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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nakagawa, A."

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Search Summary

This query matches 228 Structures.

Refinements

Structure Determination Methodology

experimental (228)

Scientific Name of Source Organism

	Homo sapiens (36)
	Mus musculus (30)
	Fusarium oxysporum (12)
	Danio rerio (11)
	Escherichia coli K-12 (10)
	Pyrococcus furiosus (10)
	Bombyx mori (9)
	Arabidopsis thaliana (7)
	Solanum tuberosum (6)
	Bos taurus (5)

More...

Taxonomy

	Eukaryota (152)
	Bacteria (35)
	Riboviria (27)
	Archaea (11)
	Duplodnaviria (6)
	other sequences (4)
	Eukaryota (eukaryotes) (2)
	unclassified sequences (1)

Experimental Method

	X-RAY DIFFRACTION (217)
	ELECTRON MICROSCOPY (9)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (228)
	RNA (2)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (24)
	1.5 - 2.0 (62)
	2.0 - 2.5 (68)
	2.5 - 3.0 (30)
	3.0 - 3.5 (23)
	3.5 - 4.0 (16)
	> 4.5 (1)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (14)
	2000 - 2004 (30)
	2005 - 2009 (37)
	2010 - 2014 (67)
	2015 - 2019 (56)
	2020 - 2024 (23)

Enzyme Classification Name

	Transferases (44)
	Oxidoreductases (28)
	Hydrolases (34)
	Lyases (15)
	Ligases (5)
	Isomerases (4)

Membrane Protein Annotation

	PDBTM (15)
	mpstruc (14)
	OPM (12)
	MemProtMD (8)

Symmetry Type

	Asymmetric (138)
	Cyclic (99)
	Icosahedral (8)
	Dihedral (3)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a/b) (44)
	All alpha proteins (41)
	All beta proteins (37)
	Alpha and beta proteins (a+b) (25)
	Artifacts (18)
	Membrane and cell surface proteins and peptides (5)
	Low resolution protein structures (1)
	Multi-domain proteins (alpha and beta) (1)
	Peptides (1)

AllSelected

1 to 25 of 228 Structures

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1BK7 \| pdb_00001bk7	Download File View File

RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD

Nakagawa, A., Tanaka, I.

(1999) Biochim Biophys Acta 1433: 253-260

Released	1999-07-23
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Momordica charantia
Macromolecule	PROTEIN (RIBONUCLEASE MC1) (protein)

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1C53 \| pdb_00001c53	Download File View File

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

Nakagawa, A., Higuchi, Y., Yasuoka, N., Katsube, Y., Yaga, T.

(1990) J Biochem 108: 701-703

Released	1993-10-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	CYTOCHROME C553 (protein)
Unique Ligands	HEM

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1DPT \| pdb_00001dpt	Download File View File

D-DOPACHROME TAUTOMERASE

Sugimoto, H., Taniguchi, M., Nakagawa, A., Tanaka, I.

(1999) Biochemistry 38: 3268-3279

Released	1999-03-30
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Homo sapiens
Macromolecule	D-DOPACHROME TAUTOMERASE (protein)

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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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1EL1 \| pdb_00001el1	Download File View File

X-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (HOLO-TYPE)

Koshiba, T., Yao, M., Tanaka, I., Nitta, K.

To be published

Released	2001-03-13
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Canis lupus familiaris
Macromolecule	LYSOZYME C (protein)
Unique Ligands	CA

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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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1F2D \| pdb_00001f2d	Download File View File

1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE

Yao, M., Ose, T., Sugimoto, H., Horiuchi, A., Nakagawa, A., Yokoi, D., Murakami, T., Honma, M., Wakatsuki, S., Tanaka, I.

(2000) J Biological Chem 275: 34557-34565

Released	2000-12-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Cyberlindnera saturnus
Macromolecule	1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE (protein)
Unique Ligands	PLP, SO4

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1FIM \| pdb_00001fim	Download File View File

MACROPHAGE MIGRATION INHIBITORY FACTOR

Suzuki, M., Sugimoto, H., Nakagawa, A., Tanaka, I.

(1996) Nat Struct Biol 3: 259-266

Released	1996-07-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Rattus norvegicus
Macromolecule	MACROPHAGE MIGRATION INHIBITORY FACTOR (protein)

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1GCJ \| pdb_00001gcj	Download File View File

N-TERMINAL FRAGMENT OF IMPORTIN-BETA

Lee, S.J., Imamoto, N., Sakai, H., Nakagawa, A., Kose, S., Koike, M., Yamamoto, M., Kumasaka, T., Yoneda, Y., Tsukihara, T.

(2000) J Mol Biology 302: 251-264

Released	2000-10-18
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mus musculus
Macromolecule	IMPORTIN BETA (protein)

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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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1GEQ \| pdb_00001geq	Download File View File

Entropic stabilization of the tryptophan synthase A-subunit from a hyperthermophile, pyrococcus furiosus: X-ray analysis and calorimetry

Yutani, K., Yamagata, Y.

(2001) J Biological Chem 276: 11062-11071

Released	2000-12-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus furiosus
Macromolecule	TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT (protein)

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1HUS \| pdb_00001hus	Download File View File

RIBOSOMAL PROTEIN S7

Hosaka, H., Nakagawa, A., Tanaka, I.

(1997) Structure 5: 1199-1208

Released	1998-01-28
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	RIBOSOMAL PROTEIN S7 (protein)

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1J0D \| pdb_00001j0d	Download File View File

ACC deaminase mutant complexed with ACC

Ose, T., Fujino, A., Yao, M., Honma, M., Tanaka, I.

(2003) J Biological Chem 278: 41069-41076

Released	2003-05-12
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Cyberlindnera saturnus
Macromolecule	1-aminocyclopropane-1-carboxylate deaminase (protein)
Unique Ligands	5PA

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1J0E \| pdb_00001j0e	Download File View File

ACC deaminase mutant reacton intermediate

Ose, T., Fujino, A., Yao, M., Honma, M., Tanaka, I.

(2003) J Biological Chem 278: 41069-41076

Released	2003-05-12
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Cyberlindnera saturnus
Macromolecule	1-aminocyclopropane-1-carboxylate deaminase (protein)
Unique Ligands	1AC

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1J1F \| pdb_00001j1f	Download File View File

Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP

Numata, T., Suzuki, A., Kakuta, Y., Kimura, K., Yao, M., Tanaka, I., Yoshida, Y., Ueda, T., Kimura, M.

(2003) Biochemistry 42: 5270-5278

Released	2003-05-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Momordica charantia
Macromolecule	RIBONUCLEASE MC1 (protein)
Unique Ligands	5GP

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1J1G \| pdb_00001j1g	Download File View File

Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP

Numata, T., Suzuki, A., Kakuta, Y., Kimura, K., Yao, M., Tanaka, I., Yoshida, Y., Ueda, T., Kimura, M.

(2003) Biochemistry 42: 5270-5278

Released	2003-05-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Momordica charantia
Macromolecule	Ribonuclease MC1 (protein)
Unique Ligands	5GP

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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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1K9A \| pdb_00001k9a	Download File View File

Crystal structure analysis of full-length carboxyl-terminal Src kinase at 2.5 A resolution

Ogawa, A., Takayama, Y., Nagata, A., Chong, K.T., Takeuchi, S., Sakai, H., Nakagawa, A., Nada, S., Okada, M., Tsukihara, T.

(2002) J Biological Chem 277: 14351-14354

Released	2002-03-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Rattus norvegicus
Macromolecule	Carboxyl-terminal Src kinase (protein)

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1MR8 \| pdb_00001mr8	Download File View File

MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8 FROM HUMAN

Ishikawa, K., Nakagawa, A., Tanaka, I., Nishihira, J.

(2000) Acta Crystallogr D Biol Crystallogr 56: 559-566

Released	2000-05-17
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8 (protein)
Unique Ligands	CA

1 to 25 of 228 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

1BK7 | pdb_00001bk7

1C53 | pdb_00001c53

1DPT | pdb_00001dpt

1EHE | pdb_00001ehe

1EHF | pdb_00001ehf

1EHG | pdb_00001ehg

1EL1 | pdb_00001el1

1F24 | pdb_00001f24

1F25 | pdb_00001f25

1F26 | pdb_00001f26

1F2D | pdb_00001f2d

1FIM | pdb_00001fim

1GCJ | pdb_00001gcj

1GEI | pdb_00001gei

1GEJ | pdb_00001gej

1GEQ | pdb_00001geq

1HUS | pdb_00001hus

1J0D | pdb_00001j0d

1J0E | pdb_00001j0e

1J1F | pdb_00001j1f

1J1G | pdb_00001j1g

1JFB | pdb_00001jfb

1JFC | pdb_00001jfc

1K9A | pdb_00001k9a

1MR8 | pdb_00001mr8