3VRT
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![BU of 3vrt by Molmil](/molmil-images/mine/3vrt) | VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3 | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Nakabayashi, M, Yoshimoto, N, Inaba, Y, Itoh, T, Ito, N, Yamamoto, K. | Deposit date: | 2012-04-14 | Release date: | 2012-05-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands J.Med.Chem., 55, 2012
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3WT7
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![BU of 3wt7 by Molmil](/molmil-images/mine/3wt7) | Crystal structure of VDR-LBD complexed with 22R-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1 ,25-dihydroxyvitamin D3 | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | Deposit date: | 2014-04-08 | Release date: | 2014-06-11 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group. J.Med.Chem., 57, 2014
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3WT6
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![BU of 3wt6 by Molmil](/molmil-images/mine/3wt6) | A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: Active vitamin D analogues with 22R-alkyl group | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | Deposit date: | 2014-04-08 | Release date: | 2014-06-11 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group. J.Med.Chem., 57, 2014
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3WC6
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![BU of 3wc6 by Molmil](/molmil-images/mine/3wc6) | Carboxypeptidase B in complex with 2nd zinc | Descriptor: | ACETATE ION, Carboxypeptidase B, ZINC ION | Authors: | Yoshimoto, N, Itoh, T, Inaba, Y, Yamamoto, K. | Deposit date: | 2013-05-24 | Release date: | 2013-10-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme. J.Med.Chem., 56, 2013
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3X1H
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![BU of 3x1h by Molmil](/molmil-images/mine/3x1h) | hPPARgamma Ligand binding domain in complex with 5-oxo-tricosahexaenoic acid | Descriptor: | (7E,11Z,14Z,17Z,20Z)-5-oxotricosa-7,11,14,17,20-pentaenoic acid, Peroxisome proliferator-activated receptor gamma | Authors: | Egawa, D, Itoh, T, Yamamoto, K. | Deposit date: | 2014-11-18 | Release date: | 2015-04-08 | Last modified: | 2022-08-24 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Characterization of covalent bond formation between PPAR gamma and oxo-fatty acids. Bioconjug.Chem., 26, 2015
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3X1I
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![BU of 3x1i by Molmil](/molmil-images/mine/3x1i) | hPPARgamma Ligand binding domain in complex with 6-oxo-tetracosahexaenoic acid | Descriptor: | (8E,12Z,15Z,18Z,21Z)-6-oxotetracosa-8,12,15,18,21-pentaenoic acid, Peroxisome proliferator-activated receptor gamma | Authors: | Egawa, D, Itoh, T, Yamamoto, K. | Deposit date: | 2014-11-18 | Release date: | 2015-04-08 | Last modified: | 2022-08-24 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Characterization of covalent bond formation between PPAR gamma and oxo-fatty acids. Bioconjug.Chem., 26, 2015
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7EFL
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![BU of 7efl by Molmil](/molmil-images/mine/7efl) | Crystal structure of the gastric proton pump K791S in (BYK)E2BeF state | Descriptor: | (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... | Authors: | Abe, K, Yamamoto, K, Irie, K. | Deposit date: | 2021-03-22 | Release date: | 2021-09-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.4 Å) | Cite: | Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun, 12, 2021
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7EFM
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![BU of 7efm by Molmil](/molmil-images/mine/7efm) | Crystal structure of the gastric proton pump K791S/E820D/Y340N in (BYK)E2BeF state | Descriptor: | (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... | Authors: | Abe, K, Yamamoto, K, Irie, K. | Deposit date: | 2021-03-22 | Release date: | 2021-09-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun, 12, 2021
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7EFN
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![BU of 7efn by Molmil](/molmil-images/mine/7efn) | Crystal structure of the gastric proton pump K791S/E820D/Y340N/E936V in (BYK)E2BeF state | Descriptor: | (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... | Authors: | Abe, K, Yamamoto, K, Irie, K. | Deposit date: | 2021-03-22 | Release date: | 2021-09-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun, 12, 2021
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9B70
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![BU of 9b70 by Molmil](/molmil-images/mine/9b70) | Cryo-EM structure of MraY in complex with analogue 2 | Descriptor: | (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{S})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid, MraYAA nanobody, Phospho-N-acetylmuramoyl-pentapeptide-transferase | Authors: | Hao, A, Lee, S.-Y. | Deposit date: | 2024-03-26 | Release date: | 2024-06-26 | Method: | ELECTRON MICROSCOPY (2.88 Å) | Cite: | Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target. Nat Commun, 15, 2024
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9B71
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![BU of 9b71 by Molmil](/molmil-images/mine/9b71) | Cryo-EM structure of MraY in complex with analogue 3 | Descriptor: | (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]-2-[[4-[[[(2~{S})-5-carbamimidamido-2-(hexadecanoylamino)pentanoyl]amino]methyl]phenyl]methylamino]propanoic acid, MraYAA Nanobody, Phospho-N-acetylmuramoyl-pentapeptide-transferase | Authors: | Hao, A, Lee, S.-Y. | Deposit date: | 2024-03-26 | Release date: | 2024-06-26 | Method: | ELECTRON MICROSCOPY (2.7 Å) | Cite: | Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target. Nat Commun, 15, 2024
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6JXI
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![BU of 6jxi by Molmil](/molmil-images/mine/6jxi) | Rb+-bound E2-MgF state of the gastric proton pump (Tyr799Trp) | Descriptor: | 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHOLESTEROL, ... | Authors: | Abe, K, Irie, K. | Deposit date: | 2019-04-23 | Release date: | 2019-08-14 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | A single K + -binding site in the crystal structure of the gastric proton pump. Elife, 8, 2019
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6JXH
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![BU of 6jxh by Molmil](/molmil-images/mine/6jxh) | K+-bound E2-MgF state of the gastric proton pump (Tyr799Trp) | Descriptor: | 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHOLESTEROL, ... | Authors: | Abe, K, Irie, K. | Deposit date: | 2019-04-23 | Release date: | 2019-08-14 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | A single K + -binding site in the crystal structure of the gastric proton pump. Elife, 8, 2019
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6JXJ
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![BU of 6jxj by Molmil](/molmil-images/mine/6jxj) | Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp) | Descriptor: | 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHOLESTEROL, ... | Authors: | Abe, K, Irie, K. | Deposit date: | 2019-04-23 | Release date: | 2019-08-14 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | A single K + -binding site in the crystal structure of the gastric proton pump. Elife, 8, 2019
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4JAW
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![BU of 4jaw by Molmil](/molmil-images/mine/4jaw) | Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifidum complexed with LNB-thiazoline | Descriptor: | 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL, Lacto-N-biosidase, SULFATE ION, ... | Authors: | Ito, T, Katayama, T, Stubbs, K.A, Fushinobu, S. | Deposit date: | 2013-02-19 | Release date: | 2013-03-20 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum J.Biol.Chem., 288, 2013
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2VSR
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![BU of 2vsr by Molmil](/molmil-images/mine/2vsr) | hPPARgamma Ligand binding domain in complex with 9-(S)-HODE | Descriptor: | (9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid, PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA | Authors: | Itoh, T, Fairall, L, Schwabe, J.W.R. | Deposit date: | 2008-04-29 | Release date: | 2008-08-19 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Structural Basis for the Activation of Pparg by Oxidised Fatty Acids Nat.Struct.Mol.Biol., 15, 2008
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2VV2
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![BU of 2vv2 by Molmil](/molmil-images/mine/2vv2) | hPPARgamma Ligand binding domain in complex with 5-HEPA | Descriptor: | (5R,6E,8Z,11Z,14Z,17Z)-5-hydroxyicosa-6,8,11,14,17-pentaenoic acid, PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA | Authors: | Itoh, T, Fairall, L, Schwabe, J.W.R. | Deposit date: | 2008-06-02 | Release date: | 2008-08-19 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Structural Basis for the Activation of Pparg by Oxidised Fatty Acids Nat.Struct.Mol.Biol., 15, 2008
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2VV4
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![BU of 2vv4 by Molmil](/molmil-images/mine/2vv4) | hPPARgamma Ligand binding domain in complex with 6-oxoOTE | Descriptor: | (8E,10S,12Z)-10-hydroxy-6-oxooctadeca-8,12-dienoic acid, (8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12-dienoic acid, PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA | Authors: | Itoh, T, Fairall, L, Schwabe, J.W.R. | Deposit date: | 2008-06-02 | Release date: | 2008-08-19 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural Basis for the Activation of Pparg by Oxidised Fatty Acids Nat.Struct.Mol.Biol., 15, 2008
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2VST
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![BU of 2vst by Molmil](/molmil-images/mine/2vst) | hPPARgamma Ligand binding domain in complex with 13-(S)-HODE | Descriptor: | (9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid, PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA | Authors: | Itoh, T, Fairall, L, Schwabe, J.W.R. | Deposit date: | 2008-04-29 | Release date: | 2008-08-19 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural Basis for the Activation of Pparg by Oxidised Fatty Acids Nat.Struct.Mol.Biol., 15, 2008
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2VV0
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![BU of 2vv0 by Molmil](/molmil-images/mine/2vv0) | hPPARgamma Ligand binding domain in complex with DHA | Descriptor: | DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID, PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA | Authors: | Itoh, T, Fairall, L, Schwabe, J.W.R. | Deposit date: | 2008-06-02 | Release date: | 2008-08-19 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Structural Basis for the Activation of Pparg by Oxidised Fatty Acids Nat.Struct.Mol.Biol., 15, 2008
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8CXR
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![BU of 8cxr by Molmil](/molmil-images/mine/8cxr) | Crystal structure of MraY bound to a sphaerimicin analogue | Descriptor: | (1S,4R,5S,6R,7S,9S,10S,11S,13S,14R)-9-[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]-14-(hexadecanoyloxy)-5,6,13-trihydroxy-8,16-dioxa-2,11-diazatricyclo[9.3.1.1~4,7~]hexadecane-10-carboxylic acid, MraYAA nanobody, Phospho-N-acetylmuramoyl-pentapeptide-transferase | Authors: | Mashalidis, E.H, Lee, S.Y. | Deposit date: | 2022-05-22 | Release date: | 2023-03-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3.65 Å) | Cite: | Synthesis of macrocyclic nucleoside antibacterials and their interactions with MraY. Nat Commun, 13, 2022
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6J79
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![BU of 6j79 by Molmil](/molmil-images/mine/6j79) | Fusion protein of heme oxygenase-1 and NADPH-cytochrome P450 reductase (13aa) | Descriptor: | FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, Heme oxygenase 1,NADPH--cytochrome P450 reductase, ... | Authors: | Sugishima, M, Wada, K. | Deposit date: | 2019-01-17 | Release date: | 2019-04-10 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.331 Å) | Cite: | Crystal structure of a NADPH-cytochrome P450 oxidoreductase (CYPOR) and heme oxygenase 1 fusion protein implies a conformational change in CYPOR upon NADPH/NADP+binding. Febs Lett., 593, 2019
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6T9C
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![BU of 6t9c by Molmil](/molmil-images/mine/6t9c) | |
5B3T
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![BU of 5b3t by Molmil](/molmil-images/mine/5b3t) | |
5B3V
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![BU of 5b3v by Molmil](/molmil-images/mine/5b3v) | |