8I8F
| Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1 | Descriptor: | (2R,4S)-5,5-dimethyl-2-[(1R)-1-(2-naphthalen-1-yloxyethanoylamino)-2-oxidanyl-2-oxidanylidene-ethyl]-1,3-thiazolidine-4-carboxylic acid, Metallo beta lactamase NDM-1, ZINC ION | Authors: | Shi, X, Liu, W. | Deposit date: | 2023-02-04 | Release date: | 2024-02-07 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design. Int.J.Biol.Macromol., 262, 2024
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8GPE
| Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin G | Descriptor: | (2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid, Metallo beta lactamase NDM-1, POTASSIUM ION, ... | Authors: | Shi, X, Dai, Y, Zhang, Q, Liu, W. | Deposit date: | 2022-08-26 | Release date: | 2023-08-30 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design. Int.J.Biol.Macromol., 262, 2024
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8GPC
| Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed ampicillin | Descriptor: | (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid, Metallo beta lactamase NDM-1, SODIUM ION, ... | Authors: | Shi, X, Dai, Y, Zhang, Q, Liu, W. | Deposit date: | 2022-08-26 | Release date: | 2023-08-30 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design. Int.J.Biol.Macromol., 262, 2024
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8GPD
| Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin V | Descriptor: | (2R,4S)-5,5-dimethyl-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-phenoxyethanoylamino)ethyl]-1,3-thiazolidine-4-carboxylic acid, Metallo beta lactamase NDM-1, POTASSIUM ION, ... | Authors: | Shi, X, Dai, Y, Zhang, Q, Liu, W. | Deposit date: | 2022-08-26 | Release date: | 2023-08-30 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design. Int.J.Biol.Macromol., 262, 2024
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3EA3
| Crystal Structure of the Y246S/Y247S/Y248S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C from Bacillus Thuringiensis | Descriptor: | 1-phosphatidylinositol phosphodiesterase, MANGANESE (II) ION | Authors: | Shi, X, Shao, C, Zhang, X, Zambonelli, C, Redfied, A.G, Head, J.F, Seaton, B.A, Roberts, M.F. | Deposit date: | 2008-08-24 | Release date: | 2009-04-14 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Modulation of Bacillus thuringiensis Phosphatidylinositol-specific Phospholipase C Activity by Mutations in the Putative Dimerization Interface. J.Biol.Chem., 284, 2009
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3EA2
| Crystal Structure of the Myo-inositol bound Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C from Bacillus Thuringiensis | Descriptor: | 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE, 1-phosphatidylinositol phosphodiesterase, ZINC ION | Authors: | Shi, X, Shao, C, Zhang, X, Zambonelli, C, Redfied, A.G, Head, J.F, Seaton, B.A, Roberts, M.F. | Deposit date: | 2008-08-24 | Release date: | 2009-04-14 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Modulation of bacillus thuringiensis phosphatidylinositol-specific phospholipase C activity by mutations in the putative dimerization interface. J.Biol.Chem., 284, 2009
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3EA1
| Crystal Structure of the Y247S/Y251S Mutant of Phosphatidylinositol-Specific Phospholipase C from Bacillus Thuringiensis | Descriptor: | 1-phosphatidylinositol phosphodiesterase, ZINC ION | Authors: | Shi, X, Shao, C, Zhang, X, Zambonelli, C, Redfied, A.G, Head, J.F, Seaton, B.A, Roberts, M.F. | Deposit date: | 2008-08-24 | Release date: | 2009-04-14 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Modulation of bacillus thuringiensis phosphatidylinositol-specific phospholipase C activity by mutations in the putative dimerization interface. J.Biol.Chem., 284, 2009
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8GYZ
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3D69
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5GWT
| 4-hydroxyisoleucine dehydrogenase mutant complexed with NADH and succinate | Descriptor: | 4-hydroxyisolecuine dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SUCCINIC ACID | Authors: | Shi, X, Miyakawa, T, Nakamura, A, Tanokura, M. | Deposit date: | 2016-09-13 | Release date: | 2017-10-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Engineering a short-chain dehydrogenase/reductase for the stereoselective production of (2S,3R,4S)-4-hydroxyisoleucine with three asymmetric centers. Sci Rep, 7, 2017
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5GWR
| 4-hydroxyisoleucine dehydrogenase complexed with NADH | Descriptor: | 1,2-ETHANEDIOL, 4-hydroxyisolecuine dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | Authors: | Shi, X, Miyakawa, T, Nakamura, A, Tanokura, M. | Deposit date: | 2016-09-13 | Release date: | 2017-10-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Engineering a short-chain dehydrogenase/reductase for the stereoselective production of (2S,3R,4S)-4-hydroxyisoleucine with three asymmetric centers Sci Rep, 7, 2017
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5GWS
| 4-hydroxyisoleucine dehydrogenase complexed with NADH and succinate | Descriptor: | 4-hydroxyisolecuine dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SUCCINIC ACID | Authors: | Shi, X, Miyakawa, T, Nakamura, A, Tanokura, M. | Deposit date: | 2016-09-13 | Release date: | 2017-10-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Engineering a short-chain dehydrogenase/reductase for the stereoselective production of (2S,3R,4S)-4-hydroxyisoleucine with three asymmetric centers. Sci Rep, 7, 2017
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1VPT
| AS11 VARIANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE | Descriptor: | S-ADENOSYLMETHIONINE, VP39 | Authors: | Hodel, A.E, Gershon, P.D, Shi, X, Quiocho, F.A. | Deposit date: | 1996-03-20 | Release date: | 1996-08-17 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends. Cell(Cambridge,Mass.), 85, 1996
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5GMJ
| Crystal Structure of GRASP55 GRASP domain in complex with JAM-B C-terminus | Descriptor: | Golgi reassembly-stacking protein 2, Junctional adhesion molecule B | Authors: | Shi, N, Shi, X, Morelli, X, Betzi, S, Huang, X. | Deposit date: | 2016-07-14 | Release date: | 2017-05-24 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.986 Å) | Cite: | Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis PLoS Genet., 13, 2017
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5GMI
| Crystal Structure of GRASP55 GRASP domain in complex with JAM-C C-terminus | Descriptor: | Golgi reassembly-stacking protein 2, Junctional adhesion molecule C | Authors: | Shi, N, Shi, X, Morelli, X, Betzi, S, Huang, X. | Deposit date: | 2016-07-14 | Release date: | 2017-05-24 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.71 Å) | Cite: | Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis PLoS Genet., 13, 2017
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5GML
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4TT4
| Crystal structure of ATAD2A bromodomain complexed with H3(1-21)K14Ac peptide | Descriptor: | ATPase family AAA domain-containing protein 2, CHLORIDE ION, Histone H3(1-21)K4Ac, ... | Authors: | Poncet-Montange, G, Zhan, Y, Bardenhagen, J, Petrocchi, A, Leo, E, Shi, X, Lee, G, Leonard, P, Geck Do, M, Cardozo, M, Palmer, W, Andersen, J, Jones, P, Ladbury, J. | Deposit date: | 2014-06-19 | Release date: | 2014-12-24 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Biochem.J., 466, 2015
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4TT2
| Crystal structure of ATAD2A bromodomain complexed with H4(1-20)K5Ac peptide | Descriptor: | ATPase family AAA domain-containing protein 2, Histone H4K5Ac | Authors: | Poncet-Montange, G, Zhan, Y, Bardenhagen, J, Petrocchi, A, Leo, E, Shi, X, Lee, G, Leonard, P, Geck Do, M, Cardozo, M, Palmer, W, Andersen, J, Jones, P, Ladbury, J. | Deposit date: | 2014-06-19 | Release date: | 2014-12-24 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Biochem.J., 466, 2015
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4TU6
| Crystal structure of apo ATAD2A bromodomain with N1064 alternate conformation | Descriptor: | ATPase family AAA domain-containing protein 2, SULFATE ION | Authors: | Poncet-Montange, G, Zhan, Y, Bardenhagen, J, Petrocchi, A, Leo, E, Shi, X, Lee, G, Leonard, P, Geck Do, M, Cardozo, M, Palmer, W, Andersen, J, Jones, P, Ladbury, J. | Deposit date: | 2014-06-23 | Release date: | 2014-12-24 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.27 Å) | Cite: | Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Biochem.J., 466, 2015
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4TU4
| Crystal structure of ATAD2A bromodomain complexed with 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(phenylsulfonyl)amino]benzoicacid | Descriptor: | 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(phenylsulfonyl)amino]benzoic acid, ATPase family AAA domain-containing protein 2, CHLORIDE ION, ... | Authors: | Poncet-Montange, G, Zhan, Y, Bardenhagen, J, Petrocchi, A, Leo, E, Shi, X, Lee, G, Leonard, P, Geck Do, M, Cardozo, M, Palmer, W, Andersen, J, Jones, P, Ladbury, J. | Deposit date: | 2014-06-23 | Release date: | 2014-12-24 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.73 Å) | Cite: | Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Biochem.J., 466, 2015
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4TT6
| Crystal structure of ATAD2A bromodomain double mutant N1063A-Y1064A in apo form | Descriptor: | ATPase family AAA domain-containing protein 2, CHLORIDE ION, GLYCEROL, ... | Authors: | Poncet-Montange, G, Zhan, Y, Bardenhagen, J, Petrocchi, A, Leo, E, Shi, X, Lee, G, Leonard, P, Geck Do, M, Cardozo, M, Palmer, W, Andersen, J, Jones, P, Ladbury, J. | Deposit date: | 2014-06-19 | Release date: | 2014-12-24 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Biochem.J., 466, 2015
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4TTE
| Crystal structure of ATAD2A bromodomain complexed with methyl 3-amino-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzoate | Descriptor: | ATPase family AAA domain-containing protein 2, CHLORIDE ION, GLYCEROL, ... | Authors: | Poncet-Montange, G, Zhan, Y, Bardenhagen, J, Petrocchi, A, Leo, E, Shi, X, Lee, G, Leonard, P, Geck Do, M, Cardozo, M, Palmer, W, Andersen, J, Jones, P, Ladbury, J. | Deposit date: | 2014-06-20 | Release date: | 2014-12-24 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Biochem.J., 466, 2015
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8KD7
| Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA | Descriptor: | 167bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... | Authors: | Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Chang, X, Chao, W.C.H, He, J. | Deposit date: | 2023-08-09 | Release date: | 2023-09-13 | Last modified: | 2023-10-11 | Method: | ELECTRON MICROSCOPY (3.09 Å) | Cite: | Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
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8KD4
| Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 | Descriptor: | 187bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... | Authors: | Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Zhang, X, Chao, W.C.H, He, J. | Deposit date: | 2023-08-09 | Release date: | 2023-09-13 | Last modified: | 2023-10-11 | Method: | ELECTRON MICROSCOPY (2.93 Å) | Cite: | Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
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8KD2
| Rpd3S in complex with 187bp nucleosome | Descriptor: | 187bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... | Authors: | Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Zhang, X, Chao, W.C.H, He, J. | Deposit date: | 2023-08-09 | Release date: | 2023-09-13 | Last modified: | 2023-10-11 | Method: | ELECTRON MICROSCOPY (3.02 Å) | Cite: | Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
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