PDB: 13480 resultsInfo pagesStatus searchChemie searchBIRD

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5EWG	Ternary complex of human DNA polymerase eta inserting rATP opposite an 8-Oxodeoxyguanosine Lesion Descriptor: ADENOSINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'), ... Authors: Su, Y, Egli, M, Guengerich, F.P. Deposit date: 2015-11-20 Release date: 2016-01-13 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.75 Å) Cite: Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta. J.Biol.Chem., 291, 2016
5EWF	Ternary complex of human DNA polymerase eta inserting rCTP opposite an 8-Oxodeoxyguanosine Lesion Descriptor: CALCIUM ION, CYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'), ... Authors: Su, Y, Egli, M, Guengerich, F.P. Deposit date: 2015-11-20 Release date: 2016-01-13 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.782 Å) Cite: Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta. J.Biol.Chem., 291, 2016
5EWE	Ternary complex of human DNA polymerase eta inserting rCTP opposite template G Descriptor: CALCIUM ION, CYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'), ... Authors: Su, Y, Egli, M, Guengerich, F.P. Deposit date: 2015-11-20 Release date: 2016-01-13 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.66 Å) Cite: Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta. J.Biol.Chem., 291, 2016
7Q2J	Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer Descriptor: Elongin-B, Elongin-C, N-[5-[4-[[5-[[(2S)-3,3-dimethyl-1-[(2S,4R)-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-5-oxidanylidene-pentyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1H-pyridine-3-carboxamide, ... Authors: Kraemer, A, Doelle, A, Schwalm, M.P, Adhikari, B, Wolf, E, Knapp, S, Structural Genomics Consortium (SGC) Deposit date: 2021-10-25 Release date: 2021-11-24 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization. Cell Chem Biol, 30, 2023
3H4D	Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*AP*GP*GP*AP*CP*CP*(DOC)), 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T), ... Authors: Jain, R, Nair, D.T, Johnson, R.E, Prakash, L, Prakash, S, Aggarwal, A.K. Deposit date: 2009-04-18 Release date: 2009-07-21 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Replication across template T/U by human DNA polymerase-iota. Structure, 17, 2009
8IDF	Crystal structure of human TUT1 complexed with U6 snRNA Descriptor: RNA (53-MER), Speckle targeted PIP5K1A-regulated poly(A) polymerase, ZINC ION Authors: Yamashita, S, Tomita, K. Deposit date: 2023-02-13 Release date: 2023-08-09 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (3.7 Å) Cite: Mechanism of U6 snRNA oligouridylation by human TUT1. Nat Commun, 14, 2023
3H4B	Ternary complex of human DNA polymerase iota with template U/T and incoming dATP Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3', 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T)-3', ... Authors: Jain, R, Nair, D.T, Johnson, R.E, Prakash, L, Prakash, S, Aggarwal, A.K. Deposit date: 2009-04-18 Release date: 2009-07-21 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Replication across template T/U by human DNA polymerase-iota. Structure, 17, 2009
3WFP	tRNA processing enzyme (apo form 2) Descriptor: Poly A polymerase, SULFATE ION Authors: Yamashita, S, Takeshita, D, Tomita, K. Deposit date: 2013-07-23 Release date: 2014-01-01 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (4.005 Å) Cite: Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase Structure, 22, 2014
3WFO	tRNA processing enzyme (apo form 1) Descriptor: Poly A polymerase, SULFATE ION Authors: Yamashita, S, Takeshita, D, Tomita, K. Deposit date: 2013-07-23 Release date: 2014-01-01 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (3.4 Å) Cite: Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase Structure, 22, 2014
2W9A	Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dGTP Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3', 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... Authors: Eoff, R.L, Zhang, H, Kosekov, I.D, Rizzo, C.J, Egli, M, Guengerich, F.P. Deposit date: 2009-01-22 Release date: 2009-05-12 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. J.Biol.Chem., 284, 2009
2W9C	Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dTTP Descriptor: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3', 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', DNA POLYMERASE IV, ... Authors: Eoff, R.L, Zhang, H, Kosekov, I.D, Rizzo, C.J, Egli, M, Guengerich, F.P. Deposit date: 2009-01-22 Release date: 2009-05-12 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. J.Biol.Chem., 284, 2009
3ISD	Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch Descriptor: 1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, 5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', ... Authors: Beard, W.A, Shock, D.D, Batra, V.K, Pedersen, L.C, Wilson, S.H. Deposit date: 2009-08-25 Release date: 2009-09-15 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2.6 Å) Cite: DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". J.Biol.Chem., 284, 2009
3JPO	Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochloromethylene triphosphate Descriptor: 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... Authors: Batra, V.K, Upton, J, Kashmerov, B, Beard, W.A, Wilson, S.H, Goodman, M.F, McKenna, C.E. Deposit date: 2009-09-04 Release date: 2010-06-02 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2 Å) Cite: Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc., 132, 2010
3JPQ	Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate Descriptor: 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... Authors: Batra, V.K, Upton, J, Kashmerov, B, Beard, W.A, Wilson, S.H, Goodman, M.F, McKenna, C.E. Deposit date: 2009-09-04 Release date: 2010-06-02 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc., 132, 2010
4QW8	TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND D-DCTP Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'), ... Authors: Gaur, V, Suo, Z. Deposit date: 2014-07-16 Release date: 2014-08-27 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.29 Å) Cite: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res., 42, 2014
4QWA	TERNARY CRYSTAL STRUCTURES OF A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS in COMPLEX WITH DNA AND (-)3TC-DP Descriptor: CALCIUM ION, DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'), DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3'), ... Authors: Gaur, V, Suo, Z. Deposit date: 2014-07-16 Release date: 2014-08-27 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res., 42, 2014
4QW9	TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)FTC-PPNP Descriptor: CALCIUM ION, DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'), DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3'), ... Authors: Gaur, V, Suo, Z. Deposit date: 2014-07-16 Release date: 2014-08-27 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res., 42, 2014
4QWC	Ternary Crystal Structures of a Y-family DNA polymerase DPO4 from Sulfobus Solfataricus in Comples with DNA and L-DCDP Descriptor: 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one, ACETATE ION, CALCIUM ION, ... Authors: Vyas, R, Suo, Z. Deposit date: 2014-07-16 Release date: 2014-08-27 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res., 42, 2014
4QWE	TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)FTC-DP Descriptor: CALCIUM ION, DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'), DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3'), ... Authors: Gaur, V, Suo, Z. Deposit date: 2014-07-16 Release date: 2014-08-27 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res., 42, 2014
4QWD	TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)3TC-PPNP Descriptor: CALCIUM ION, DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'), DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3'), ... Authors: Gaur, V, Suo, Z. Deposit date: 2014-07-16 Release date: 2014-08-27 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.05 Å) Cite: Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res., 42, 2014
1HBX	Ternary Complex of SAP-1 and SRF with specific SRE DNA Descriptor: 5'-D(*CP*AP*CP*AP*CP*CP*GP*GP*AP*AP*GP*TP*CP* CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*T)-3', 5'-D(*GP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP* GP*GP*AP*CP*TP*TP*CP*CP*GP*GP*TP*G)-3', ETS-DOMAIN PROTEIN ELK-4, ... Authors: Hassler, M, Richmond, T.J. Deposit date: 2001-04-20 Release date: 2001-06-27 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (3.15 Å) Cite: The B-Box Dominates Sap-1/Srf Interactions in the Structure of the Ternary Complex Embo J., 20, 2001
1YKE	Structure of the mediator MED7/MED21 subcomplex Descriptor: RNA polymerase II holoenzyme component SRB7, RNA polymerase II mediator complex protein MED7 Authors: Baumli, S, Hoeppner, S, Cramer, P. Deposit date: 2005-01-18 Release date: 2005-02-22 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.3 Å) Cite: A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. J.Biol.Chem., 280, 2005
1YKH	Structure of the mediator MED7/MED21 (Med7/Srb7) subcomplex Descriptor: RNA polymerase II holoenzyme component SRB7, RNA polymerase II mediator complex protein MED7 Authors: Baumli, S, Hoeppner, S, Cramer, P. Deposit date: 2005-01-18 Release date: 2005-02-22 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (3 Å) Cite: A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. J.Biol.Chem., 280, 2005
1EUY	GLUTAMINYL-TRNA SYNTHETASE COMPLEXED WITH A TRNA MUTANT AND AN ACTIVE SITE INHIBITOR Descriptor: 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE, GLUTAMINYL TRNA, GLUTAMINYL-TRNA SYNTHETASE Authors: Sherlin, L.D, Bullock, T.L, Newberry, K.J, Lipman, R.S.A, Hou, Y.-M, Beijer, B, Sproat, B.S, Perona, J.J. Deposit date: 2000-04-19 Release date: 2000-06-04 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases. J.Mol.Biol., 299, 2000
3RJJ	Ternary complex crystal structure of DNA Polymerase Beta with template 8odG provides insight into mutagenic lesion bypass Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG)P*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'), ... Authors: Batra, V.K, Beard, W.A, Wilson, S.H. Deposit date: 2011-04-15 Release date: 2012-01-18 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2 Å) Cite: Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion. Proc.Natl.Acad.Sci.USA, 109, 2012

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