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1BM1
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BU of 1bm1 by Molmil
CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE
Descriptor: BACTERIORHODOPSIN, PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER, RETINAL
Authors:Sato, H, Takeda, K, Tani, K, Hino, T, Okada, T, Nakasako, M, Kamiya, N, Kouyama, T.
Deposit date:1998-07-28
Release date:1999-04-27
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:Specific lipid-protein interactions in a novel honeycomb lattice structure of bacteriorhodopsin.
Acta Crystallogr.,Sect.D, 55, 1999
7CD0
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BU of 7cd0 by Molmil
Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of human hydroxymethylbilane synthase
Descriptor: 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid, 3-[5-(aminomethyl)-4-(carboxymethyl)-2-iodo-1H-pyrrol-3-yl]propanoic acid, Porphobilinogen deaminase
Authors:Sato, H, Sugishima, M, Wada, K, Hirabayashi, K, Tsukaguchi, M.
Deposit date:2020-06-18
Release date:2021-03-17
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.31 Å)
Cite:Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Biochem.J., 478, 2021
7CCX
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BU of 7ccx by Molmil
Crystal structure of the holo form of human hydroxymethylbilane synthase
Descriptor: 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid, Porphobilinogen deaminase
Authors:Sato, H, Sugishima, M, Wada, K, Hirabayashi, K, Tsukaguchi, M.
Deposit date:2020-06-18
Release date:2021-03-17
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Biochem.J., 478, 2021
7CCZ
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BU of 7ccz by Molmil
Crystal structure of the ES2 intermediate form of human hydroxymethylbilane synthase
Descriptor: 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid, Porphobilinogen deaminase
Authors:Sato, H, Sugishima, M, Wada, K, Hirabayashi, K, Tsukaguchi, M.
Deposit date:2020-06-18
Release date:2021-03-17
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Biochem.J., 478, 2021
7CCY
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BU of 7ccy by Molmil
Crystal structure of the 2-iodoporphobilinogen-bound holo form of human hydroxymethylbilane synthase
Descriptor: 3-[5-(aminomethyl)-4-(carboxymethyl)-2-iodo-1H-pyrrol-3-yl]propanoic acid, 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid, Porphobilinogen deaminase
Authors:Sato, H, Sugishima, M, Wada, K, Hirabayashi, K, Tsukaguchi, M.
Deposit date:2020-06-18
Release date:2021-03-17
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Biochem.J., 478, 2021
2ZVU
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BU of 2zvu by Molmil
Crystal structure of rat heme oxygenase-1 in complex with ferrous verdoheme
Descriptor: 5-OXA-PROTOPORPHYRIN IX CONTAINING FE, FORMIC ACID, Heme oxygenase 1
Authors:Sato, H, Sugishima, M, Fukuyama, K, Noguchi, M.
Deposit date:2008-11-21
Release date:2009-02-03
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of rat haem oxygenase-1 in complex with ferrous verdohaem: presence of a hydrogen-bond network on the distal side
Biochem.J., 419, 2009
1QM8
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BU of 1qm8 by Molmil
Structure of Bacteriorhodopsin at 100 K
Descriptor: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE, 2,3-DI-PHYTANYL-GLYCEROL, 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL, ...
Authors:Takeda, K, Matsui, Y, Sato, H, Hino, T, Kanamori, E, Okumura, H, Yamane, T, Kamiya, N, Kouyama, T.
Deposit date:1999-09-22
Release date:2000-08-16
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:A Novel Three-Dimensional Crystal of Bacteriorhodopsin Obtained by Successive Fusion of the Vesicular Assemblies.
J.Mol.Biol., 283, 1998
5B56
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BU of 5b56 by Molmil
Crystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex
Descriptor: Importin subunit alpha-1, Protein Vpr
Authors:Miyatake, H, Sanjoh, A, Matusda, G, Murakami, T, Murakami, H, Hagiwara, K, Yokoyama, M, Sato, H, Miyamoto, Y, Dohmae, N, Aida, Y.
Deposit date:2016-04-25
Release date:2016-06-01
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Molecular Mechanism of HIV-1 Vpr for Binding to Importin-alpha
J.Mol.Biol., 428, 2016
2RVP
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BU of 2rvp by Molmil
Solution structure of DNA Containing Metallo-Base-Pair
Descriptor: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), SILVER ION
Authors:Dairaku, T, Furuita, K, Sato, H, Sebera, J, Nakashima, K, Kondo, J, Yamanaka, D, Kondo, Y, Okamoto, I, Ono, A, Sychrovsky, V, Kojima, C, Tanaka, Y.
Deposit date:2016-03-22
Release date:2016-08-31
Last modified:2023-06-14
Method:SOLUTION NMR
Cite:Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.
Chemistry, 22, 2016
1DZE
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BU of 1dze by Molmil
Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K
Descriptor: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE, 2,3-DI-PHYTANYL-GLYCEROL, 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL, ...
Authors:Takeda, K, Matsui, Y, Sato, H, Hino, T, Kanamori, E, Okumura, H, Yamane, T, Iizuka, T, Kamiya, N, Adachi, S, Kouyama, T.
Deposit date:2000-02-25
Release date:2000-08-16
Last modified:2023-12-06
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal Structure of the M Intermediate of Bacteriorhodopsin: Allosteric Structural Changes Mediated by Sliding Movement of a Transmembrane Helix
J.Mol.Biol., 341, 2004
6J7A
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BU of 6j7a by Molmil
Fusion protein of heme oxygenase-1 and NADPH cytochrome P450 reductase (17aa)
Descriptor: FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, Heme oxygenase 1,NADPH--cytochrome P450 reductase, ...
Authors:Sugishima, M, Sato, H, Wada, K, Yamamoto, K.
Deposit date:2019-01-17
Release date:2019-04-10
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (3.269 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
6J7I
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BU of 6j7i by Molmil
Fusion protein of heme oxygenase-1 and NADPH cytochrome P450 reductase (15aa)
Descriptor: FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, Heme oxygenase 1,NADPH--cytochrome P450 reductase, ...
Authors:Sugishima, M, Sato, H, Wada, K, Yamamoto, K.
Deposit date:2019-01-18
Release date:2019-04-10
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (3.3 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
1WTG
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BU of 1wtg by Molmil
Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-biphenylalanine-Gln-p-aminobenzamidine
Descriptor: 2-(3-BIPHENYL-4-YL-2-ETHANESULFONYLAMINO-PROPIONYLAMINO)-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIMIDOYL-BENZYLAMIDE), CALCIUM ION, Coagulation factor VII, ...
Authors:Kadono, S, Sakamoto, S, Kikuchi, Y, Oh-Eda, M, Yabuta, N, Kitazawa, K, Yoshihashi, T, Suzuki, T, Koga, T, Hattori, K, Shiraishi, T, Kodama, M, Haramura, H, Ono, Y, Esaki, T, Sato, H, Watanabe, Y, Itoh, S, Ohta, M, Kozono, T.
Deposit date:2004-11-23
Release date:2005-11-23
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Novel interactions of large P3 moiety and small P4 moiety in the binding of the peptide mimetic factor VIIa inhibitor
Biochem.Biophys.Res.Commun., 326, 2005
2ZZU
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BU of 2zzu by Molmil
Human Factor VIIA-Tissue Factor Complexed with ethylsulfonamide-D-5-(3-carboxybenzyloxy)-Trp-Gln-p-aminobenzamidine
Descriptor: 3-[[3-[(2R)-3-[[(2S)-5-amino-1-[(4-carbamimidoylphenyl)methylamino]-1,5-dioxo-pentan-2-yl]amino]-2-(ethylsulfonylamino)-3-oxo-propyl]-1H-indol-5-yl]oxymethyl]benzoic acid, CALCIUM ION, Factor VII heavy chain, ...
Authors:Kadono, S, Sakamoto, A, Kikuchi, Y, Oh-Eda, M, Yabuta, N, Koga, T, Hattori, K, Shiraishi, T, Haramura, M, Sato, H, Ohta, M, Kozono, T.
Deposit date:2009-02-25
Release date:2009-03-24
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Design and synthesis of peptidomimetic factor VIIa inhibitors
Chem.Pharm.Bull., 58, 2010
1WUN
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BU of 1wun by Molmil
Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-Trp-Gln-p-aminobenzamidine
Descriptor: CALCIUM ION, Coagulation factor VII, N-(ETHYLSULFONYL)TRYPTOPHYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}GLUTAMAMIDE, ...
Authors:Kadono, S, Sakamoto, A, Kikuchi, Y, Oh-eda, M, Yabuta, N, Yoshihashi, K, Kitazawa, T, Suzuki, T, Koga, T, Hattori, K, Shiraishi, T, Haramura, M, Kodama, H, Ono, Y, Esaki, T, Sato, H, Watanabe, Y, Itoh, S, Ohta, M, Kozono, T.
Deposit date:2004-12-08
Release date:2005-12-08
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor
Biochem.Biophys.Res.Commun., 327, 2005
1WSS
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BU of 1wss by Molmil
Human Factor Viia-Tissue Factor in Complex with peptide-mimetic inhibitor that has two charged groups in P2 and P4
Descriptor: CALCIUM ION, Coagulation factor VII, N-[(3-CARBOXYBENZYL)SULFONYL]ISOLEUCYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}-5-IMINOORNITHINAMIDE, ...
Authors:Kadono, S, Sakamoto, A, Kikuchi, Y, Oh-Eda, M, Yabuta, N, Koga, T, Hattori, K, Shiraishi, T, Haramura, M, Kodama, H, Ono, Y, Esaki, T, Sato, H, Watanabe, Y, Itoh, S, Ohta, M, Kozono, T.
Deposit date:2004-11-10
Release date:2005-11-10
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4.
Acta Crystallogr.,Sect.F, 61, 2005
1WV7
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BU of 1wv7 by Molmil
Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-5-propoxy-Trp-Gln-p-aminobenzamidine
Descriptor: CALCIUM ION, Coagulation factor VII, N-(ETHYLSULFONYL)-5-PROPOXY-L-TRYPTOPHYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}-L-GLUTAMAMIDE, ...
Authors:Kadono, S, Sakamoto, A, Kikuchi, Y, Oh-eda, M, Yabuta, N, Yoshihashi, K, Kitazawa, T, Suzuki, T, Koga, T, Hattori, K, Shiraishi, T, Haramura, M, Kodama, H, Ono, Y, Esaki, T, Sato, H, Watanabe, Y, Itoh, S, Ohta, M, Kozono, T.
Deposit date:2004-12-11
Release date:2005-12-11
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor
Biochem.Biophys.Res.Commun., 327, 2005
7YRP
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BU of 7yrp by Molmil
Crystal structure of VIM-28 metallo-beta-lactamase
Descriptor: CITRATE ANION, GLYCEROL, Metallo-beta-lactamase VIM-28, ...
Authors:Shimizu-Ibuka, A, Sato, H.
Deposit date:2022-08-10
Release date:2023-06-21
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structure of VIM-28 metallo-beta-lactamase
To Be Published
2ZWL
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BU of 2zwl by Molmil
Human factor viia-tissue factor complexed with highly selective peptide inhibitor
Descriptor: 2-[[(2R)-1-[[(2S)-5-amino-1-[(4-carbamimidoylphenyl)methylamino]-1,5-dioxo-pentan-2-yl]amino]-3-(1H-indol-3-yl)-1-oxo-propan-2-yl]sulfamoyl]ethanoic acid, CALCIUM ION, Factor VII heavy chain, ...
Authors:Kadono, S, Sakamoto, A, Kikuchi, Y, Oh-Eda, M, Yabuta, N, Koga, T, Hattori, K, Shiraishi, T, Haramura, M, Sato, H, Ohta, M, Kozono, T.
Deposit date:2008-12-16
Release date:2009-01-20
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Human factor viia-tissue factor complexed with highly selective peptide inhibitor
To be Published
2D6C
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BU of 2d6c by Molmil
Crystal structure of myoglobin reconstituted with iron porphycene
Descriptor: IMIDAZOLE, Myoglobin, PORPHYCENE CONTAINING FE
Authors:Hayashi, T, Murata, D, Makino, M, Sugimoto, H, Matsuo, T, Sato, H, Shiro, Y, Hisaeda, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-11-11
Release date:2006-10-31
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.26 Å)
Cite:Crystal structure and peroxidase activity of myoglobin reconstituted with iron porphycene
Inorg.Chem., 45, 2006
3WKT
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BU of 3wkt by Molmil
Complex structure of an open form of NADPH-cytochrome P450 reductase and heme oxygenase-1
Descriptor: FLAVIN MONONUCLEOTIDE, FLAVIN-ADENINE DINUCLEOTIDE, Heme oxygenase 1, ...
Authors:Sugishima, M, Sato, H, Higashimoto, Y, Harada, J, Wada, K, Fukuyama, K, Noguchi, M.
Deposit date:2013-10-31
Release date:2014-01-29
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (4.3 Å)
Cite:Structural basis for the electron transfer from an open form of NADPH-cytochrome P450 oxidoreductase to heme oxygenase.
Proc.Natl.Acad.Sci.USA, 111, 2014
1YWN
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BU of 1ywn by Molmil
Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine
Descriptor: N-{4-[4-AMINO-6-(4-METHOXYPHENYL)FURO[2,3-D]PYRIMIDIN-5-YL]PHENYL}-N'-[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]UREA, Vascular endothelial growth factor receptor 2
Authors:Miyazaki, Y, Matsunaga, S, Tang, J, Maeda, Y, Nakano, M, Philippe, R.J, Shibahara, M, Liu, W, Sato, H, Wang, L, Nolte, R.T.
Deposit date:2005-02-18
Release date:2005-08-23
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:Novel 4-amino-furo[2,3-d]pyrimidines as Tie-2 and VEGFR2 dual inhibitors
Bioorg.Med.Chem.Lett., 15, 2005
5B3T
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BU of 5b3t by Molmil
Crystal structure of apo-form biliverdin reductase from Synechocystis sp. PCC 6803
Descriptor: Biliverdin reductase, PHOSPHATE ION
Authors:Takao, H, Wada, K.
Deposit date:2016-03-12
Release date:2017-02-15
Last modified:2021-08-11
Method:X-RAY DIFFRACTION (2.099 Å)
Cite:A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity
Nat Commun, 8, 2017
5B3V
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BU of 5b3v by Molmil
Crystal structure of biliverdin reductase in complex with biliverdin and NADP+ from Synechocystis sp. PCC 6803
Descriptor: BILIVERDINE IX ALPHA, Biliverdin reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Authors:Takao, H, Wada, K.
Deposit date:2016-03-13
Release date:2017-02-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.594 Å)
Cite:A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity
Nat Commun, 8, 2017
5B3U
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BU of 5b3u by Molmil
Crystal structure of biliverdin reductase in complex with NADP+ from Synechocystis sp. PCC 6803
Descriptor: Biliverdin reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PHOSPHATE ION
Authors:Takao, H, Wada, K.
Deposit date:2016-03-13
Release date:2017-02-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.698 Å)
Cite:A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity
Nat Commun, 8, 2017

 

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