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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Nagata, K."

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Search Summary

This query matches 99 Structures.

Refinements

Structure Determination Methodology

experimental (99)

Scientific Name of Source Organism

	Homo sapiens (15)
	Mus musculus (8)
	Sphingobium sp. MI1205 (8)
	Thermus thermophilus HB8 (8)
	Sulfurisphaera tokodaii str. 7 (5)
	Drosophila melanogaster (4)
	Candida parapsilosis (3)
	Gluconobacter frateurii (3)
	Pyrococcus horikoshii (3)
	Thermus thermophilus (3)

More...

Taxonomy

	Eukaryota (42)
	Bacteria (39)
	Archaea (13)
	Eukaryota (eukaryotes) (4)
	Riboviria (2)

Experimental Method

	X-RAY DIFFRACTION (81)
	SOLUTION NMR (17)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (99)
	DNA (5)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (38)
	2.0 - 2.5 (26)
	2.5 - 3.0 (13)
	3.0 - 3.5 (3)

Release Date

	1990 - 1994 (3)
	1995 - 1999 (3)
	2000 - 2004 (8)
	2005 - 2009 (24)
	2010 - 2014 (41)
	2015 - 2019 (6)
	2020 - 2024 (12)
	2025 - 2029 (2)

Enzyme Classification Name

	Hydrolases (22)
	Oxidoreductases (13)
	Lyases (4)
	Isomerases (2)
	Ligases (2)
	Transferases (2)
	Translocases (1)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (73)
	Cyclic (26)
	Dihedral (9)

SCOP Classification

	Alpha and beta proteins (a/b) (21)
	Alpha and beta proteins (a+b) (12)
	All beta proteins (7)
	All alpha proteins (7)
	Artifacts (7)
	Small proteins (7)
	Membrane and cell surface proteins and peptides (1)
	Multi-domain proteins (alpha and beta) (1)
	Peptides (1)

AllSelected

1 to 25 of 99 Structures

Page 1 of 4

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1BOM \| pdb_00001bom	Download File View File

THREE-DIMENSIONAL STRUCTURE OF BOMBYXIN-II, AN INSULIN-RELATED BRAIN-SECRETORY PEPTIDE OF THE SILKMOTH BOMBYX MORI: COMPARISON WITH INSULIN AND RELAXIN

Nagata, K., Hatanaka, H., Kohda, D., Inagaki, F.

(1995) J Mol Biology 253: 749-758

Released	1994-11-01
Method	SOLUTION NMR
Organisms	Bombyx mori
Macromolecule	BOMBYXIN-II,BOMBYXIN A-2 (protein) BOMBYXIN-II,BOMBYXIN A-6 (protein)

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1BON \| pdb_00001bon	Download File View File

THREE-DIMENSIONAL STRUCTURE OF BOMBYXIN-II, AN INSULIN-RELATED BRAIN-SECRETORY PEPTIDE OF THE SILKMOTH BOMBYX MORI: COMPARISON WITH INSULIN AND RELAXIN

Nagata, K., Hatanaka, H., Kohda, D., Inagaki, F., Structural Proteomics in Europe (SPINE)

(1995) J Mol Biology 253: 749-758

Released	1995-01-26
Method	SOLUTION NMR
Organisms	Bombyx mori
Macromolecule	BOMBYXIN-II,BOMBYXIN A-2 (protein) BOMBYXIN-II,BOMBYXIN A-6 (protein)

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1EQK \| pdb_00001eqk	Download File View File

SOLUTION STRUCTURE OF ORYZACYSTATIN-I, A CYSTEINE PROTEINASE INHIBITOR OF THE RICE, ORYZA SATIVA L. JAPONICA

Nagata, K., Kudo, N., Abe, K., Arai, S., Tanokura, M.

(2000) Biochemistry 39: 14753-14760

Released	2001-01-10
Method	SOLUTION NMR
Organisms	Oryza sativa Japonica Group
Macromolecule	ORYZACYSTATIN-I (protein)

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1GCP \| pdb_00001gcp	Download File View File

CRYSTAL STRUCTURE OF VAV SH3 DOMAIN

Nishida, M., Nagata, K., Hachimori, Y., Ogura, K., Inagaki, F.

(2001) EMBO J 20: 2995-3007

Released	2001-08-08
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	VAV PROTO-ONCOGENE (protein)

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1GCQ \| pdb_00001gcq	Download File View File

CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS

Nishida, M., Nagata, K., Hachimori, Y., Ogura, K., Inagaki, F.

(2001) EMBO J 20: 2995-3007

Released	2001-08-08
Method	X-RAY DIFFRACTION 1.68 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 (protein) VAV PROTO-ONCOGENE (protein)
Unique Ligands	MRD

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1HRE \| pdb_00001hre	Download File View File

SOLUTION STRUCTURE OF THE EPIDERMAL GROWTH FACTOR-LIKE DOMAIN OF HEREGULIN-ALPHA, A LIGAND FOR P180ERB4

Nagata, K., Kohda, D., Hatanaka, H., Ichikawa, S., Inagaki, F.

(1994) EMBO J 13: 3517-3523

Released	1994-10-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HEREGULIN ALPHA (protein)

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1HRF \| pdb_00001hrf	Download File View File

SOLUTION STRUCTURE OF THE EPIDERMAL GROWTH FACTOR-LIKE DOMAIN OF HEREGULIN-ALPHA, A LIGAND FOR P180ERB4

Nagata, K., Kohda, D., Hatanaka, H., Ichikawa, S., Inagaki, F.

(1994) EMBO J 13: 3517-3523

Released	1994-10-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HEREGULIN ALPHA (protein)

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1IX5 \| pdb_00001ix5	Download File View File

Solution structure of the Methanococcus thermolithotrophicus FKBP

Suzuki, R., Nagata, K., Kawakami, M., Nemoto, N., Furutani, M., Adachi, K., Maruyama, T., Tanokura, M.

(2003) J Mol Biology 328: 1149-1160

Released	2003-06-10
Method	SOLUTION NMR
Organisms	Methanothermococcus thermolithotrophicus
Macromolecule	FKBP (protein)

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1J0T \| pdb_00001j0t	Download File View File

The solution structure of molt-inhibiting hormone from the kuruma prawn

Katayama, H., Nagata, K., Ohira, T., Yumoto, F., Tanokura, M., Nagasawa, H.

(2003) J Biological Chem 278: 9620-9623

Released	2002-12-11
Method	SOLUTION NMR
Organisms	Penaeus japonicus
Macromolecule	MOLT-INHIBITING HORMONE (protein)

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1K1Z \| pdb_00001k1z	Download File View File

Solution structure of N-terminal SH3 domain mutant(P33G) of murine Vav

Ogura, K., Nagata, K., Horiuchi, M., Ebisui, E., Hasuda, T., Yuzawa, S., Nishida, M., Hatanaka, H., Inagaki, F.

(2002) J Biomol NMR 22: 37-46

Released	2001-10-10
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	vav (protein)

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1MKC \| pdb_00001mkc	Download File View File

C-TERMINAL DOMAIN OF MIDKINE

Iwasaki, W., Nagata, K., Hatanaka, H., Ogura, K., Inui, T., Kimura, T., Muramatsu, T., Yoshida, K., Tasumi, M., Inagaki, F.

(1997) EMBO J 16: 6936-6946

Released	1999-03-23
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PROTEIN (MIDKINE) (protein)

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1MKN \| pdb_00001mkn	Download File View File

N-TERMINAL HALF OF MIDKINE

Iwasaki, W., Nagata, K., Hatanaka, H., Ogura, K., Inui, T., Kimura, T., Muramatsu, T., Yoshida, K., Tasumi, M., Inagaki, F.

(1997) EMBO J 16: 6936-6946

Released	1999-03-23
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PROTEIN (MIDKINE) (protein)

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1R5Z \| pdb_00001r5z	Download File View File

Crystal Structure of Subunit C of V-ATPase

Iwata, M., Imamura, H., Stambouli, E., Ikeda, C., Tamakoshi, M., Nagata, K., Makyio, H., Hankamer, B., Barber, J., Yoshida, M., Yokoyama, K., Iwata, S.

(2004) Proc Natl Acad Sci U S A 101: 59-64

Released	2004-01-13
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Thermus thermophilus
Macromolecule	V-type ATP synthase subunit C (protein)

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1V46 \| pdb_00001v46	Download File View File

Solution Structure of CCAP (Crustacean Cardioactive Peptide) from Drosophila melanogaster

Nagata, K., Tanokura, M.

To be published

Released	2004-12-14
Method	SOLUTION NMR
Organisms	Manduca sexta
Macromolecule	Cardioactive Peptide (protein)

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1WTB \| pdb_00001wtb	Download File View File

Complex structure of the C-terminal RNA-binding domain of hnRNP D (AUF1) with telomere DNA

Enokizono, Y., Konishi, Y., Nagata, K., Ouhashi, K., Uesugi, S., Ishikawa, F., Katahira, M.

(2005) J Biological Chem 280: 18862-18870

Released	2005-04-05
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Heterogeneous nuclear ribonucleoprotein D0 (protein) 5'-D(PTPAPGPG)-3' (nucleic acid)

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1X0F \| pdb_00001x0f	Download File View File

Complex structure of the C-terminal RNA-binding domain of hnRNP D(AUF1) with telomeric DNA

Enokizono, Y., Konishi, Y., Nagata, K., Ouhashi, K., Uesugi, S., Ishikawa, F., Katahira, M.

(2005) J Biological Chem 280: 18862-18870

Released	2005-04-05
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Heterogeneous nuclear ribonucleoprotein D0 (protein) 5'-D(PTPAPGPG)-3' (nucleic acid)

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1X25 \| pdb_00001x25	Download File View File

Crystal Structure of a Member of YjgF Family from Sulfolobus Tokodaii (ST0811)

Miyakawa, T., Lee, W.C., Hatano, K., Kato, Y., Sawano, Y., Miyazono, K., Nagata, K., Tanokura, M.

(2006) Proteins 62: 557-561

Released	2006-02-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	Hypothetical UPF0076 protein ST0811 (protein)

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1Y49 \| pdb_00001y49	Download File View File

Solution Structure of CCAP (Crustacean Cardioactive Peptide) from Drosophila melanogaster

Nagata, K., Tanokura, M.

To be published

Released	2005-11-30
Method	SOLUTION NMR
Organisms	Drosophila melanogaster
Macromolecule	Cardioactive peptide (protein)

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1ZOV \| pdb_00001zov	Download File View File

Crystal Structure of Monomeric Sarcosine Oxidase from Bacillus sp. NS-129

Nagata, K., Sasaki, H., Ohtsuka, J., Hua, M., Okai, M., Kubota, K., Kamo, M., Ito, K., Ichikawa, T., Koyama, Y., Tanokura, M.

(2005) Proc Jpn Acad Ser B Phys Biol Sci 81: 220-224

Released	2006-05-23
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Bacillus sp. NS-129
Macromolecule	Monomeric sarcosine oxidase (protein)
Unique Ligands	CL, FAD

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2D36 \| pdb_00002d36	Download File View File

The Crystal Structure of Flavin Reductase HpaC

Okai, M., Kudo, N., Lee, W.C., Kamo, M., Nagata, K., Tanokura, M.

(2006) Biochemistry 45: 5103-5110

Released	2006-05-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	hypothetical NADH-dependent FMN oxidoreductase (protein)
Unique Ligands	FMN

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2D37 \| pdb_00002d37	Download File View File

The Crystal Structure of Flavin Reductase HpaC complexed with NAD+

Okai, M., Kudo, N., Lee, W.C., Kamo, M., Nagata, K., Tanokura, M.

(2006) Biochemistry 45: 5103-5110

Released	2006-05-30
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	hypothetical NADH-dependent FMN oxidoreductase (protein)
Unique Ligands	FMN, NAD

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2D38 \| pdb_00002d38	Download File View File

The Crystal Structure of Flavin Reductase HpaC complexed with NADP+

Okai, M., Kudo, N., Lee, W.C., Kamo, M., Nagata, K., Tanokura, M.

(2006) Biochemistry 45: 5103-5110

Released	2006-05-30
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	hypothetical NADH-dependent FMN oxidoreductase (protein)
Unique Ligands	FMN, NAP

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2D7J \| pdb_00002d7j	Download File View File

Crystal Structure Analysis of Glutamine Amidotransferase from Pyrococcus horikoshii OT3

Maruoka, S., Lee, W.C., Kamo, M., Kudo, N., Nagata, K., Tanokura, M.

(2005) Proc Jpn Acad Ser B Phys Biol Sci 81: 459-462

Released	2006-11-21
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	GMP synthase [glutamine-hydrolyzing] subunit A (protein)