3C PROTEINASE Authors: Bergmann, E.M, James, M.N.G. Deposit date: 1996-10-23 Release date: 1996-12-23 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2 Å) Cite: The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition. J.Virol., 71, 1997
6AOC	Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase Descriptor: 1,2-ETHANEDIOL, 6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione, MANGANESE (II) ION, ... Authors: Kirby, K.A, Sarafianos, S.G. Deposit date: 2017-08-15 Release date: 2018-08-08 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H. Eur J Med Chem, 141, 2017
4F5Q	Closed ternary complex of R283K DNA polymerase beta Descriptor: 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ... Authors: Freudenthal, B.D, Beard, W.A, Wilson, S.H. Deposit date: 2012-05-13 Release date: 2012-12-12 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.25 Å) Cite: Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
4F5R	Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit Descriptor: 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, 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'), ... Authors: Freudenthal, B.D, Beard, W.A, Wilson, S.H. Deposit date: 2012-05-13 Release date: 2012-12-12 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
3K2P	HIV-1 Reverse Transcriptase Isolated RnaseH Domain with the Inhibitor beta-thujaplicinol Bound at the Active Site Descriptor: 2,7-dihydroxy-4-(propan-2-yl)cyclohepta-2,4,6-trien-1-one, MANGANESE (II) ION, Reverse Transcriptase Authors: Pauly, T.A, Himmel, D.M, Maegley, K, Arnold, E. Deposit date: 2009-09-30 Release date: 2010-02-09 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (2.04 Å) Cite: Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site. Structure, 17, 2009
2N0Y	NMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH Descriptor: Non-structural protein NS-S, RNA polymerase II transcription factor B subunit 1 Authors: Cyr, N, de la Fuente, C, Lecoq, L, Guendel, I, Chabot, P.R, Kehn-Hall, K, Omichinski, J.G. Deposit date: 2015-03-18 Release date: 2015-04-22 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: A Omega XaV motif in the Rift Valley fever virus NSs protein is essential for degrading p62, forming nuclear filaments and virulence. Proc.Natl.Acad.Sci.USA, 112, 2015
7TO2	Cryo-EM structure of RIG-I bound to the internal sites of p3SLR30 (+ATP) Descriptor: ADENOSINE-5'-DIPHOSPHATE, Antiviral innate immune response receptor RIG-I, MAGNESIUM ION, ... Authors: Wang, W, Pyle, A.M. Deposit date: 2022-01-22 Release date: 2022-11-02 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands. Mol.Cell, 82, 2022
5DDY	Binary complex of human Polymerase lambda with dCTP Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA polymerase lambda, MAGNESIUM ION, ... Authors: Liu, M.S, Tsai, M.D. Deposit date: 2015-08-25 Release date: 2016-02-24 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (3.36 Å) Cite: Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda J.Am.Chem.Soc., 138, 2016
8ILE	The crystal structure of dGTPalphaSe-Rp:DNApre-II:Pol X substrate ternary complex Descriptor: DNA (5'-D(*CP*TP*GP*GP*AP*TP*CP*CP*A)-3'), MANGANESE (II) ION, Repair DNA polymerase X, ... Authors: Qin, T, Gan, J.H, Huang, Z. Deposit date: 2023-03-03 Release date: 2024-01-10 Method: X-RAY DIFFRACTION (3 Å) Cite: Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom. Int J Mol Sci, 24, 2023
8ILF	The crystal structure of dGTPalphaSe-Sp:DNApre-II:Pol X substrate ternary complex Descriptor: DNA (5'-D(*CP*TP*GP*GP*AP*TP*CP*CP*A)-3'), MANGANESE (II) ION, Repair DNA polymerase X, ... Authors: Qin, T, Zhao, Q.W, Gan, J.H, Huang, Z. Deposit date: 2023-03-03 Release date: 2024-01-17 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom. Int J Mol Sci, 24, 2023
2HOJ	Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions Descriptor: MAGNESIUM ION, MANGANESE (II) ION, THIAMINE DIPHOSPHATE, ... Authors: Edwards, T.E, Ferre-D'Amare, A.R. Deposit date: 2006-07-14 Release date: 2006-09-19 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition Structure, 14, 2006
4N56	Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA Descriptor: 5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3', 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3', DNA polymerase I, ... Authors: Wu, E.Y. Deposit date: 2013-10-09 Release date: 2015-01-21 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.2 Å) Cite: A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase. Biochemistry, 54, 2015
2LBR	Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR Descriptor: RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*UP*AP*(6IA)P*AP*(PSU)P*CP*CP*CP*C)-3') Authors: Denmon, A.P, Wang, J, Nikonowicz, E.P. Deposit date: 2011-04-05 Release date: 2011-08-03 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Conformation Effects of Base Modification on the Anticodon Stem-Loop of Bacillus subtilis tRNA(Tyr). J.Mol.Biol., 412, 2011
3PY8	Crystal structure of a mutant of the large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with DNA and ddCTP Descriptor: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, DNA (5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'), ... Authors: Schnur, A, Marx, A, Welte, W, Diederichs, K. Deposit date: 2010-12-12 Release date: 2011-06-15 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.74 Å) Cite: Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity. Chembiochem, 12, 2011
1K6O	Crystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex Descriptor: 5'-D(*CP*AP*CP*AP*GP*GP*AP*TP*GP*TP*CP*CP*AP*TP*AP*TP*TP*AP*GP*GP*AP*CP*A)-3', 5'-D(*TP*GP*TP*CP*CP*TP*AP*AP*TP*AP*TP*GP*GP*AP*CP*AP*TP*CP*CP*TP*GP*TP*G)-3', ETS-domain protein ELK-4, ... Authors: Mo, Y, Ho, W, Johnston, K, Marmorstein, R. Deposit date: 2001-10-16 Release date: 2002-01-17 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (3.19 Å) Cite: Crystal structure of a ternary SAP-1/SRF/c-fos SRE DNA complex. J.Mol.Biol., 314, 2001
2PFQ	Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA polymerase lambda, Downstream Primer, ... Authors: Garcia-Diaz, M, Bebenek, K, Krahn, J.M, Pedersen, L.C, Kunkel, T.A. Deposit date: 2007-04-05 Release date: 2007-05-15 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair, 6, 2007
4Q8E	Human DNA polymerase eta inserting dCMPNPP opposite a phenanthriplatin adducted G Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, 5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3', 5'-D(*CP*AP*TP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3', ... Authors: Gregory, M.T, Yang, W. Deposit date: 2014-04-26 Release date: 2014-07-02 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (1.549 Å) Cite: Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage. Proc.Natl.Acad.Sci.USA, 111, 2014
2PFO	DNA Polymerase lambda in complex with DNA and dUPNPP Descriptor: 1,2-ETHANEDIOL, 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, DNA polymerase lambda, ... Authors: Garcia-Diaz, M, Bebenek, K, Krahn, J.M, Pedersen, L.C, Kunkel, T.A. Deposit date: 2007-04-05 Release date: 2007-05-15 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2 Å) Cite: Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair, 6, 2007
4Q8F	Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted G Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, 5'-D(*AP*GP*TP*GP*TP*GP*AP*C)-3', 5'-D(*CP*AP*TP*CP*GP*TP*CP*AP*CP*AP*CP*T)-3', ... Authors: Gregory, M.T, Yang, W. Deposit date: 2014-04-26 Release date: 2014-07-02 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.797 Å) Cite: Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage. Proc.Natl.Acad.Sci.USA, 111, 2014
3SJJ	RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+ Descriptor: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3', 5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', ... Authors: Wang, M, Wang, J, Konigsberg, W.H. Deposit date: 2011-06-21 Release date: 2011-10-12 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.38 Å) Cite: Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase. Biochemistry, 50, 2011
1NOM	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR) Descriptor: DNA POLYMERASE BETA, MANGANESE (II) ION Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-19 Release date: 1996-11-15 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (3 Å) Cite: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry, 35, 1996

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