PDB: 4130 resultsInfo pagesStatus searchChemie searchBIRD

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3RR5	DNA ligase from the archaeon Thermococcus sp. 1519 Descriptor: DNA ligase, MAGNESIUM ION Authors: Petrova, T, Bezsudnova, E.Y, Boyko, K.M, Mardanov, A.V, Popov, V.O, Polyakov, K.M, Ravin, N.V, Shabalin, I.G, Skryabin, K.G, Stekhanova, T.N, Kovalchuk, M.V. Deposit date: 2011-04-29 Release date: 2012-04-11 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (3.018 Å) Cite: ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain. Acta Crystallogr.,Sect.F, 68, 2012
6GDR	DNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases Descriptor: ADENOSINE MONOPHOSPHATE, DNA, DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3'), ... Authors: Williamson, A, Grigic, M, Leiros, H.K.S. Deposit date: 2018-04-24 Release date: 2018-07-25 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (2.33 Å) Cite: DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases. Nucleic Acids Res., 46, 2018
7D9K	DNA binding domain of human DNA Ligase IV - Wild type Descriptor: DNA ligase 4 Authors: Maddi, E.R, Raghavan, S.C, Natesh, R. Deposit date: 2020-10-13 Release date: 2021-02-24 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Hypomorphic mutations in human DNA ligase IV lead to compromised DNA binding efficiency, hydrophobicity and thermal stability. Protein Eng.Des.Sel., 34, 2021
7D9Y	DNA binding domain of human DNA Ligase IV mutant - A3V Descriptor: DNA ligase 4 Authors: Maddi, E.R, Raghavan, S.C, Natesh, R. Deposit date: 2020-10-14 Release date: 2021-02-24 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (2.76 Å) Cite: Hypomorphic mutations in human DNA ligase IV lead to compromised DNA binding efficiency, hydrophobicity and thermal stability. Protein Eng.Des.Sel., 34, 2021
4EQ5	DNA ligase from the archaeon Thermococcus sibiricus Descriptor: ADENOSINE MONOPHOSPHATE, DNA ligase Authors: Petrova, T, Bezsudnova, E.Y, Dorokhov, B.D, Slutskaya, E.S, Polyakov, K.M, Dorovatovskiy, P.V, Ravin, N.V, Skryabin, K.G, Kovalchuk, M.V, Popov, V.O. Deposit date: 2012-04-18 Release date: 2012-05-09 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeon Thermococcus sibiricus. Acta Crystallogr.,Sect.F, 68, 2012
9YHV	DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxorG:C captured at pre-catalytic stage Descriptor: DNA (5'-D(P*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3'), DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(8GM))-3'), DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... Authors: KanalElamparithi, B, Caglayan, M. Deposit date: 2025-10-01 Release date: 2025-12-31 Method: X-RAY DIFFRACTION (2.81 Å) Cite: Processing of DNA single-strand breaks with oxidatively damaged ends by LIG1. Nucleic Acids Res., 53, 2025
9YHY	DNA ligase 1 wild-type in complex with nick containing 3'-8oxodG:C captured at pre-catalytic stage Descriptor: DNA (5'-D(P*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3'), DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(8OG))-3'), DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... Authors: KanalElamparithi, B, Caglayan, M. Deposit date: 2025-10-01 Release date: 2025-12-31 Method: X-RAY DIFFRACTION (2.76 Å) Cite: Processing of DNA single-strand breaks with oxidatively damaged ends by LIG1. Nucleic Acids Res., 53, 2025
9YHX	DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxodG:C captured at pre-catalytic stage Descriptor: DNA (5'-D(P*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3'), DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(8OG))-3'), DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... Authors: KanalElamparithi, B, Caglayan, M. Deposit date: 2025-10-01 Release date: 2025-12-31 Method: X-RAY DIFFRACTION (2.96 Å) Cite: Processing of DNA single-strand breaks with oxidatively damaged ends by LIG1. Nucleic Acids Res., 53, 2025
4GLX	DNA ligase A in complex with inhibitor Descriptor: 2-amino-6-bromo-7-(trifluoromethyl)-1,8-naphthyridine-3-carboxamide, DNA (26-MER), DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3'), ... Authors: Prade, L, Lange, R, Tidten-Luksch, N, Chambovey, A. Deposit date: 2012-08-15 Release date: 2012-10-10 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Structure-guided design, synthesis and biological evaluation of novel DNA ligase inhibitors with in vitro and in vivo anti-staphylococcal activity. Bioorg.Med.Chem.Lett., 22, 2012
4GLW	DNA ligase A in complex with inhibitor Descriptor: 7-methoxy-6-methylpteridine-2,4-diamine, BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE, DNA ligase, ... Authors: Prade, L, Lange, R, Tidten-Luksch, N, Chambovey, A. Deposit date: 2012-08-15 Release date: 2012-10-10 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2 Å) Cite: Structure-guided design, synthesis and biological evaluation of novel DNA ligase inhibitors with in vitro and in vivo anti-staphylococcal activity. Bioorg.Med.Chem.Lett., 22, 2012
7RPX	Archaeal DNA ligase and heterotrimeric PCNA in complex with end-joined DNA Descriptor: DNA ligase, DNA polymerase sliding clamp 1, DNA polymerase sliding clamp 2, ... Authors: Sverzhinsky, A, Pascal, J.M. Deposit date: 2021-08-04 Release date: 2021-11-17 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (4.2 Å) Cite: Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure, 30, 2022
3JSN	Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus Descriptor: DNA ligase Authors: Han, S, Chang, J.S, Griffor, M. Deposit date: 2009-09-10 Release date: 2009-12-15 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus. Acta Crystallogr.,Sect.F, 65, 2009
8VDS	DNA Ligase 1 with nick DNA 3'rG:C Descriptor: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA ligase 1, DNA/RNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-R(P*G)-D(P*GP*TP*CP*GP*GP*AP*C)-3') Authors: KanalElamparithi, B, Gulkis, M, Caglayan, M. Deposit date: 2023-12-17 Release date: 2024-05-22 Method: X-RAY DIFFRACTION (2.79 Å) Cite: Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA. J.Biol.Chem., 300, 2024
8VDT	DNA Ligase 1 with nick DNA 3'rA:T Descriptor: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*TP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA ligase 1, DNA/RNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-R(P*A)-D(P*GP*TP*CP*GP*GP*AP*C)-3'), ... Authors: KanalElamparithi, B, Gulkis, M, Caglayan, M. Deposit date: 2023-12-17 Release date: 2024-05-22 Method: X-RAY DIFFRACTION (2.78 Å) Cite: Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA. J.Biol.Chem., 300, 2024
3GDE	The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus Descriptor: DNA ligase, PHOSPHATE ION Authors: Kim, D.J, Kim, H.-W, Kim, O, Kim, H.S, Lee, S.J, Suh, S.W. Deposit date: 2009-02-24 Release date: 2009-12-15 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.3 Å) Cite: ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation Acta Crystallogr.,Sect.F, 65, 2009
1UW0	Solution structure of the zinc-finger domain from DNA ligase IIIa Descriptor: DNA LIGASE III, ZINC ION Authors: Kulczyk, A.W, Yang, J.-C, Neuhaus, D. Deposit date: 2004-01-27 Release date: 2004-08-05 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Solution Structure and DNA Binding of the Zinc-Finger Domain from DNA Ligase Iiialpha J.Mol.Biol., 341, 2004
1TAE	Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal Descriptor: DNA ligase, NAD-dependent, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... Authors: Gajiwala, K.S, Pinko, C. Deposit date: 2004-05-19 Release date: 2004-11-23 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal. STRUCTURE, 12, 2004
3JSL	Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus Descriptor: DNA ligase, SULFATE ION Authors: Han, S, Chang, J.S, Griffor, M. Deposit date: 2009-09-10 Release date: 2009-12-15 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus. Acta Crystallogr.,Sect.F, 65, 2009
4HTP	Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide Descriptor: DNA ligase 4, Protein artemis Authors: De Ioannes, P.E, Aggarwal, A.K. Deposit date: 2012-11-01 Release date: 2012-12-26 Last modified: 2024-10-09 Method: X-RAY DIFFRACTION (2.2502 Å) Cite: Structural Basis of DNA Ligase IV-Artemis Interaction in Nonhomologous End-Joining. Cell Rep, 2, 2012
4HTO	Crystal structure of the DBD domain of human DNA ligase IV Apo form Descriptor: DNA ligase 4, PHOSPHATE ION Authors: De Ioannes, P.E, Aggarwal, A.K. Deposit date: 2012-11-01 Release date: 2012-12-26 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.8068 Å) Cite: Structural Basis of DNA Ligase IV-Artemis Interaction in Nonhomologous End-Joining. Cell Rep, 2, 2012
8AK4	Structure of the C-terminally truncated NAD+-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans Descriptor: DNA ligase, MANGANESE (II) ION, ZINC ION Authors: Fernandes, A, Williamson, A.K, Matias, P.M, Moe, E. Deposit date: 2022-07-29 Release date: 2023-09-27 Last modified: 2026-03-04 Method: X-RAY DIFFRACTION (3.36 Å) Cite: Structure/function studies of the NAD + -dependent DNA ligase from the poly-extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding. Extremophiles, 27, 2023
10YI	XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Descriptor: 601 I strand (non-damaged strand), 601 J strand (damaged strand 1), 601 K strand (damaged strand 2), ... Authors: Boesch, D.J, Weaver, T.M. Deposit date: 2026-02-12 Release date: 2026-03-18 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 To Be Published
10YF	DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Descriptor: 601 I strand (non-damaged strand), 601 J strand (damaged strand 1), 601 K strand (damaged strand 2), ... Authors: Boesch, D.J, Weaver, T.M. Deposit date: 2026-02-12 Release date: 2026-03-18 Method: ELECTRON MICROSCOPY (3 Å) Cite: DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 To Be Published
10YE	DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Descriptor: 601 I strand (non-damaged strand), 601 J strand (damaged strand), 601 K strand (damaged strand), ... Authors: Boesch, D.J, Weaver, T.M. Deposit date: 2026-02-12 Release date: 2026-03-18 Method: ELECTRON MICROSCOPY (2.5 Å) Cite: DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 To Be Published
10YH	DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Descriptor: 601 I strand (non-damaged strand), 601 J strand (damaged strand 1), 601 K strand (damaged strand 2), ... Authors: Boesch, D.J, Weaver, T.M. Deposit date: 2026-02-12 Release date: 2026-03-18 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 To Be Published

 

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