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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Shimizu, H."

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Search Summary

This query matches 118 Structures.

Refinements

Structure Determination Methodology

experimental (118)

Scientific Name of Source Organism

	Homo sapiens (21)
	Fusarium oxysporum (15)
	Ignavibacterium album JCM 16511 (12)
	Rattus norvegicus (10)
	Mus musculus (8)
	Saccharomyces cerevisiae (6)
	Trypanosoma cruzi (6)
	Bos taurus (5)
	Ascaris suum (4)
	Bacteroides xylanisolvens XB1A (3)

More...

Taxonomy

	Eukaryota (83)
	Bacteria (31)
	Riboviria (4)

Experimental Method

	X-RAY DIFFRACTION (112)
	ELECTRON MICROSCOPY (3)
	SOLUTION NMR (3)

Polymer Entity Type

Protein (118)

Refinement Resolution (Å)

	1.0 - 1.5 (13)
	1.5 - 2.0 (50)
	2.0 - 2.5 (32)
	2.5 - 3.0 (14)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)
	> 4.5 (3)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (2)
	2000 - 2004 (41)
	2005 - 2009 (20)
	2010 - 2014 (15)
	2015 - 2019 (16)
	2020 - 2024 (17)
	2025 - 2029 (6)

Enzyme Classification Name

	Oxidoreductases (55)
	Hydrolases (9)
	Transferases (8)
	Ligases (2)

Membrane Protein Annotation

	MemProtMD (7)
	PDBTM (7)
	mpstruc (2)
	OPM (3)

Symmetry Type

	Asymmetric (65)
	Cyclic (51)
	Tetrahedral (2)

SCOP Classification

	All alpha proteins (41)
	Alpha and beta proteins (a+b) (21)
	Alpha and beta proteins (a/b) (8)
	All beta proteins (5)
	Artifacts (1)
	Small proteins (1)

AllSelected

1 to 25 of 118 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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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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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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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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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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1IFA \| pdb_00001ifa	Download File View File

THREE-DIMENSIONAL CRYSTAL STRUCTURE OF RECOMBINANT MURINE INTERFERON-BETA

Mitsui, Y., Senda, T., Matsuda, S., Kawano, G., Nakamura, K.T., Shimizu, H.

(1992) EMBO J 11: 3193-3201

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mus musculus
Macromolecule	INTERFERON-BETA (protein)
Unique Ligands	ASN

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1IQC \| pdb_00001iqc	Download File View File

Crystal structure of Di-Heme Peroxidase from Nitrosomonas europaea

Shimizu, H.

(2001) Biochemistry 40: 13483-13490

Released	2002-01-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nitrosomonas europaea
Macromolecule	di-heme peroxidase (protein)
Unique Ligands	CA, GOL, HEC, MG

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1JFB \| pdb_00001jfb	Download File View File

X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferric resting state at atomic resolution

Shimizu, H., Adachi, S., Park, S.Y., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Acta Crystallogr D Biol Crystallogr 58: 81-89

Released	2001-12-20
Method	X-RAY DIFFRACTION 1 Å
Organisms	Fusarium oxysporum
Macromolecule	nitric-oxide reductase cytochrome P450 55A1 (protein)
Unique Ligands	GOL, HEM

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1JFC \| pdb_00001jfc	Download File View File

X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferrous CO state at atomic resolution

Shimizu, H., Adachi, S., Park, S.Y., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Acta Crystallogr D Biol Crystallogr 58: 81-89

Released	2001-12-20
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Fusarium oxysporum
Macromolecule	nitric-oxide reductase Cytochrome P450 55A1 (protein)
Unique Ligands	CMO, GOL, HEM

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1LZX \| pdb_00001lzx	Download File View File

Rat neuronal NOS heme domain with NG-hydroxy-L-arginine bound

Li, H., Shimizu, H., Flinspach, M., Jamal, J., Yang, W., Xian, M., Cai, T., Wen, E.Z., Jia, Q., Wang, P.G., Poulos, T.L.

(2002) Biochemistry 41: 13868-13875

Released	2002-11-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Rattus norvegicus
Macromolecule	Nitric-oxide synthase (protein)
Unique Ligands	ACT, H4B, HAR, HEM, ZN

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1LZZ \| pdb_00001lzz	Download File View File

Rat neuronal NOS heme domain with N-isopropyl-N'-hydroxyguanidine bound

Li, H., Shimizu, H., Flinspach, M., Jamal, J., Yang, W., Xian, M., Cai, T., Wen, E.Z., Jia, Q., Wang, P.G., Poulos, T.L.

(2002) Biochemistry 41: 13868-13875

Released	2002-11-27
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Rattus norvegicus
Macromolecule	Nitric-oxide synthase (protein)
Unique Ligands	ACT, H4B, HEM, IHG, ZN

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1M00 \| pdb_00001m00	Download File View File

Rat neuronal NOS heme domain with N-butyl-N'-hydroxyguanidine bound

Li, H., Shimizu, H., Flinspach, M., Jamal, J., Yang, W., Xian, M., Cai, T., Wen, E.Z., Jia, Q., Wang, P.G., Poulos, T.L.

(2002) Biochemistry 41: 13868-13875

Released	2002-11-27
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Rattus norvegicus
Macromolecule	Nitric-oxide synthase (protein)
Unique Ligands	ACT, BHH, H4B, HEM, ZN

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1MK8 \| pdb_00001mk8	Download File View File

Crystal Structure of a Mutant Cytochrome c Peroxidase showing a Novel Trp-Tyr Covalent Cross-link

Bhaskar, B., Immoos, C.E., Shimizu, H., Farmer, P.J., Poulos, T.L.

(2003) J Mol Biology 328: 157-166

Released	2003-04-08
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cytochrome c Peroxidase (protein)
Unique Ligands	HEM

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1MKQ \| pdb_00001mkq	Download File View File

Crystal Structure of the Mutant Variant of Cytochrome c Peroxidase in the 'Open' Uncross-linked form

Bhaskar, B., Immoos, C.E., Shimizu, H., Farmer, P.J., Poulos, T.L.

(2003) J Mol Biology 328: 157-166

Released	2003-04-08
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cytochrome c Peroxidase (protein)
Unique Ligands	HEM, MPD