1P8L
 
 | | New Crystal Structure of Chlorella Virus DNA Ligase-Adenylate | | Descriptor: | ADENOSINE MONOPHOSPHATE, PBCV-1 DNA ligase | | Authors: | Odell, M, Malinina, L, Teplova, M, Shuman, S. | | Deposit date: | 2003-05-07 | | Release date: | 2003-08-26 | | Last modified: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Analysis of the DNA Joining Repertoire of Chlorella Virus DNA ligase and a New Crystal Structure of the Ligase-Adenylate Intermediate
Nucleic Acids Res., 31, 2003
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7RPW
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7RPX
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2CFM
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1JH5
 | | Crystal Structure of sTALL-1 of TNF family ligand | | Descriptor: | TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B | | Authors: | Liu, Y, Xu, L, Opalka, N, Shu, H.-B, Zhang, G. | | Deposit date: | 2001-06-27 | | Release date: | 2002-02-08 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystal structure of sTALL-1 reveals a virus-like assembly of TNF family ligands.
Cell(Cambridge,Mass.), 108, 2002
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6Q1V
 | | Human DNA Ligase 1 (E592R) Bound to an Adenylated, hydroxyl terminated DNA nick | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, ADENOSINE MONOPHOSPHATE, ... | | Authors: | Schellenberg, M.J, Williams, R.S, Tumbale, P.S, Riccio, A.A. | | Deposit date: | 2019-08-06 | | Release date: | 2019-12-11 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Two-tiered enforcement of high-fidelity DNA ligation.
Nat Commun, 10, 2019
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5Z7X
 | | Crystal structure of Striga hermonthica HTL4 (ShHTL4) | | Descriptor: | 1,2-ETHANEDIOL, Hyposensitive to light 4, MAGNESIUM ION | | Authors: | Xu, Y, Miyakawa, T, Nakamura, A, Tanokura, M. | | Deposit date: | 2018-01-30 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.055 Å) | | Cite: | Structural analysis of HTL and D14 proteins reveals the basis for ligand selectivity in Striga.
Nat Commun, 9, 2018
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1IOV
 | | COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE | | Descriptor: | 2-[(1-AMINO-ETHYL)-PHOSPHATE-PHOSPHINOYLOXY]-BUTYRIC ACID, ADENOSINE-5'-DIPHOSPHATE, D-ALA:D-ALA LIGASE, ... | | Authors: | Knox, J.R, Moews, P.C, Fan, C. | | Deposit date: | 1996-09-20 | | Release date: | 1997-02-12 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant.
Biochemistry, 36, 1997
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4LH7
 | | Crystal structure of a LigA inhibitor | | Descriptor: | 4-aminothieno[3,2-c]pyridine-2,7-dicarboxamide, BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE, DNA ligase, ... | | Authors: | Boriack-Sjodin, P.A, Prince, D.B. | | Deposit date: | 2013-06-30 | | Release date: | 2013-12-25 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Identification through structure-based methods of a bacterial NAD(+)-dependent DNA ligase inhibitor that avoids known resistance mutations.
Bioorg.Med.Chem.Lett., 24, 2014
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4LH6
 | | Crystal structure of a LigA inhibitor | | Descriptor: | 4-amino-2-bromothieno[3,2-c]pyridine-7-carboxamide, ACETATE ION, BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE, ... | | Authors: | Benenato, K, Wang, H, Mcguire, H.M, Davis, H, Gao, N, Prince, D.B, Jahic, H, Stokes, S.S, Boriack-Sjodin, P.A. | | Deposit date: | 2013-06-30 | | Release date: | 2013-12-25 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Identification through structure-based methods of a bacterial NAD(+)-dependent DNA ligase inhibitor that avoids known resistance mutations.
Bioorg.Med.Chem.Lett., 24, 2014
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8Q7R
 | | Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide | | Descriptor: | 5-azanyl-1-oxidanyl-pentan-2-one, Cullin-2, E3 ubiquitin-protein ligase RBX1, ... | | Authors: | Liwocha, J, Prabu, J.R, Kleiger, G, Schulman, B.A. | | Deposit date: | 2023-08-16 | | Release date: | 2024-02-21 | | Last modified: | 2024-04-24 | | Method: | ELECTRON MICROSCOPY (3.71 Å) | | Cite: | Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting.
Mol.Cell, 84, 2024
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1ZAU
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6TTU
 | | Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 | | Descriptor: | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY, Cullin-1, E3 ubiquitin-protein ligase RBX1, ... | | Authors: | Baek, K, Prabu, J.R, Schulman, B.A. | | Deposit date: | 2019-12-30 | | Release date: | 2020-02-12 | | Last modified: | 2020-03-04 | | Method: | ELECTRON MICROSCOPY (3.7 Å) | | Cite: | NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly.
Nature, 578, 2020
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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 | | 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
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7UFP
 | | Structure of a pseudomurein peptide ligase type E from Methanothermus fervidus | | Descriptor: | Mur ligase middle domain protein, SULFATE ION, URIDINE-5'-DIPHOSPHATE | | Authors: | Carbone, V, Schofield, L.R, Sutherland-Smith, A.J, Ronimus, R.S, Subedi, B.P. | | Deposit date: | 2022-03-23 | | Release date: | 2022-10-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases.
Microbiology (Reading, Engl.), 168, 2022
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7TZI
 | | Structure of a pseudomurein peptide ligase type E from Methanothermobacter thermautotrophicus | | Descriptor: | Mur ligase family protein | | Authors: | Carbone, V, Schofield, L.R, Sutherland-Smith, A.J, Ronimus, R.S, Subedi, B.P. | | Deposit date: | 2022-02-15 | | Release date: | 2022-10-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.911 Å) | | Cite: | Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases.
Microbiology (Reading, Engl.), 168, 2022
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5MIY
 | | Crystal structure of the E3 ubiquitin ligase RavN from Legionella pneumophila | | Descriptor: | 1,2-ETHANEDIOL, E3 ubiquitin ligase RavN, SODIUM ION, ... | | Authors: | Lucas, M, Abascal-Palacios, G, Rojas, A.L, Hierro, A. | | Deposit date: | 2016-11-29 | | Release date: | 2018-05-23 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (1.717 Å) | | Cite: | RavN is a member of a previously unrecognized group of Legionella pneumophila E3 ubiquitin ligases.
PLoS Pathog., 14, 2018
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6WH1
 | | Structure of the complex of human DNA ligase III-alpha and XRCC1 BRCT domains | | Descriptor: | DNA ligase 3 alpha, X-ray repair cross complementing protein 1 variant | | Authors: | Pourfarjam, Y, Ellenberger, T, Tainer, J.A, Tomkinson, A.E, Kim, I.K. | | Deposit date: | 2020-04-07 | | Release date: | 2020-12-02 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase III alpha within a flexible DNA repair complex.
Nucleic Acids Res., 49, 2021
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8JEB
 | | Crystal structure of CGL1 from Crassostrea gigas, mannotetraose-bound form (CGL1/Man(alpha)1-2Man(alpha)1-2Man(alpha)1-6Man) | | Descriptor: | ACETIC ACID, MAGNESIUM ION, Natterin-3, ... | | Authors: | Unno, H, Hatakeyama, T. | | Deposit date: | 2023-05-15 | | Release date: | 2023-10-25 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Mannose oligosaccharide recognition of CGL1, a mannose-specific lectin containing DM9 motifs from Crassostrea gigas, revealed by X-ray crystallographic analysis.
J.Biochem., 175, 2023
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6FX4
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8R5H
 | | Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 | | Descriptor: | (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide, 5-azanylpentan-2-one, Bromodomain-containing protein 4, ... | | Authors: | Liwocha, J, Prabu, J.R, Kleiger, G, Schulman, B.A. | | Deposit date: | 2023-11-16 | | Release date: | 2024-02-21 | | Last modified: | 2024-04-17 | | Method: | ELECTRON MICROSCOPY (3.44 Å) | | Cite: | Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting.
Mol.Cell, 84, 2024
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6DML
 | | A multiconformer ligand model of 3,5 dimethylisoxaxole bound to the bromodomain of human BRD4 | | Descriptor: | 1,2-ETHANEDIOL, 4-((2-(tert-butyl)phenyl)amino)-7-(3,5-dimethylisoxazol-4-yl)-6-methoxy-1,5-naphthyridine-3-carboxylic acid, Bromodomain-containing protein 4 | | Authors: | Hudson, B.M, van Zundert, G, Keedy, D.A, Fonseca, R, Heliou, A, Suresh, P, Borrelli, K, Day, T, Fraser, J.S, van den Bedem, H. | | Deposit date: | 2018-06-05 | | Release date: | 2018-12-19 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
J. Med. Chem., 61, 2018
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4RMC
 | | Crystal Structure of human retinoid X receptor alpha-ligand binding domain complex with 9cUAB76 and the coactivator peptide GRIP-1 | | Descriptor: | (3S,7S,8E)-8-[3-ethyl-2-(3-methylbutyl)cyclohex-2-en-1-ylidene]-3,7-dimethyloctanoic acid, Nuclear receptor coactivator 2, Retinoic acid receptor RXR-alpha | | Authors: | Xia, G, Muccio, D.D. | | Deposit date: | 2014-10-21 | | Release date: | 2015-09-16 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Conformationally Defined Rexinoids and Their Efficacy in the Prevention of Mammary Cancers.
J.Med.Chem., 58, 2015
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6DMJ
 | | A multiconformer ligand model of inhibitor 53W bound to CREB binding protein bromodomain | | Descriptor: | 5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[2-(4-methoxyphenyl)ethyl]-1-[2-(morpholin-4-yl)ethyl]-1H-benzimidazole, Bromodomain-containing protein 4 | | Authors: | Hudson, B.M, van Zundert, G, Keedy, D.A, Fonseca, R, Heliou, A, Suresh, P, Borrelli, K, Day, T, Fraser, J.S, van den Bedem, H. | | Deposit date: | 2018-06-05 | | Release date: | 2018-12-19 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.15 Å) | | Cite: | qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
J. Med. Chem., 61, 2018
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6DMK
 | | A multiconformer ligand model of an isoxazolyl-benzimidazole ligand bound to the bromodomain of human CREBBP | | Descriptor: | 1,2-ETHANEDIOL, 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazole, CREB-binding protein, ... | | Authors: | Hudson, B.M, van Zundert, G, Keedy, D.A, Fonseca, R, Heliou, A, Suresh, P, Borrelli, K, Day, T, Fraser, J.S, van den Bedem, H. | | Deposit date: | 2018-06-05 | | Release date: | 2018-12-19 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.66 Å) | | Cite: | qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
J. Med. Chem., 61, 2018
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