6KZX
 
 | | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | | Descriptor: | 3-[[8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid, DNA gyrase subunit B | | Authors: | Mima, M, Takeuchi, T, Ushiyama, F. | | Deposit date: | 2019-09-25 | | Release date: | 2020-05-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation.
Acs Omega, 5, 2020
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6L01
 | | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | | Descriptor: | 2-[3-[[8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]phenyl]ethanoic acid, DNA gyrase subunit B | | Authors: | Mima, M, Takeuchi, T, Ushiyama, F. | | Deposit date: | 2019-09-25 | | Release date: | 2020-05-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation.
Acs Omega, 5, 2020
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6KZZ
 | | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | | Descriptor: | 4-[[8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid, DNA gyrase subunit B | | Authors: | Mima, M, Takeuchi, T, Ushiyama, F. | | Deposit date: | 2019-09-25 | | Release date: | 2020-05-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation.
Acs Omega, 5, 2020
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4XIU
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1NK2
 | | VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, 20 STRUCTURES | | Descriptor: | DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3'), DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3'), HOMEOBOX PROTEIN VND | | Authors: | Gruschus, J.M, Tsao, D.H.H, Wang, L.-H, Nirenberg, M, Ferretti, J.A. | | Deposit date: | 1998-05-06 | | Release date: | 1999-02-23 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.
Biochemistry, 36, 1997
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1HCQ
 | | THE CRYSTAL STRUCTURE OF THE ESTROGEN RECEPTOR DNA-BINDING DOMAIN BOUND TO DNA: HOW RECEPTORS DISCRIMINATE BETWEEN THEIR RESPONSE ELEMENTS | | Descriptor: | DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)-3'), DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)-3'), PROTEIN (ESTROGEN RECEPTOR), ... | | Authors: | Schwabe, J.W.R, Chapman, L, Finch, J.T, Rhodes, D. | | Deposit date: | 1995-01-04 | | Release date: | 1995-11-23 | | Last modified: | 2022-12-21 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements.
Cell(Cambridge,Mass.), 75, 1993
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1HWT
 | | STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN | | Descriptor: | DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3'), PROTEIN (HEME ACTIVATOR PROTEIN), ... | | Authors: | King, D.A, Zhang, L, Guarente, L, Marmorstein, R. | | Deposit date: | 1998-09-17 | | Release date: | 1999-11-10 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein.
Nat.Struct.Biol., 6, 1999
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2HAP
 | | STRUCTURE OF A HAP1-18/DNA COMPLEX REVEALS THAT PROTEIN/DNA INTERACTIONS CAN HAVE DIRECT ALLOSTERIC EFFECTS ON TRANSCRIPTIONAL ACTIVATION | | Descriptor: | DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3'), DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3'), PROTEIN (HEME ACTIVATOR PROTEIN), ... | | Authors: | King, D.A, Zhang, L, Guarente, L, Marmorstein, R. | | Deposit date: | 1998-09-17 | | Release date: | 1999-11-10 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structure of HAP1-18-DNA implicates direct allosteric effect of protein-DNA interactions on transcriptional activation.
Nat.Struct.Biol., 6, 1999
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8SY7
 | | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-STP base pair in the active site | | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | | Authors: | Shan, Z, Lyumkis, D, Oh, J, Wang, D. | | Deposit date: | 2023-05-24 | | Release date: | 2023-12-27 | | Method: | ELECTRON MICROSCOPY (2.65 Å) | | Cite: | A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
Nat Commun, 14, 2023
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4QTR
 | | Computational design of co-assembling protein-DNA nanowires | | Descriptor: | DNA (5'-D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3'), DNA (5'-D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3'), dualENH | | Authors: | Mou, Y, Mayo, S.L. | | Deposit date: | 2014-07-08 | | Release date: | 2015-07-29 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Computational design of co-assembling protein-DNA nanowires.
Nature, 525, 2015
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8V5M
 | | Tetramer core subcomplex (conformation 1) of Xenopus laevis DNA polymerase alpha-primase | | Descriptor: | DNA polymerase alpha catalytic subunit, DNA polymerase alpha subunit B, DNA primase, ... | | Authors: | Mullins, E.A, Chazin, W.J, Eichman, B.F. | | Deposit date: | 2023-11-30 | | Release date: | 2023-12-20 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (9.22 Å) | | Cite: | A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase.
Nat.Struct.Mol.Biol., 31, 2024
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8V5O
 | | Tetramer core subcomplex (conformation 3) of Xenopus laevis DNA polymerase alpha-primase | | Descriptor: | DNA polymerase alpha catalytic subunit, DNA polymerase alpha subunit B, DNA primase, ... | | Authors: | Mullins, E.A, Chazin, W.J, Eichman, B.F. | | Deposit date: | 2023-11-30 | | Release date: | 2023-12-20 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (8.99 Å) | | Cite: | A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase.
Nat.Struct.Mol.Biol., 31, 2024
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8V5N
 | | Tetramer core subcomplex (conformation 2) of Xenopus laevis DNA polymerase alpha-primase | | Descriptor: | DNA polymerase alpha catalytic subunit, DNA polymerase alpha subunit B, DNA primase, ... | | Authors: | Mullins, E.A, Chazin, W.J, Eichman, B.F. | | Deposit date: | 2023-11-30 | | Release date: | 2023-12-20 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (8.56 Å) | | Cite: | A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase.
Nat.Struct.Mol.Biol., 31, 2024
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4Z6F
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4Z6D
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5MDN
 | | Structure of the family B DNA polymerase from the hyperthermophilic archaeon Pyrobaculum calidifontis | | Descriptor: | DNA polymerase, MAGNESIUM ION | | Authors: | Guo, J, Zhang, W, Coker, A.R, Wood, S.P, Cooper, J.B, Rashid, N, Akhtar, M. | | Deposit date: | 2016-11-12 | | Release date: | 2016-12-14 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structure of the family B DNA polymerase from the hyperthermophilic archaeon Pyrobaculum calidifontis.
Acta Crystallogr D Struct Biol, 73, 2017
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4Z6E
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4Z6C
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8G9L
 | | DNA initiation subcomplex of Xenopus laevis DNA polymerase alpha-primase | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA polymerase alpha catalytic subunit, DNA primase large subunit, ... | | Authors: | Mullins, E.A, Durie, C.L, Ohi, M.D, Chazin, W.J, Eichman, B.F. | | Deposit date: | 2023-02-21 | | Release date: | 2023-04-12 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase.
Nat.Struct.Mol.Biol., 31, 2024
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3CO7
 | | Crystal Structure of FoxO1 DBD Bound to DBE2 DNA | | Descriptor: | DNA (5'-D(*DCP*DAP*DAP*DAP*DAP*DTP*DGP*DTP*DAP*DAP*DAP*DCP*DAP*DAP*DGP*DA)-3'), DNA (5'-D(*DTP*DCP*DTP*DTP*DGP*DTP*DTP*DTP*DAP*DCP*DAP*DTP*DTP*DTP*DTP*DG)-3'), Forkhead box protein O1 | | Authors: | Brent, M.M, Anand, R, Marmorstein, R. | | Deposit date: | 2008-03-27 | | Release date: | 2008-09-16 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.91 Å) | | Cite: | Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification.
Structure, 16, 2008
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6UR9
 | | DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddGTP (nGTP), and Ca2+ | | Descriptor: | 3'-amino-2',3'-dideoxyguanosine 5'-(tetrahydrogen triphosphate), CALCIUM ION, DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... | | Authors: | Zhang, W, Lelyveld, V.S, Szostak, J.W. | | Deposit date: | 2019-10-22 | | Release date: | 2020-03-18 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.
Proc.Natl.Acad.Sci.USA, 117, 2020
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6US5
 | | DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, 3'-amino primer, dGpNHpp analog, and Mn2+ | | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3'), DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3'), ... | | Authors: | Zhang, W, Lelyveld, V.S, Szostak, J.W. | | Deposit date: | 2019-10-24 | | Release date: | 2020-03-18 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.
Proc.Natl.Acad.Sci.USA, 117, 2020
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6Y42
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1IF1
 | | INTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA | | Descriptor: | DNA (26-MER), PROTEIN (INTERFERON REGULATORY FACTOR 1) | | Authors: | Escalante, C.R, Yie, J, Thanos, D, Aggarwal, A. | | Deposit date: | 1997-09-12 | | Release date: | 1998-02-25 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structure of IRF-1 with bound DNA reveals determinants of interferon regulation.
Nature, 391, 1998
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1OCT
 | | CRYSTAL STRUCTURE OF THE OCT-1 POU DOMAIN BOUND TO AN OCTAMER SITE: DNA RECOGNITION WITH TETHERED DNA-BINDING MODULES | | Descriptor: | DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3'), PROTEIN (OCT-1 POU DOMAIN) | | Authors: | Klemm, J.D, Rould, M.A, Aurora, R, Herr, W, Pabo, C.O. | | Deposit date: | 1994-05-09 | | Release date: | 1994-08-31 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules.
Cell(Cambridge,Mass.), 77, 1994
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