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1C53
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BU of 1c53 by Molmil
S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD
Descriptor: CYTOCHROME C553, PROTOPORPHYRIN IX CONTAINING FE
Authors:Nakagawa, A, Higuchi, Y, Yasuoka, N, Katsube, Y, Yaga, T.
Deposit date:1991-08-26
Release date:1993-10-31
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:S-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from Desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method.
J.Biochem.(Tokyo), 108, 1990
1BK7
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BU of 1bk7 by Molmil
RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD
Descriptor: PROTEIN (RIBONUCLEASE MC1)
Authors:Nakagawa, A, Tanaka, I.
Deposit date:1998-07-15
Release date:1999-07-23
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution.
Biochim.Biophys.Acta, 1433, 1999
1RL2
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BU of 1rl2 by Molmil
RIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERMOPHILUS
Descriptor: PROTEIN (RIBOSOMAL PROTEIN L2)
Authors:Nakagawa, A, Hosaka, H, Nakashima, T, Tanaka, I.
Deposit date:1999-03-25
Release date:1999-04-02
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome.
EMBO J., 18, 1999
1UF2
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BU of 1uf2 by Molmil
The Atomic Structure of Rice dwarf Virus (RDV)
Descriptor: Core protein P3, Outer capsid protein P8, Structural protein P7
Authors:Nakagawa, A, Miyazaki, N, Taka, J, Naitow, H, Ogawa, A, Fujimoto, Z, Mizuno, H, Higashi, T, Watanabe, Y, Omura, T, Cheng, R.H, Tsukihara, T.
Deposit date:2003-05-23
Release date:2003-10-14
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins.
Structure, 11, 2003
4NI0
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BU of 4ni0 by Molmil
Quaternary R3 CO-liganded hemoglobin structure in complex with a thiol containing compound
Descriptor: 5-[(2S)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione, CARBON MONOXIDE, Hemoglobin subunit alpha, ...
Authors:Safo, M.K, Meadows, J, Ko, T.-P, Nakagawa, A, Zapol, W.
Deposit date:2013-11-05
Release date:2014-08-20
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Identification of a Small Molecule that Increases Hemoglobin Oxygen Affinity and Reduces SS Erythrocyte Sickling.
Acs Chem.Biol., 9, 2014
4NI1
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BU of 4ni1 by Molmil
Quaternary R CO-liganded hemoglobin structure in complex with a thiol containing compound
Descriptor: 5-[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione, CARBON MONOXIDE, Hemoglobin subunit alpha, ...
Authors:Safo, M.K, Meadows, J, Ko, T.-P, Nakagawa, A, Zapol, W.
Deposit date:2013-11-05
Release date:2014-09-17
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Identification of a Small Molecule that Increases Hemoglobin Oxygen Affinity and Reduces SS Erythrocyte Sickling.
Acs Chem.Biol., 9, 2014
1O5W
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BU of 1o5w by Molmil
The structure basis of specific recognitions for substrates and inhibitors of rat monoamine oxidase A
Descriptor: Amine oxidase [flavin-containing] A, FLAVIN-ADENINE DINUCLEOTIDE, N-[3-(2,4-DICHLOROPHENOXY)PROPYL]-N-METHYL-N-PROP-2-YNYLAMINE
Authors:Ma, J, Yoshimura, M, Yamashita, E, Nakagawa, A, Ito, A, Tsukihara, T.
Deposit date:2003-10-06
Release date:2004-04-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structure of rat monoamine oxidase a and its specific recognitions for substrates and inhibitors.
J.Mol.Biol., 338, 2004
4P76
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BU of 4p76 by Molmil
Cellular response to a crystal-forming protein
Descriptor: Photoconvertible fluorescent protein, SODIUM ION
Authors:Tsutsui, H, Jinno, Y, Shoda, K, Tomita, A, Matsuda, M, Yamashita, E, Katayama, H, Nakagawa, A, Miyawaki, A.
Deposit date:2014-03-26
Release date:2015-04-29
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:A diffraction-quality protein crystal processed as an autophagic cargo
Mol.Cell, 58, 2015
2ROM
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BU of 2rom by Molmil
CRYSTAL STRUCTURE OF NITRIC REDUCTASE FROM DENITRIFYING FUNGUS FUSARIUM OXYSPORUM COMPLEX WITH CARBON MONOXIDE
Descriptor: CARBON MONOXIDE, CYTOCHROME P450, PROTOPORPHYRIN IX CONTAINING FE
Authors:Park, S.-Y, Nakagawa, A.
Deposit date:1997-03-24
Release date:1997-10-15
Last modified:2024-02-21
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum.
Nat.Struct.Biol., 4, 1997
2RSY
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BU of 2rsy by Molmil
Solution structure of the SH2 domain of Csk in complex with a phosphopeptide from Cbp
Descriptor: Phosphoprotein associated with glycosphingolipid-enriched microdomains 1, Tyrosine-protein kinase CSK
Authors:Tanaka, H, Akagi, K, Oneyama, C, Tanaka, M, Sasaki, Y, Kanou, T, Lee, Y, Yokogawa, D, Debenecker, M, Nakagawa, A, Okada, M, Ikegami, T.
Deposit date:2012-09-10
Release date:2013-04-10
Last modified:2019-12-25
Method:SOLUTION NMR
Cite:Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains.
J.Biol.Chem., 288, 2013
3VPQ
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BU of 3vpq by Molmil
Crystal structure of Bombyx mori sigma-class glutathione transferase in complex with glutathione
Descriptor: DI(HYDROXYETHYL)ETHER, GLUTATHIONE, Glutathione S-transferase sigma, ...
Authors:Yamamoto, K, Higashiura, A, Nakagawa, A, Suzuki, M.
Deposit date:2012-03-08
Release date:2013-03-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.702 Å)
Cite:Crystal structure of a Bombyx mori sigma-class glutathione transferase exhibiting prostaglandin E synthase activity
Biochim.Biophys.Acta, 1830, 2013
3VUR
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BU of 3vur by Molmil
Crystal structure of Bombyx mori sigma-class glutathione transferase in complex with glutathionesulfonic acid
Descriptor: GLUTATHIONE SULFONIC ACID, Glutathione S-transferase sigma, PENTAETHYLENE GLYCOL
Authors:Yamamoto, K, Higashiura, A, Nakagawa, A, Suzuki, M.
Deposit date:2012-07-05
Release date:2013-07-10
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.365 Å)
Cite:Crystal structure of Bombyx mori sigma-class glutathione transferase in complex with glutathionesulfonic acid
TO BE PUBLISHED
6IOL
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BU of 6iol by Molmil
Cryo-EM structure of multidrug efflux pump MexAB-OprM (60 degree state)
Descriptor: Multidrug resistance protein MexA, Multidrug resistance protein MexB, Outer membrane protein OprM
Authors:Tsutsumi, K, Yonehara, R, Nakagawa, A, Yamashita, E.
Deposit date:2018-10-30
Release date:2019-04-03
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (3.76 Å)
Cite:Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism.
Nat Commun, 10, 2019
1DPT
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BU of 1dpt by Molmil
D-DOPACHROME TAUTOMERASE
Descriptor: D-DOPACHROME TAUTOMERASE
Authors:Sugimoto, H, Taniguchi, M, Nakagawa, A, Tanaka, I.
Deposit date:1998-05-11
Release date:1999-03-30
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Crystal structure of human D-dopachrome tautomerase, a homologue of macrophage migration inhibitory factor, at 1.54 A resolution.
Biochemistry, 38, 1999
3VMZ
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BU of 3vmz by Molmil
Crystal Structure of a parallel coiled-coil dimerization domain from the voltage-gated proton channel (oxidation/H2O2)
Descriptor: Voltage-gated hydrogen channel 1
Authors:Fujiwara, Y, Takeshita, K, Kobayashi, M, Okamura, Y, Nakagawa, A.
Deposit date:2011-12-19
Release date:2013-01-30
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Crystal Structure of a Parallel Coiled-Coil Dimerization Domain from the Voltage-Gated Proton Channel (Oxidation/H2O2)
To be Published
3VRP
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BU of 3vrp by Molmil
Crystal structure of the tyrosine kinase binding domain of Cbl-c in complex with phospho-EGFR peptide
Descriptor: CALCIUM ION, Epidermal growth factor receptor, Signal transduction protein CBL-C
Authors:Takeshita, K, Tezuka, T, Isozaki, Y, Yamashita, E, Suzuki, M, Yamanashi, Y, Yamamoto, T, Nakagawa, A.
Deposit date:2012-04-13
Release date:2013-03-06
Method:X-RAY DIFFRACTION (1.52 Å)
Cite:Structural flexibility regulates phosphopeptide-binding activity of the tyrosine kinase binding domain of Cbl-c.
J.Biochem., 152, 2012
3VMY
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BU of 3vmy by Molmil
Crystal Structure of a parallel coiled-coil dimerization domain from the voltage-gated proton channel (REDUCTION/DTT)
Descriptor: Voltage-gated hydrogen channel 1
Authors:Fujiwara, Y, Takeshita, K, Kobayashi, M, Okamura, Y, Nakagawa, A.
Deposit date:2011-12-19
Release date:2013-01-30
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.47 Å)
Cite:Crystal Structure of a Parallel Coiled-Coil Dimerization Domain from the Voltage-Gated Proton Channel (Reduction/Dtt)
To be Published
3VQF
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BU of 3vqf by Molmil
Crystal Structure Analysis of the PDZ Domain Derived from the Tight Junction Regulating Protein
Descriptor: E3 ubiquitin-protein ligase LNX
Authors:Akiyoshi, Y, Hamada, D, Goda, N, Tenno, T, Narita, H, Nakagawa, A, Furuse, M, Suzuki, M, Hiroaki, H.
Deposit date:2012-03-22
Release date:2013-03-27
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.199 Å)
Cite:Structural basis for down regulation of tight junction by PDZ-domain containing E3-Ubiquitin ligase
To be Published
3VTO
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BU of 3vto by Molmil
The crystal structure of the C-terminal domain of Mu phage central spike
Descriptor: CALCIUM ION, CHLORIDE ION, FE (III) ION, ...
Authors:Harada, K, Yamashita, E, Nakagawa, A, Takeda, S.
Deposit date:2012-06-01
Release date:2013-02-06
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.44 Å)
Cite:Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion
Biochim.Biophys.Acta, 1834, 2013
4WY3
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BU of 4wy3 by Molmil
Structure of SARS-3CL protease complex with a phenylbenzoyl (R,S)-N-decalin type inhibitor
Descriptor: (2S)-2-({[(3R,4aS,8aR)-2-(biphenyl-4-ylcarbonyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal, 3C-like proteinase
Authors:Akaji, K, Teruya, K, Shimamoto, Y, Sanjho, A, Yamashita, E, Nakagawa, A.
Deposit date:2014-11-15
Release date:2015-02-18
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors.
Bioorg.Med.Chem., 23, 2015
5H5L
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BU of 5h5l by Molmil
Structure of prostaglandin synthase D of Nilaparvata lugens
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLUTATHIONE, ...
Authors:Yamamoto, K, Higashiura, A, Suzuki, S, Nakagawa, A.
Deposit date:2016-11-07
Release date:2017-09-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.999 Å)
Cite:Molecular structure of a prostaglandin D synthase requiring glutathione from the brown planthopper, Nilaparvata lugens
Biochem. Biophys. Res. Commun., 492, 2017
1QSH
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BU of 1qsh by Molmil
MAGNESIUM(II)-AND ZINC(II)-PROTOPORPHYRIN IX'S STABILIZE THE LOWEST OXYGEN AFFINITY STATE OF HUMAN HEMOGLOBIN EVEN MORE STRONGLY THAN DEOXYHEME
Descriptor: PROTEIN (HEMOGLOBIN ALPHA CHAIN), PROTEIN (HEMOGLOBIN BETA CHAIN), PROTOPORPHYRIN IX CONTAINING FE, ...
Authors:Miyazaki, G, Morimoto, H, Yun, K.-M, Park, S.-Y, Nakagawa, A, Minagawa, H, Shibayama, N.
Deposit date:1999-06-22
Release date:1999-07-02
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme.
J.Mol.Biol., 292, 1999
1QSI
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BU of 1qsi by Molmil
MAGNESIUM(II)-AND ZINC(II)-PROTOPORPHYRIN IX'S STABILIZE THE LOWEST OXYGEN AFFINITY STATE OF HUMAN HEMOGLOBIN EVEN MORE STRONGLY THAN DEOXYHEME
Descriptor: CARBON MONOXIDE, PROTEIN (HEMOGLOBIN ALPHA CHAIN), PROTEIN (HEMOGLOBIN BETA CHAIN), ...
Authors:Miyazaki, G, Morimoto, H, Yun, K.-M, Park, S.-Y, Nakagawa, A, Minagawa, H, Shibayama, N.
Deposit date:1999-06-22
Release date:1999-07-02
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme.
J.Mol.Biol., 292, 1999
5X6U
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BU of 5x6u by Molmil
Crystal structure of human heteropentameric complex
Descriptor: Ragulator complex protein LAMTOR1, Ragulator complex protein LAMTOR2, Ragulator complex protein LAMTOR3, ...
Authors:Yonehara, R, Nada, S, Nakai, T, Nakai, M, Kitamura, A, Ogawa, A, Nakatsumi, H, Nakayama, K.I, Li, S, Standley, D.M, Yamashita, E, Nakagawa, A, Okada, M.
Deposit date:2017-02-23
Release date:2017-12-06
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis for the assembly of the Ragulator-Rag GTPase complex.
Nat Commun, 8, 2017
5X6V
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BU of 5x6v by Molmil
Crystal structure of human heteroheptameric complex
Descriptor: ACETATE ION, Ragulator complex protein LAMTOR1, Ragulator complex protein LAMTOR2, ...
Authors:Yonehara, R, Nada, S, Nakai, T, Nakai, M, Kitamura, A, Ogawa, A, Nakatsumi, H, Nakayama, K.I, Li, S, Standley, D.M, Yamashita, E, Nakagawa, A, Okada, M.
Deposit date:2017-02-23
Release date:2017-12-06
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.02 Å)
Cite:Structural basis for the assembly of the Ragulator-Rag GTPase complex.
Nat Commun, 8, 2017

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