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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yamaguchi, H."

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Search Summary

This query matches 129 Structures.

Refinements

Structure Determination Methodology

experimental (129)

Scientific Name of Source Organism

	Bos taurus (32)
	Arthrobacter globiformis (25)
	Homo sapiens (13)
	Thermus thermophilus (7)
	Solanum lycopersicum (6)
	Chlorobaculum tepidum TLS (5)
	Gallus gallus (5)
	Staphylococcus aureus subsp. aureus Mu50 (5)
	Mus musculus (4)
	Escherichia coli (3)

More...

Taxonomy

	Bacteria (64)
	Eukaryota (59)
	Riboviria (5)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (121)
	ELECTRON MICROSCOPY (5)
	SOLUTION NMR (3)

Polymer Entity Type

	Protein (128)
	DNA (1)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (6)
	1.5 - 2.0 (60)
	2.0 - 2.5 (32)
	2.5 - 3.0 (21)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (12)
	2000 - 2004 (19)
	2005 - 2009 (25)
	2010 - 2014 (41)
	2015 - 2019 (15)
	2020 - 2024 (15)
	2025 - 2029 (1)

Enzyme Classification Name

	Oxidoreductases (41)
	Hydrolases (41)
	Transferases (21)
	Translocases (5)
	Lyases (7)
	Ligases (4)
	Isomerases (3)

Membrane Protein Annotation

	MemProtMD (5)
	PDBTM (5)

Symmetry Type

	Asymmetric (64)
	Cyclic (62)
	Dihedral (16)

SCOP Classification

	Membrane and cell surface proteins and peptides (5)
	Alpha and beta proteins (a+b) (49)
	All beta proteins (50)
	Alpha and beta proteins (a/b) (21)
	Artifacts (11)
	All alpha proteins (10)
	Small proteins (5)

AllSelected

1 to 25 of 129 Structures

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1AV4 \| pdb_00001av4	Download File View File

CRYSTAL STRUCTURES OF THE COPPER-CONTAINING AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS IN THE HOLO-AND APO-FORMS: IMPLICATIONS FOR THE BIOGENESIS OF TOPA QUINONE

Wilce, M.C.J., Guss, J.M., Freeman, H.C.

(1997) Biochemistry 36: 16116-16133

Released	1998-03-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Arthrobacter globiformis
Macromolecule	AMINE OXIDASE (protein)
Unique Ligands	CU

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1AVK \| pdb_00001avk	Download File View File

CRYSTAL STRUCTURES OF THE COPPER-CONTAINING AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS IN THE HOLO-AND APO-FORMS: IMPLICATIONS FOR THE BIOGENESIS OF TOPA QUINONE

Wilce, M.C.J., Guss, J.M., Freeman, H.C., Tanizawa, K., Yamaguchi, H.

(1997) Biochemistry 36: 16116-16133

Released	1998-03-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Arthrobacter globiformis
Macromolecule	AMINE OXIDASE (protein)

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1AVL \| pdb_00001avl	Download File View File

CRYSTAL STRUCTURES OF THE COPPER-CONTAINING AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS IN THE HOLO-AND APO-FORMS: IMPLICATIONS FOR THE BIOGENESIS OF TOPA QUINONE

Wilce, M.C.J., Guss, J.M., Freeman, H.C.

(1997) Biochemistry 36: 16116-16133

Released	1998-03-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Arthrobacter globiformis
Macromolecule	AMINE OXIDASE (protein)
Unique Ligands	CU

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1GLV \| pdb_00001glv	Download File View File

THREE-DIMENSIONAL STRUCTURE OF THE GLUTATHIONE SYNTHETASE FROM ESCHERICHIA COLI B AT 2.0 ANGSTROMS RESOLUTION

Yamaguchi, H., Kato, H., Tanaka, T., Katsube, Y.

(1993) J Mol Biology 229: 1083-1100

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli
Macromolecule	GLUTATHIONE SYNTHASE (protein)

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1GSA \| pdb_00001gsa	Download File View File

STRUCTURE OF GLUTATHIONE SYNTHETASE COMPLEXED WITH ADP AND GLUTATHIONE

Hara, T., Kato, H., Nishioka, T., Katsube, Y., Oda, J.

(1996) Biochemistry 35: 11967-11974

Released	1996-06-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli B
Macromolecule	GLUTATHIONE SYNTHETASE (protein)
Unique Ligands	ADP, GSH, MG, SO4

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1GSH \| pdb_00001gsh	Download File View File

STRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 7.5

Matsuda, K., Kato, H., Yamaguchi, H., Nishioka, T., Katsube, Y., Oda, J.

(1996) Protein Eng 9: 1083-1092

Released	1996-07-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli B
Macromolecule	GLUTATHIONE BIOSYNTHETIC LIGASE (protein)

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1IA9 \| pdb_00001ia9	Download File View File

CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (AMPPNP COMPLEX)

Yamaguchi, H., Matsushita, M., Nairn, A.C., Kuriyan, J.

(2001) Mol Cell 7: 1047-1057

Released	2001-06-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	TRANSIENT RECEPTOR POTENTIAL-RELATED PROTEIN (protein)
Unique Ligands	ANP, DTT, ZN

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1IAH \| pdb_00001iah	Download File View File

CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (ADP-MG COMPLEX)

Yamaguchi, H., Matsushita, M., Nairn, A.C., Kuriyan, J.

(2001) Mol Cell 7: 1047-1057

Released	2001-06-06
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus
Macromolecule	TRANSIENT RECEPTOR POTENTIAL-RELATED PROTEIN (protein)
Unique Ligands	ADP, DTT, MG, ZN

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1IAJ \| pdb_00001iaj	Download File View File

CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (APO)

Yamaguchi, H., Matsushita, M., Nairn, A.C., Kuriyan, J.

(2001) Mol Cell 7: 1047-1057

Released	2001-06-06
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mus musculus
Macromolecule	TRANSIENT RECEPTOR POTENTIAL-RELATED PROTEIN (protein)
Unique Ligands	ZN

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1IQX \| pdb_00001iqx	Download File View File

CRYSTAL STRUCTURE OF COBALT-SUBSTITUTED AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS

Kishishita, S., Okajima, T., Mure, M., Kim, M., Yamaguchi, H., Hirota, S., Suzuki, S., Kuroda, S., Tanizawa, K.

(2003) J Am Chem Soc 125: 1041-1055

Released	2003-02-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Arthrobacter globiformis
Macromolecule	CO(II)-SUBSTITUTED AMINE OXIDASE (protein)
Unique Ligands	CO

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1IQY \| pdb_00001iqy	Download File View File

CRYSTAL STRUCTURE OF NICKEL-SUBSTITUTED AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS

Kishishita, S., Okajima, T., Mure, M., Kim, M., Yamaguchi, H., Hirota, S., Kuroda, S., Tanizawa, K.

(2003) J Am Chem Soc 125: 1041-1055

Released	2003-02-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Arthrobacter globiformis
Macromolecule	AMINE OXIDASE (protein)
Unique Ligands	NI

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1IU7 \| pdb_00001iu7	Download File View File

HOLO FORM OF COPPER-CONTAINING AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS

Kishishita, S., Okajima, T., Kim, M., Yamaguchi, H., Hirota, S., Suzuki, S., Kuroda, S., Tanizawa, K., Mure, M.

(2003) J Am Chem Soc 125: 1041-1055

Released	2003-02-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Arthrobacter globiformis
Macromolecule	AMINE OXIDASE (protein)
Unique Ligands	CU

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1IUG \| pdb_00001iug	Download File View File

The crystal structure of aspartate aminotransferase which belongs to subgroup IV from Thermus thermophilus

Katsura, Y., Shirouzu, M., Yamaguchi, H., Ishitani, R., Nureki, O., Kuramitsu, S., Hayashi, H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Proteins 55: 487-492

Released	2003-11-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	putative aspartate aminotransferase (protein)
Unique Ligands	PO4

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1IUH \| pdb_00001iuh	Download File View File

Crystal structure of TT0787 of thermus thermophilus HB8

Kato, M., Sakai, H., Shirouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) J Mol Biology 329: 903-911

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus
Macromolecule	2'-5' RNA Ligase (protein)

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1IVU \| pdb_00001ivu	Download File View File

Crystal structure of copper amine oxidase from Arthrobacter globiformis: Initial intermediate in topaquinone biogenesis

Kim, M., Okajima, T., Kishishita, S., Yoshimura, M., Kawamori, A., Tanizawa, K., Yamaguchi, H.

(2002) Nat Struct Biol 9: 591-596

Released	2002-08-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Arthrobacter globiformis
Macromolecule	amine oxidase (protein)
Unique Ligands	CU

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1IVV \| pdb_00001ivv	Download File View File

Crystal structure of copper amine oxidase from Arthrobacter globiformis: Early intermediate in topaquinone biogenesis

Kim, M., Okajima, T., Kishishita, S., Yoshimura, M., Kawamori, A., Tanizawa, K., Yamaguchi, H.

(2002) Nat Struct Biol 9: 591-596

Released	2002-08-07
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Arthrobacter globiformis
Macromolecule	amine oxidase (protein)
Unique Ligands	CU

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1IVW \| pdb_00001ivw	Download File View File

Crystal structure of copper amine oxidase from Arthrobacter globiformis: Late intermediate in topaquinone biogenesis

Kim, M., Okajima, T., Kishishita, S., Yoshimura, M., Kawamori, A., Tanizawa, K., Yamaguchi, H.

(2002) Nat Struct Biol 9: 591-596

Released	2002-08-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Arthrobacter globiformis
Macromolecule	amine oxidase (protein)
Unique Ligands	CU

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1IVX \| pdb_00001ivx	Download File View File

Crystal structure of copper amine oxidase from Arthrobacter globiformis: Holo form generated by biogenesis in crystal.

Kim, M., Okajima, T., Kishishita, S., Yoshimura, M., Kawamori, A., Tanizawa, K., Yamaguchi, H.

(2002) Nat Struct Biol 9: 591-596

Released	2002-08-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Arthrobacter globiformis
Macromolecule	amine oxidase (protein)
Unique Ligands	CU

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1OCC \| pdb_00001occ	Download File View File

STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE

Tsukihara, T., Aoyama, H., Yamashita, E., Tomizaki, T., Yamaguchi, H., Shinzawa-Itoh, K., Nakashima, R., Yaono, R., Yoshikawa, S.

(1996) Science 272: 1136-1144

Released	1996-12-07
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CU, HEA, MG, ZN

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1OCO \| pdb_00001oco	Download File View File

BOVINE HEART CYTOCHROME C OXIDASE IN CARBON MONOXIDE-BOUND STATE

Tsukihara, T., Yao, M.

(1998) Science 280: 1723-1729

Released	1999-07-22
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CMO, CU, HEA, MG, NA, ZN

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1OCR \| pdb_00001ocr	Download File View File

BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE

Tsukihara, T., Yao, M.

(1998) Science 280: 1723-1729

Released	1999-07-29
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CU, HEA, MG, NA, ZN

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1OCZ \| pdb_00001ocz	Download File View File

BOVINE HEART CYTOCHROME C OXIDASE IN AZIDE-BOUND STATE

Tsukihara, T., Yao, M.

(1998) Science 280: 1723-1729

Released	1999-07-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	AZI, CU, HEA, MG, NA, ZN

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1UFA \| pdb_00001ufa	Download File View File

Crystal structure of TT1467 from Thermus thermophilus HB8

Idaka, M., Terada, T., Murayama, K., Yamaguchi, H., Nureki, O., Ishitani, R., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2003-11-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	TT1467 protein (protein)

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1UFB \| pdb_00001ufb	Download File View File

Crystal structure of TT1696 from Thermus thermophilus HB8

Idaka, M., Murayama, K., Yamaguchi, H., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2003-11-28
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus
Macromolecule	TT1696 protein (protein)

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1UFL \| pdb_00001ufl	Download File View File

Crystal Structure of TT1020 from Thermus thermophilus HB8

Wang, H., Sakai, H., Hori-Takemoto, C., Kaminishi, T., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Struct Biol 149: 99-110

Released	2003-11-30
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Nitrogen regulatory protein P-II (protein)

1 to 25 of 129 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

1AV4 | pdb_00001av4

1AVK | pdb_00001avk

1AVL | pdb_00001avl

1GLV | pdb_00001glv

1GSA | pdb_00001gsa

1GSH | pdb_00001gsh

1IA9 | pdb_00001ia9

1IAH | pdb_00001iah

1IAJ | pdb_00001iaj

1IQX | pdb_00001iqx

1IQY | pdb_00001iqy

1IU7 | pdb_00001iu7

1IUG | pdb_00001iug

1IUH | pdb_00001iuh

1IVU | pdb_00001ivu

1IVV | pdb_00001ivv

1IVW | pdb_00001ivw

1IVX | pdb_00001ivx

1OCC | pdb_00001occ

1OCO | pdb_00001oco

1OCR | pdb_00001ocr

1OCZ | pdb_00001ocz

1UFA | pdb_00001ufa

1UFB | pdb_00001ufb

1UFL | pdb_00001ufl