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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nakamura, H."

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Search Summary

This query matches 170 Structures.

Refinements

Structure Determination Methodology

experimental (170)

Scientific Name of Source Organism

	Homo sapiens (36)
	Escherichia coli (23)
	Fusarium oxysporum (15)
	Human immunodeficiency virus 1 (11)
	Mus musculus (11)
	Thermotoga maritima (10)
	Pyrococcus furiosus (9)
	Penicillium brasilianum (8)
	Striga hermonthica (7)
	Corynebacterium diphtheriae NCTC 13129 (6)

More...

Taxonomy

	Eukaryota (95)
	Bacteria (63)
	Riboviria (11)
	Archaea (9)
	Eukaryota (eukaryotes) (2)

Experimental Method

	X-RAY DIFFRACTION (145)
	SOLUTION NMR (25)

Polymer Entity Type

	Protein (167)
	DNA (6)
	NA-hybrid (3)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (12)
	1.5 - 2.0 (52)
	2.0 - 2.5 (41)
	2.5 - 3.0 (26)
	3.0 - 3.5 (12)
	3.5 - 4.0 (2)

Release Date

	1990 - 1994 (24)
	1995 - 1999 (25)
	2000 - 2004 (26)
	2005 - 2009 (22)
	2010 - 2014 (20)
	2015 - 2019 (33)
	2020 - 2024 (20)

Enzyme Classification Name

	Hydrolases (42)
	Oxidoreductases (24)
	Transferases (18)
	Lyases (16)
	Isomerases (3)

Membrane Protein Annotation

	OPM (8)
	PDBTM (8)
	MemProtMD (2)
	mpstruc (2)

Symmetry Type

	Asymmetric (136)
	Cyclic (32)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (47)
	All alpha proteins (38)
	Alpha and beta proteins (a+b) (12)
	All beta proteins (2)
	Artifacts (7)
	Peptides (5)

AllSelected

1 to 25 of 170 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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1DHH \| pdb_00001dhh	Download File View File

NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC)

Nishizaki, T., Iwai, S., Ohkubo, T., Kojima, C., Nakamura, H., Kyogoku, Y., Ohtsuka, E.

(1996) Biochemistry 35: 4016-4025

Released	1996-04-03
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(GPTPCPAPTPCPTPCPC)-3') (nucleic acid) DNA/RNA (5'-D(GPG)-R(PAPGPAPU)-D(PGPAPC)-3') (hybrid)

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1DRN \| pdb_00001drn	Download File View File

NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC)

Nishizaki, T., Iwai, S., Ohkubo, T., Kojima, C., Nakamura, H., Kyogoku, Y., Ohtsuka, E.

(1996) Biochemistry 35: 4016-4025

Released	1996-04-03
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(GPTPCPAPTPCPTPCPC)-3') (nucleic acid) DNA/RNA (5'-D(GPGPAPGPA)-R(PUPGPAPC)-3') (hybrid)

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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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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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1GIB \| pdb_00001gib	Download File View File

MU-CONOTOXIN GIIIB, NMR

Hill, J.M., Alewood, P.F., Craik, D.J.

(1996) Biochemistry 35: 8824-8835

Released	1996-11-08
Method	SOLUTION NMR
Organisms	Conus geographus
Macromolecule	MU-CONOTOXIN GIIIB (protein)

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1GOA \| pdb_00001goa	Download File View File

COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION

Ishikawa, K., Kimura, S., Nakamura, H., Morikawa, K., Kanaya, S.

(1993) Biochemistry 32: 7136-7142

Released	1994-01-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	RIBONUCLEASE H (protein)

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1GOB \| pdb_00001gob	Download File View File

COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION

Ishikawa, K., Kimura, S., Nakamura, H., Morikawa, K., Kanaya, S.

(1993) Biochemistry 32: 7136-7142

Released	1994-01-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	RIBONUCLEASE H (protein)

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1GOC \| pdb_00001goc	Download File View File

COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION

Ishikawa, K., Kimura, S., Nakamura, H., Morikawa, K., Kanaya, S.

(1993) Biochemistry 32: 7136-7142

Released	1994-01-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	RIBONUCLEASE H (protein)

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1HJR \| pdb_00001hjr	Download File View File

ATOMIC STRUCTURE OF THE RUVC RESOLVASE: A HOLLIDAY JUNCTION-SPECIFIC ENDONUCLEASE FROM E. COLI

Ariyoshi, M., Vassylyev, D.G., Morikawa, K.

(1994) Cell 78: 1063-1072

Released	1995-02-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	HOLLIDAY JUNCTION RESOLVASE (RUVC) (protein)

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1HNR \| pdb_00001hnr	Download File View File

H-NS (DNA-BINDING DOMAIN)

Shindo, H., Iwaki, T., Ieda, R., Kurumizaka, H., Ueguchi, C., Mizuno, T., Morikawa, S., Nakamura, H., Kuboniwa, H.

(1995) FEBS Lett 360: 125-131

Released	1995-07-10
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	H-NS (protein)

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1HNS \| pdb_00001hns	Download File View File

H-NS (DNA-BINDING DOMAIN)

Shindo, H., Iwaki, T., Ieda, R., Kurumizaka, H., Ueguchi, C., Mizuno, T., Morikawa, S., Nakamura, H., Kuboniwa, H.

(1995) FEBS Lett 360: 125-131

Released	1995-07-10
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	H-NS (protein)

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1I1Z \| pdb_00001i1z	Download File View File

MUTANT HUMAN LYSOZYME (Q86D)

Kuroki, R.

(1998) J Biological Chem 273: 34310-34315

Released	2001-02-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)

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1I20 \| pdb_00001i20	Download File View File

MUTANT HUMAN LYSOZYME (A92D)

Kuroki, R.

(1998) J Biological Chem 273: 34310-34315

Released	2001-02-28
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)

1 to 25 of 170 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

1DHH | pdb_00001dhh

1DRN | pdb_00001drn

1EHE | pdb_00001ehe

1EHF | pdb_00001ehf

1EHG | pdb_00001ehg

1EW0 | pdb_00001ew0

1F24 | pdb_00001f24

1F25 | pdb_00001f25

1F26 | pdb_00001f26

1GEI | pdb_00001gei

1GEJ | pdb_00001gej

1GEQ | pdb_00001geq

1GIB | pdb_00001gib

1GOA | pdb_00001goa

1GOB | pdb_00001gob

1GOC | pdb_00001goc

1HJR | pdb_00001hjr

1HNR | pdb_00001hnr

1HNS | pdb_00001hns

1I1Z | pdb_00001i1z

1I20 | pdb_00001i20