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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Shiro, Y."

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Search Summary

This query matches 232 Structures.

Refinements

Structure Determination Methodology

experimental (232)

Scientific Name of Source Organism

	Fusarium oxysporum (25)
	Homo sapiens (18)
	Priestia megaterium (17)
	Pseudomonas aeruginosa PAO1 (17)
	Thermotoga maritima (10)
	Aquifex aeolicus VF5 (9)
	Pyrococcus horikoshii OT3 (8)
	Sphingomonas paucimobilis (7)
	Thermus thermophilus HB8 (7)
	Corynebacterium diphtheriae NCTC 13129 (6)

More...

Taxonomy

	Bacteria (152)
	Eukaryota (69)
	Archaea (15)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (224)
	ELECTRON MICROSCOPY (6)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (232)
	DNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (30)
	1.5 - 2.0 (83)
	2.0 - 2.5 (69)
	2.5 - 3.0 (28)
	3.0 - 3.5 (16)
	3.5 - 4.0 (2)
	4.0 - 4.5 (1)
	> 4.5 (1)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (2)
	2000 - 2004 (39)
	2005 - 2009 (76)
	2010 - 2014 (29)
	2015 - 2019 (49)
	2020 - 2024 (36)

Enzyme Classification Name

	Oxidoreductases (107)
	Lyases (19)
	Transferases (20)
	Hydrolases (12)
	Translocases (8)

Membrane Protein Annotation

	PDBTM (28)
	mpstruc (9)
	OPM (18)
	MemProtMD (16)

Symmetry Type

	Asymmetric (154)
	Cyclic (83)
	Dihedral (10)
	Tetrahedral (1)

SCOP Classification

	All alpha proteins (98)
	Alpha and beta proteins (a/b) (24)
	Alpha and beta proteins (a+b) (15)
	All beta proteins (10)
	Artifacts (11)
	Multi-domain proteins (alpha and beta) (1)
	Membrane and cell surface proteins and peptides (2)
	Designed proteins (1)

AllSelected

1 to 25 of 232 Structures

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1CL6 \| pdb_00001cl6	Download File View File

CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE REDUCTASE AND ITS SER286 MUTANTS AT CRYOGENIC TEMPERATURE

Park, S.-Y., Shiro, Y.

(2000) J Biological Chem 275: 4816-4826

Released	2000-03-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 (protein)
Unique Ligands	HEM, NO

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1CMJ \| pdb_00001cmj	Download File View File

CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE REDUCTASE AND THEIR SER286 MUTANTS AT CRYOGENIC TEMPERATURE

Park, S.-Y., Shiro, Y.

(2000) J Biological Chem 275: 4816-4826

Released	2000-03-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 (protein)
Unique Ligands	HEM, NO

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1CMN \| pdb_00001cmn	Download File View File

CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE REDUCTASE AND THEIR SER286 MUTANTS AT CRYOGENIC TEMPERATURE

Park, S.-Y., Shiro, Y.

(2000) J Biological Chem 275: 4816-4826

Released	2000-03-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 (protein)
Unique Ligands	HEM, NO

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1D06 \| pdb_00001d06	Download File View File

STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION

Miyatake, H., Mukai, M., Park, S.-Y., Adachi, S., Tamura, K., Nakamura, H., Nakamura, K., Tsuchiya, T., Iizuka, T., Shiro, Y.

(2000) J Mol Biology 301: 415-431

Released	2000-03-15
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Sinorhizobium meliloti
Macromolecule	nitrogen fixation regulatory protein fixL (protein)
Unique Ligands	HEM

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1EHE \| pdb_00001ehe	Download File View File

CRYSTAL STRUCTURES OF CYTOCHROME P450NOR AND ITS MUTANTS (SER286 VAL, THR) IN THE FERRIC RESTING STATE AT CRYOGENIC TEMPERATURE: A COMPARATIVE ANALYSIS WITH MONOOXYGENASE CYTOCHROME P450S

Shimizu, H., Park, S.

(2000) J Inorg Biochem 81: 191-205

Released	2000-08-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450NOR (protein)
Unique Ligands	HEM

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1EHF \| pdb_00001ehf	Download File View File

CRYSTAL STRUCTURES OF CYTOCHROME P450NOR AND ITS MUTANTS (SER286 VAL, THR) IN THE FERRIC RESTING STATE AT CRYOGENIC TEMPERATURE: A COMPARATIVE ANALYSIS WITH MONOOXYGENASE CYTOCHROME P450S

Shimizu, H., Park, S.

(2000) J Inorg Biochem 81: 191-205

Released	2000-08-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450NOR (protein)
Unique Ligands	HEM

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1EHG \| pdb_00001ehg	Download File View File

CRYSTAL STRUCTURES OF CYTOCHROME P450NOR AND ITS MUTANTS (SER286 VAL, THR) IN THE FERRIC RESTING STATE AT CRYOGENIC TEMPERATURE: A COMPARATIVE ANALYSIS WITH MONOOXYGENASE CYTOCHROME P450S

Shimizu, H., Park, S.

(2000) J Inorg Biochem 81: 191-205

Released	2000-08-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450NOR (protein)
Unique Ligands	HEM

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1EW0 \| pdb_00001ew0	Download File View File

CRYSTAL STRUCTURE ANALYSIS OF THE SENSOR DOMAIN OF RMFIXL(FERROUS FORM)

Miyatake, H., Mukai, M., Park, S.-Y., Adachi, S., Tamura, K., Nakamura, H., Nakamura, K., Tsuchiya, T., Iizuka, T., Shiro, Y.

(2000) J Mol Biology 301: 415-431

Released	2000-05-10
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Sinorhizobium meliloti
Macromolecule	FIXL (protein)
Unique Ligands	HEM

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1F24 \| pdb_00001f24	Download File View File

CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ALA MUTANTS OF CYTOCHROME P450NOR

Shimizu, H., Park, S.-Y.

(2000) J Inorg Biochem 82: 103-111

Released	2000-11-23
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Fusarium oxysporum
Macromolecule	NITRIC OXIDE REDUCTASE (protein)
Unique Ligands	GOL, HEM, NO

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1F25 \| pdb_00001f25	Download File View File

CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ASN MUTANTS OF CYTOCHROME P450NOR

Shimizu, H., Park, S.-Y.

(2000) J Inorg Biochem 82: 103-111

Released	2000-11-23
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Fusarium oxysporum
Macromolecule	NITRIC OXIDE REDUCTASE (protein)
Unique Ligands	GOL, HEM, NO

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1F26 \| pdb_00001f26	Download File View File

CRYSTAL STRUCTURE OF NO COMPLEX OF THR243VAL MUTANTS OF CYTOCHROME P450NOR

Shimizu, H., Park, S.-Y.

(2000) J Inorg Biochem 82: 103-111

Released	2000-11-23
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Fusarium oxysporum
Macromolecule	NITRIC OXIDE REDUCTASE (protein)
Unique Ligands	GOL, HEM, NO

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1GCU \| pdb_00001gcu	Download File View File

CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A

Kikuchi, A., Park, S.Y., Shiro, Y.

(2001) Nat Struct Biol 8: 221-225

Released	2001-02-08
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Rattus norvegicus
Macromolecule	BILIVERDIN REDUCTASE A (protein)

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1GDV \| pdb_00001gdv	Download File View File

CRYSTAL STRUCTURE OF CYTOCHROME C6 FROM RED ALGA PORPHYRA YEZOENSIS AT 1.57 A RESOLUTION

Yamada, S., Park, S.-Y., Shimizu, H., Shiro, Y., Oku, T.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1577-1582

Released	2001-04-06
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Pyropia yezoensis
Macromolecule	CYTOCHROME C6 (protein)
Unique Ligands	HEC

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1GEB \| pdb_00001geb	Download File View File

X-RAY CRYSTAL STRUCTURE AND CATALYTIC PROPERTIES OF THR252ILE MUTANT OF CYTOCHROME P450CAM

Hishiki, T., Shimada, H., Nagano, S., Park, S.-Y., Ishimura, Y.

(2000) J Biochem 128: 965-974

Released	2000-11-15
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450-CAM (protein)
Unique Ligands	CAM, HEM

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1GED \| pdb_00001ged	Download File View File

A positive charge route for the access of nadh to heme formed in the distal heme pocket of cytochrome p450nor

Kudo, T., Takaya, N., Park, S.-Y., Shiro, Y., Shoun, H.

(2001) J Biological Chem 276: 5020-5026

Released	2000-11-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 55A1 (protein)
Unique Ligands	BR, HEM

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1GEI \| pdb_00001gei	Download File View File

STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM

Lee, D.-S., Park, S.-Y., Yamane, K., Shiro, Y.

(2001) Biochemistry 40: 2669-2677

Released	2000-11-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 55A1 (protein)
Unique Ligands	HEM, NBN

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1GEJ \| pdb_00001gej	Download File View File

STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM

lee, D.-S., Park, S.-Y., Yamane, K., Shiro, Y.

(2001) Biochemistry 40: 2669-2677

Released	2000-12-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 55A1 (protein)
Unique Ligands	HEM, NBN

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1GEK \| pdb_00001gek	Download File View File

STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM

Lee, D.-S., Park, S.-Y., Yamane, K., Shiro, Y.

(2001) Biochemistry 40: 2669-2677

Released	2000-12-06
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450CAM (protein)
Unique Ligands	HEM, NBN

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1GEM \| pdb_00001gem	Download File View File

STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM

Lee, D.-S., Park, S.-Y., Yamane, K., Shiro, Y.

(2001) Biochemistry 40: 2669-2677

Released	2000-12-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450CAM (protein)
Unique Ligands	HEM, NBN

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1IO7 \| pdb_00001io7	Download File View File

THERMOPHILIC CYTOCHROME P450 (CYP119) FROM SULFOLOBUS SOLFATARICUS: HIGH RESOLUTION STRUCTURAL ORIGIN OF ITS THERMOSTABILITY AND FUNCTIONAL PROPERTIES

Park, S.-Y., Yamane, K., Adachi, S., Shiro, Y., Sligar, S.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Inorg Biochem 91: 491-501

Released	2001-02-28
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Saccharolobus solfataricus
Macromolecule	CYTOCHROME P450 CYP119 (protein)
Unique Ligands	HEM

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1IO8 \| pdb_00001io8	Download File View File

Thermophilic cytochrome P450 (CYP119) from sulfolobus solfataricus: High resolution structural origin of its thermostability and functional properties

Park, S.-Y., Yamane, K., Adachi, S., Shiro, Y., Sligar, S.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Inorg Biochem 91: 491-501

Released	2001-03-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharolobus solfataricus
Macromolecule	CYTOCHROME P450 CYP119 (protein)
Unique Ligands	HEM

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1IO9 \| pdb_00001io9	Download File View File

THERMOPHILIC CYTOCHROME P450 (CYP119) FROM SULFOLOBUS SOLFATARICUS: HIGH RESOLUTION STRUCTURAL ORIGIN OF ITS THERMOSTABILITY AND FUNCTIONAL PROPERTIES

Park, S.-Y., Yamane, K., Adachi, S., Shiro, Y., Sligar, S.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Inorg Biochem 91: 491-501

Released	2001-03-07
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Saccharolobus solfataricus
Macromolecule	CYTOCHROME P450 CYP119 (protein)
Unique Ligands	HEM

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1IW0 \| pdb_00001iw0	Download File View File

Crystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed with heme in the ferric state

Hirotsu, S., Unno, M., Chu, G.C., Lee, D.S., Park, S.Y., Shiro, Y., Ikeda-Saito, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 11937-11947

Released	2003-04-08
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Corynebacterium diphtheriae
Macromolecule	Heme oxygenase (protein)
Unique Ligands	HEM, SO4
Unique branched monosaccharides	FRU, GLC

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1IW1 \| pdb_00001iw1	Download File View File

Crystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed with heme in the ferrous state

Hirotsu, S., Unno, M., Chu, G.C., Lee, D.S., Park, S.Y., Shiro, Y., Ikeda-Saito, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 11937-11947

Released	2003-04-04
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Corynebacterium diphtheriae
Macromolecule	Heme oxygenase (protein)
Unique Ligands	HEM, SO4
Unique branched monosaccharides	FRU, GLC

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1IW6 \| pdb_00001iw6	Download File View File

Crystal Structure of the Ground State of Bacteriorhodopsin

Kouyama, T., Okumura, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 324: 469-481

Released	2002-12-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Halobacterium salinarum
Macromolecule	bacteriorhodopsin (protein)
Unique Ligands	L2P, L3P, RET
Unique branched monosaccharides	GAL, GLC, MAN

1 to 25 of 232 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1CL6 | pdb_00001cl6

1CMJ | pdb_00001cmj

1CMN | pdb_00001cmn

1D06 | pdb_00001d06

1EHE | pdb_00001ehe

1EHF | pdb_00001ehf

1EHG | pdb_00001ehg

1EW0 | pdb_00001ew0

1F24 | pdb_00001f24

1F25 | pdb_00001f25

1F26 | pdb_00001f26

1GCU | pdb_00001gcu

1GDV | pdb_00001gdv

1GEB | pdb_00001geb

1GED | pdb_00001ged

1GEI | pdb_00001gei

1GEJ | pdb_00001gej

1GEK | pdb_00001gek

1GEM | pdb_00001gem

1IO7 | pdb_00001io7

1IO8 | pdb_00001io8

1IO9 | pdb_00001io9

1IW0 | pdb_00001iw0

1IW1 | pdb_00001iw1

1IW6 | pdb_00001iw6