1WVP
 
 | | Structure of chemically modified myoglobin with distal N-tetrazolyl-histidine E7(64) | | Descriptor: | Myoglobin, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION | | Authors: | Makino, M, Sugimoto, H, Kamiya, N, Shiro, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-12-23 | | Release date: | 2005-01-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.53 Å) | | Cite: | Heme environmental structure of a novel artificial myoglobin with a closed heme pocket: site-specific chemical modification producing distal N-tetrazolylhistidine E7 by cyanogen bromide and azide ion
J.Am.Chem.Soc., 113, 1991
|
|
4U72
 | | Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant) | | Descriptor: | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, 4-PHENYL-1H-IMIDAZOLE, Indoleamine 2,3-dioxygenase 1, ... | | Authors: | Sugimoto, H, Horitani, M, Kometani, E, Shiro, Y. | | Deposit date: | 2014-07-30 | | Release date: | 2015-09-02 | | Last modified: | 2020-01-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Conformation and Mobility of Active Site Loop is Critical for Substrate Binding and Inhibition in Human Indoleamine 2,3-Dioxygenase
to be published
|
|
4U74
 | | Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (G262A mutant) | | Descriptor: | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, 4-PHENYL-1H-IMIDAZOLE, Indoleamine 2,3-dioxygenase 1, ... | | Authors: | Sugimoto, H, Horitani, M, Kometani, E, Shiro, Y. | | Deposit date: | 2014-07-30 | | Release date: | 2015-09-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.31 Å) | | Cite: | Conformation and Mobility of Active Site Loop is Critical for Substrate Binding and Inhibition in Human Indoleamine 2,3-Dioxygenase
to be published
|
|
5XA4
 | | Crystal Structure of HasAp with Fe-5,15-Diazaporphyrin | | Descriptor: | 10,20-Diphenyl-5,15-diaza-porphyrin containing FE, Heme acquisition protein HasAp | | Authors: | Shoji, O, Uehara, H, Sugimoto, H, Shiro, Y, Watanabe, Y. | | Deposit date: | 2017-03-10 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Structures of the Heme Acquisition Protein HasA with Iron(III)-5,15-Diphenylporphyrin and Derivatives Thereof as an Artificial Prosthetic Group
Angew. Chem. Int. Ed. Engl., 56, 2017
|
|
5XKB
 | | Crystal Structure of HasAp with Fe-5,15-bisethynyl-10,20-diphenylporphyrin | | Descriptor: | 5,15-Bisethynyl-10,20-diphenylporphyrin containing FE, Heme acquisition protein HasAp | | Authors: | Shoji, O, Uehara, H, Sugimoto, H, Shiro, Y, Watanabe, Y. | | Deposit date: | 2017-05-06 | | Release date: | 2017-12-06 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structures of the Heme Acquisition Protein HasA with Iron(III)-5,15-Diphenylporphyrin and Derivatives Thereof as an Artificial Prosthetic Group
Angew. Chem. Int. Ed. Engl., 56, 2017
|
|
5XIC
 | | Crystal Structure of HasAp with Fe-5,10,15-triphenylporphyrin | | Descriptor: | 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL, 5,10,15-Triphenylporphyrin cpntaining FE, Heme acquisition protein HasAp | | Authors: | Shoji, O, Uehara, H, Sugimoto, H, Shiro, Y, Watanabe, Y. | | Deposit date: | 2017-04-26 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structures of the Heme Acquisition Protein HasA with Iron(III)-5,15-Diphenylporphyrin and Derivatives Thereof as an Artificial Prosthetic Group
Angew. Chem. Int. Ed. Engl., 56, 2017
|
|
5GUX
 | | Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon | | Descriptor: | Antibody fab fragment heavy chain, Antibody fab fragment light chain, CALCIUM ION, ... | | Authors: | Ishii, S, Terasaka, E, Sugimoto, H, Shiro, Y, Tosha, T. | | Deposit date: | 2016-08-31 | | Release date: | 2017-08-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Dynamics of nitric oxide controlled by protein complex in bacterial system.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
|
|
5GUW
 | | Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa | | Descriptor: | CALCIUM ION, CHLORIDE ION, FE (III) ION, ... | | Authors: | Terasaka, E, Sugimoto, H, Shiro, Y, Tosha, T. | | Deposit date: | 2016-08-31 | | Release date: | 2017-08-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Dynamics of nitric oxide controlled by protein complex in bacterial system
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
|
|
6FWF
 | | Low resolution structure of Neisseria meningitidis qNOR | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric-oxide reductase, ... | | Authors: | Young, D, Antonyuk, S, Tosha, T, Hisano, T, Hasnain, S, Shiro, Y. | | Deposit date: | 2018-03-06 | | Release date: | 2018-03-14 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (4.2 Å) | | Cite: | Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme.
Sci Rep, 8, 2018
|
|
5XA3
 | | Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-prolyl-L-phenylalanine | | Descriptor: | Bifunctional cytochrome P450/NADPH-P450 reductase, DIMETHYL SULFOXIDE, PHENYLALANINE, ... | | Authors: | Shoji, O, Yanagisawa, S, Stanfield, J.K, Suzuki, K, Kasai, C, Cong, Z, Sugimoto, H, Shiro, Y, Watanabe, Y. | | Deposit date: | 2017-03-10 | | Release date: | 2018-02-21 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Direct Hydroxylation of Benzene to Phenol by Cytochrome P450BM3 Triggered by Amino Acid Derivatives.
Angew. Chem. Int. Ed. Engl., 56, 2017
|
|
5X7E
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D2 | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(E,2R,5S)-5,6-dimethyl-6-oxidanyl-hept-3-en-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydr o-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol, PROTOPORPHYRIN IX CONTAINING FE, Vitamin D3 dihydroxylase | | Authors: | Hayashi, K, Yasuda, K, Shiro, Y, Sugimoto, H, Sakaki, T. | | Deposit date: | 2017-02-25 | | Release date: | 2017-05-10 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Production of an active form of vitamin D2 by genetically engineered CYP105A1
Biochem. Biophys. Res. Commun., 486, 2017
|
|
3CV9
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R73A/R84A mutant) in complex with 1alpha,25-dihydroxyvitamin D3 | | Descriptor: | 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, Cytochrome P450-SU1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Hayashi, K, Sugimoto, H, Shinkyo, R, Yamada, M, Ikeda, S, Ikushiro, S, Kamakura, M, Shiro, Y, Sakaki, T. | | Deposit date: | 2008-04-18 | | Release date: | 2008-11-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1
Biochemistry, 47, 2008
|
|
3CV8
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84F mutant) | | Descriptor: | Cytochrome P450-SU1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Hayashi, K, Sugimoto, H, Shinkyo, R, Yamada, M, Ikeda, S, Ikushiro, S, Kamakura, M, Shiro, Y, Sakaki, T. | | Deposit date: | 2008-04-18 | | Release date: | 2008-11-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1
Biochemistry, 47, 2008
|
|
1X3U
 | | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot | | Descriptor: | Transcriptional regulatory protein fixJ | | Authors: | Kurashima-Ito, K, Kasai, Y, Hosono, K, Tamura, K, Oue, S, Isogai, M, Ito, Y, Nakamura, H, Shiro, Y. | | Deposit date: | 2005-05-10 | | Release date: | 2006-05-02 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter
Biochemistry, 44, 2005
|
|
3O0R
 | | Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment | | Descriptor: | CALCIUM ION, FE (III) ION, HEME C, ... | | Authors: | Hino, T, Matsumoto, Y, Nagano, S, Sugimoto, H, Fukumori, Y, Murata, T, Iwata, S, Shiro, Y. | | Deposit date: | 2010-07-20 | | Release date: | 2010-12-29 | | Last modified: | 2013-10-16 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural basis of biological N2O generation by bacterial nitric oxide reductase
Science, 330, 2010
|
|
5CPG
 | | R-Hydratase PhaJ1 from Pseudomonas aeruginosa in the unliganded form | | Descriptor: | (R)-specific enoyl-CoA hydratase, GLYCEROL | | Authors: | Tsuge, T, Sato, S, Hiroe, A, Ishizuka, K, Kanazawa, H, Kanagarajan, S, Shiro, Y, Hisano, T. | | Deposit date: | 2015-07-21 | | Release date: | 2015-10-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.694 Å) | | Cite: | Contribution of the Distal Pocket Residue to the Acyl-Chain-Length Specificity of (R)-Specific Enoyl-Coenzyme A Hydratases from Pseudomonas spp.
Appl.Environ.Microbiol., 81, 2015
|
|
6QQ5
 | | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) from Alcaligenes xylosoxidans | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric oxide reductase subunit B, ... | | Authors: | Gopalasingam, C.C, Johnson, R.M, Chiduza, G.N, Tosha, T, Yamamoto, M, Shiro, Y, Antonyuk, S.V, Muench, S.P, Hasnain, S.S. | | Deposit date: | 2019-02-17 | | Release date: | 2019-09-11 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy.
Sci Adv, 5, 2019
|
|
6QQ6
 | | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) Val495Ala mutant from Alcaligenes xylosoxidans | | Descriptor: | (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE, CALCIUM ION, DODECYL-BETA-D-MALTOSIDE, ... | | Authors: | Gopalasingam, C.C, Johnson, R.M, Chiduza, G.N, Tosha, T, Yamamoto, M, Shiro, Y, Antonyuk, S.V, Muench, S.P, Hasnain, S.S. | | Deposit date: | 2019-02-17 | | Release date: | 2019-09-11 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy.
Sci Adv, 5, 2019
|
|
1WN1
 | | Crystal Structure of Dipeptiase from Pyrococcus Horikoshii OT3 | | Descriptor: | COBALT (II) ION, dipeptidase | | Authors: | Jeyakanthan, J, Taka, J, Kitaguchi, Y, Shiro, Y, Yokoyama, S, Yutani, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-07-26 | | Release date: | 2005-08-09 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Crystal Structure of Dipeptiase from Pyrococcus Horikoshii OT3
To be Published
|
|
6L1X
 | | Quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis in the monomeric oxidized state with zinc complex. | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric-oxide reductase, ... | | Authors: | Jamali, M.M.A, Antonyuk, S.V, Tosha, T, Muramoto, K, Hasnain, S.S, Shiro, Y. | | Deposit date: | 2019-10-01 | | Release date: | 2020-04-01 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (3.15 Å) | | Cite: | The active form of quinol-dependent nitric oxide reductase fromNeisseria meningitidisis a dimer.
Iucrj, 7, 2020
|
|
6L3H
 | | Cryo-EM structure of dimeric quinol dependent Nitric Oxide Reductase (qNOR) from the pathogen Neisseria meninigitidis | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric-oxide reductase, ... | | Authors: | Jamali, M.M.A, Gopalasingam, C.C, Johnson, R.M, Tosha, T, Muench, S.P, Muramoto, K, Antonyuk, S.V, Shiro, Y, Hasnain, S.S. | | Deposit date: | 2019-10-11 | | Release date: | 2020-04-01 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.06 Å) | | Cite: | The active form of quinol-dependent nitric oxide reductase fromNeisseria meningitidisis a dimer.
Iucrj, 7, 2020
|
|
1GDV
 | | CRYSTAL STRUCTURE OF CYTOCHROME C6 FROM RED ALGA PORPHYRA YEZOENSIS AT 1.57 A RESOLUTION | | Descriptor: | CYTOCHROME C6, HEME C | | Authors: | Yamada, S, Park, S.-Y, Shimizu, H, Shiro, Y, Oku, T. | | Deposit date: | 2000-10-06 | | Release date: | 2001-04-06 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.57 Å) | | Cite: | Structure of cytochrome c6 from the red alga Porphyra yezoensis at 1. 57 A resolution.
Acta Crystallogr.,Sect.D, 56, 2000
|
|
1GEJ
 | | STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM | | Descriptor: | CYTOCHROME P450 55A1, N-BUTYL ISOCYANIDE, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | lee, D.-S, Park, S.-Y, Yamane, K, Shiro, Y. | | Deposit date: | 2000-11-13 | | Release date: | 2000-12-06 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural characterization of n-butyl-isocyanide complexes of cytochromes P450nor and P450cam.
Biochemistry, 40, 2001
|
|
1GEI
 | | STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM | | Descriptor: | CYTOCHROME P450 55A1, N-BUTYL ISOCYANIDE, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Lee, D.-S, Park, S.-Y, Yamane, K, Shiro, Y. | | Deposit date: | 2000-11-13 | | Release date: | 2000-11-29 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural characterization of n-butyl-isocyanide complexes of cytochromes P450nor and P450cam.
Biochemistry, 40, 2001
|
|
5GJ3
 | | Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in two-heme bound form (holo-2) | | Descriptor: | PROTOPORPHYRIN IX CONTAINING FE, Periplasmic binding protein, ZINC ION | | Authors: | Rahman, M.M, Naoe, Y, Nakamura, N, Shiro, Y, Sugimoto, H. | | Deposit date: | 2016-06-26 | | Release date: | 2017-06-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Proteins, 85, 2017
|
|
