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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Shiro, Y."

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Search Summary

This query matches 215 Structures.

Refinements

Structure Determination Methodology

experimental (215)

Scientific Name of Source Organism

	Fusarium oxysporum (17)
	Pseudomonas aeruginosa PAO1 (17)
	Homo sapiens (16)
	Priestia megaterium (16)
	Aquifex aeolicus VF5 (10)
	Thermotoga maritima (10)
	Thermus thermophilus HB8 (10)
	Sphingomonas paucimobilis (7)
	Corynebacterium diphtheriae NCTC 13129 (6)
	Mus musculus (6)

More...

Taxonomy

	Bacteria (152)
	Eukaryota (55)
	Archaea (12)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (210)
	ELECTRON MICROSCOPY (3)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (215)
	DNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (25)
	1.5 - 2.0 (83)
	2.0 - 2.5 (63)
	2.5 - 3.0 (26)
	3.0 - 3.5 (13)
	3.5 - 4.0 (2)
	4.0 - 4.5 (1)

Release Date

	1990 - 1994 (1)
	2000 - 2004 (29)
	2005 - 2009 (76)
	2010 - 2014 (36)
	2015 - 2019 (46)
	2020 - 2024 (27)

Enzyme Classification Name

	Oxidoreductases (92)
	Lyases (20)
	Transferases (20)
	Hydrolases (12)
	Translocases (4)

Membrane Protein Annotation

	PDBTM (23)
	MemProtMD (15)
	OPM (15)
	mpstruc (5)

Symmetry Type

	Asymmetric (138)
	Cyclic (80)
	Dihedral (12)
	Tetrahedral (1)

SCOP Classification

	All alpha proteins (86)
	Alpha and beta proteins (a+b) (17)
	Alpha and beta proteins (a/b) (26)
	All beta proteins (7)
	Artifacts (11)
	Multi-domain proteins (alpha and beta) (4)
	Designed proteins (1)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 25 of 215 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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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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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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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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1IWI \| pdb_00001iwi	Download File View File

Putidaredoxin-Binding Stablilizes an Active Conformer of Cytochrome P450cam in its Reduced State; Crystal Structure of Cytochrome P450cam

Nagano, S., Shimada, H., Tarumi, A., Hishiki, T., Kimata-Ariga, Y., Egawa, T., Park, S.-Y., Adachi, S., Shiro, Y., Ishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Biochemistry 42: 14507-14514

Released	2002-06-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450-CAM (protein)
Unique Ligands	CAM, HEM

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1IWJ \| pdb_00001iwj	Download File View File

Putidaredoxin-Binding Stablilizes an Active Conformer of Cytochrome P450cam in its Reduced State; Crystal Structure of Mutant(109K) Cytochrome P450cam

Nagano, S., Shimada, H., Tarumi, A., Hishiki, T., Kimata-Ariga, Y., Egawa, T., Park, S.-Y., Adachi, S., Shiro, Y., Ishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Biochemistry 42: 14507-14514

Released	2002-06-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450-CAM (protein)
Unique Ligands	CAM, HEM

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1IWK \| pdb_00001iwk	Download File View File

Putidaredoxin-Binding Stablilizes an Active Conformer of Cytochrome P450cam in its Reduced State; Crystal Structure of Mutant(112K) Cytochrome P450cam

Nagano, S., Shimada, H., Tarumi, A., Hishiki, T., Kimata-Ariga, Y., Egawa, T., Park, S.-Y., Adachi, S., Shiro, Y., Ishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Biochemistry 42: 14507-14514

Released	2002-06-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450-CAM (protein)
Unique Ligands	HEM

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1IXF \| pdb_00001ixf	Download File View File

Crystal Structure of the K intermediate of bacteriorhodopsin

Matsui, Y., Sakai, K., Murakami, M., Shiro, Y., Adachi, S., Okumura, H., Kouyama, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 324: 469-481

Released	2002-12-18
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Halobacterium salinarum
Macromolecule	bacteriorhodopsin (protein)
Unique Ligands	L2P, L3P, RET
Unique branched monosaccharides	GAL, GLC, MAN

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1IZO \| pdb_00001izo	Download File View File

Cytochrome P450 BS beta Complexed with Fatty Acid

Lee, D.S., Yamada, A., Sugimoto, H., Matsunaga, I., Ogura, H., Ichihara, K., Adachi, S., Park, S.Y., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) J Biological Chem 278: 9761-9767

Released	2003-03-18
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bacillus subtilis
Macromolecule	Cytochrome P450 152A1 (protein)
Unique Ligands	HEM, PAM

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1J3Y \| pdb_00001j3y	Download File View File

Direct observation of photolysis-induced tertiary structural changes in human hemoglobin; Crystal structure of alpha(Fe)-beta(Ni) hemoglobin (laser photolysed)

Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Proc Natl Acad Sci U S A 100: 7039-7044

Released	2003-07-22
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha Chain (protein) Hemoglobin beta Chain (protein)
Unique Ligands	2FU, CMO, HEM, HNI

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1J3Z \| pdb_00001j3z	Download File View File

Direct observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Fe-CO)-beta(Ni) hemoglobin (laser unphotolysed)

Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Proc Natl Acad Sci U S A 100: 7039-7044

Released	2003-07-22
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha Chain (protein) Hemoglobin beta Chain (protein)
Unique Ligands	2FU, CMO, HEM, HNI

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1J40 \| pdb_00001j40	Download File View File

Direct observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Ni)-beta(Fe-CO) hemoglobin (laser unphotolysed)

Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Proc Natl Acad Sci U S A 100: 7039-7044

Released	2003-07-22
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha Chain (protein) Hemoglobin beta Chain (protein)
Unique Ligands	2FU, CMO, HEM, HNI

1 to 25 of 215 Structures

Page 1 of 9

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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

1EW0 | pdb_00001ew0

1GCU | pdb_00001gcu

1GDV | pdb_00001gdv

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

1IWI | pdb_00001iwi

1IWJ | pdb_00001iwj

1IWK | pdb_00001iwk

1IXF | pdb_00001ixf

1IZO | pdb_00001izo

1J3Y | pdb_00001j3y

1J3Z | pdb_00001j3z

1J40 | pdb_00001j40