5D1P
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![BU of 5d1p by Molmil](/molmil-images/mine/5d1p) | Archaeal ATP-dependent RNA ligase - form 2 | Descriptor: | ATP-dependent RNA ligase, MAGNESIUM ION, SULFATE ION | Authors: | Murakami, K.S. | Deposit date: | 2015-08-04 | Release date: | 2016-03-09 | Last modified: | 2016-03-30 | Method: | X-RAY DIFFRACTION (2.199 Å) | Cite: | Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis. Nucleic Acids Res., 44, 2016
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4XM6
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![BU of 4xm6 by Molmil](/molmil-images/mine/4xm6) | Anthrax toxin lethal factor with ligand-induced binding pocket | Descriptor: | 1,2-ETHANEDIOL, Lethal factor, N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-(2-methylpropyl)-D-valinamide, ... | Authors: | Maize, K.M, De la Mora-Rey, T, Finzel, B.C. | Deposit date: | 2015-01-14 | Release date: | 2015-11-11 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.352 Å) | Cite: | Ligand-induced expansion of the S1' site in the anthrax toxin lethal factor. Febs Lett., 589, 2015
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6FYH
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![BU of 6fyh by Molmil](/molmil-images/mine/6fyh) | Disulfide between ubiquitin G76C and the E3 HECT ligase Huwe1 | Descriptor: | E3 ubiquitin-protein ligase HUWE1, Polyubiquitin-B, SULFATE ION, ... | Authors: | Jaeckl, M, Hartmann, M.D, Wiesner, S. | Deposit date: | 2018-03-12 | Release date: | 2018-07-11 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.906 Å) | Cite: | beta-Sheet Augmentation Is a Conserved Mechanism of Priming HECT E3 Ligases for Ubiquitin Ligation. J. Mol. Biol., 430, 2018
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8AK4
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![BU of 8ak4 by Molmil](/molmil-images/mine/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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7TZI
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![BU of 7tzi by Molmil](/molmil-images/mine/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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7UFP
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![BU of 7ufp by Molmil](/molmil-images/mine/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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8Q7R
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![BU of 8q7r by Molmil](/molmil-images/mine/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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6DMK
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![BU of 6dmk by Molmil](/molmil-images/mine/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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6DMH
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![BU of 6dmh by Molmil](/molmil-images/mine/6dmh) | A multiconformer ligand model of acylenzyme intermediate of meropenem bound to an SFC-1 E166A mutant | Descriptor: | (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid, 1,2-ETHANEDIOL, Beta-lactamase | 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 (1.3 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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1Z15
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![BU of 1z15 by Molmil](/molmil-images/mine/1z15) | Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein in superopen form | Descriptor: | Leu/Ile/Val-binding protein | Authors: | Trakhanov, S.D, Vyas, N.K, Kristensen, D.M, Ma, J, Quiocho, F.A. | Deposit date: | 2005-03-03 | Release date: | 2005-10-04 | Last modified: | 2023-08-23 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity. Biochemistry, 44, 2005
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8JEB
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![BU of 8jeb by Molmil](/molmil-images/mine/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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1Z18
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![BU of 1z18 by Molmil](/molmil-images/mine/1z18) | Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound valine | Descriptor: | CADMIUM ION, Leu/Ile/Val-binding protein, VALINE | Authors: | Trakhanov, S.D, Vyas, N.K, Kristensen, D.M, Ma, J, Quiocho, F.A. | Deposit date: | 2005-03-03 | Release date: | 2005-10-04 | Last modified: | 2023-08-23 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity. Biochemistry, 44, 2005
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7BCN
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![BU of 7bcn by Molmil](/molmil-images/mine/7bcn) | Crystal structure of the sugar acid binding protein DctPAm from Advenella mimigardefordensis strain DPN7T in complex with Xylonic acid | Descriptor: | D-xylonic acid, Putative TRAP transporter solute receptor DctP | Authors: | Schaefer, L, Meinert, C, Kobus, S, Hoeppner, A, Smits, S.H, Steinbuechel, A. | Deposit date: | 2020-12-21 | Release date: | 2021-04-14 | Last modified: | 2024-01-31 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal structure of the sugar acid-binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7 T . Febs J., 288, 2021
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4LH7
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![BU of 4lh7 by Molmil](/molmil-images/mine/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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6DML
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![BU of 6dml by Molmil](/molmil-images/mine/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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6DMJ
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![BU of 6dmj by Molmil](/molmil-images/mine/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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4LH6
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![BU of 4lh6 by Molmil](/molmil-images/mine/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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6DMI
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![BU of 6dmi by Molmil](/molmil-images/mine/6dmi) | A multiconformer ligand model of 5T5 bound to BACE-1 | Descriptor: | Beta-secretase 1, DIMETHYL SULFOXIDE, SODIUM ION, ... | 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 (1.9 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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1Z16
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![BU of 1z16 by Molmil](/molmil-images/mine/1z16) | Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound leucine | Descriptor: | CADMIUM ION, LEUCINE, Leu/Ile/Val-binding protein | Authors: | Trakhanov, S.D, Vyas, N.K, Kristensen, D.M, Ma, J, Quiocho, F.A. | Deposit date: | 2005-03-03 | Release date: | 2005-10-04 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.72 Å) | Cite: | Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity. Biochemistry, 44, 2005
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2OOB
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![BU of 2oob by Molmil](/molmil-images/mine/2oob) | |
4C5A
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![BU of 4c5a by Molmil](/molmil-images/mine/4c5a) | The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and D-cycloserine phosphate | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, D-ALANINE--D-ALANINE LIGASE, GLYCEROL, ... | Authors: | Batson, S, Majce, V, Lloyd, A.J, Rea, D, Fishwick, C.W.G, Simmons, K.J, Fulop, V, Roper, D.I. | Deposit date: | 2013-09-10 | Release date: | 2015-01-21 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine. Nat Commun, 8, 2017
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4C5B
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![BU of 4c5b by Molmil](/molmil-images/mine/4c5b) | The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ATP and D-ala-D-ala | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, CARBONATE ION, D-ALANINE, ... | Authors: | Batson, S, Majce, V, Lloyd, A.J, Rea, D, Fishwick, C.W.G, Simmons, K.J, Fulop, V, Roper, D.I. | Deposit date: | 2013-09-10 | Release date: | 2015-01-21 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine. Nat Commun, 8, 2017
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4C5C
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![BU of 4c5c by Molmil](/molmil-images/mine/4c5c) | The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ADP and D-ala-D-ala | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, D-ALANINE, D-ALANINE--D-ALANINE LIGASE, ... | Authors: | Batson, S, Majce, V, Lloyd, A.J, Rea, D, Fishwick, C.W.G, Simmons, K.J, Fulop, V, Roper, D.I. | Deposit date: | 2013-09-10 | Release date: | 2015-01-21 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine. Nat Commun, 8, 2017
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3Q4J
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![BU of 3q4j by Molmil](/molmil-images/mine/3q4j) | Structure of a small peptide ligand bound to E.coli DNA sliding clamp | Descriptor: | DNA polymerase III subunit beta, peptide ligand | Authors: | Wolff, P, Olieric, V, Briand, J.P, Chaloin, O, Dejaegere, A, Dumas, P, Ennifar, E, Guichard, G, Wagner, J, Burnouf, D. | Deposit date: | 2010-12-23 | Release date: | 2011-12-28 | Last modified: | 2013-03-20 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structure-based design of short peptide ligands binding onto the E. coli processivity ring. J.Med.Chem., 54, 2011
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3Q4L
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![BU of 3q4l by Molmil](/molmil-images/mine/3q4l) | Structure of a small peptide ligand bound to E.coli DNA sliding clamp | Descriptor: | DNA polymerase III subunit beta, SODIUM ION, peptide ligand | Authors: | Wolff, P, Olieric, V, Briand, J.P, Chaloin, O, Dejaegere, A, Dumas, P, Ennifar, E, Guichard, G, Wagner, J, Burnouf, D. | Deposit date: | 2010-12-23 | Release date: | 2011-12-28 | Last modified: | 2013-03-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Structure-based design of short peptide ligands binding onto the E. coli processivity ring. J.Med.Chem., 54, 2011
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