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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kai, Y."

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Search Summary

This query matches 44 Structures.

Refinements

Structure Determination Methodology

experimental (44)

Scientific Name of Source Organism

	Thermococcus kodakarensis KOD1 (6)
	Achromobacter cycloclastes (4)
	Bacillus subtilis (3)
	Oryza sativa Japonica Group (3)
	Adiantum capillus-veneris (2)
	Cucurbita pepo (2)
	Escherichia coli (2)
	Galdieria partita (2)
	Geobacillus zalihae (2)
	Methylomonas sp. J (2)

More...

Taxonomy

	Bacteria (22)
	Eukaryota (15)
	Archaea (7)

Experimental Method

	X-RAY DIFFRACTION (43)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (44)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (21)
	2.0 - 2.5 (10)
	2.5 - 3.0 (7)
	3.0 - 3.5 (2)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (14)
	2000 - 2004 (15)
	2005 - 2009 (11)
	2010 - 2014 (3)

Enzyme Classification Name

	Lyases (11)
	Hydrolases (7)
	Transferases (6)
	Isomerases (4)
	Oxidoreductases (2)

Membrane Protein Annotation

OPM (2)

Symmetry Type

	Asymmetric (25)
	Cyclic (11)
	Dihedral (13)

SCOP Classification

	Alpha and beta proteins (a+b) (10)
	Alpha and beta proteins (a/b) (20)
	All beta proteins (16)
	All alpha proteins (2)
	Artifacts (2)
	Multi-domain proteins (alpha and beta) (2)

AllSelected

1 to 25 of 44 Structures

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1BQK \| pdb_00001bqk	Download File View File

OXIDIZED PSEUDOAZURIN

Inoue, T., Nishio, N., Hamanaka, S., Shimomura, T., Harada, S., Suzuki, S., Kohzuma, T., Shidara, S., Iwasaki, H., Kai, Y.

(1999) J Biological Chem 274: 17845-17852

Released	1999-08-17
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Achromobacter cycloclastes
Macromolecule	PSEUDOAZURIN (protein)
Unique Ligands	CU

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1BQR \| pdb_00001bqr	Download File View File

REDUCED PSEUDOAZURIN

Inoue, T., Nishio, N., Hamanaka, S., Shimomura, T., Harada, S., Suzuki, S., Kohzuma, T., Shidara, S., Iwasaki, H., Kai, Y.

(1999) J Biological Chem 274: 17845-17852

Released	1999-08-17
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Achromobacter cycloclastes
Macromolecule	PSEUDOAZURIN (protein)
Unique Ligands	CU

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1BWV \| pdb_00001bwv	Download File View File

Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate

Sugawara, H., Yamamoto, H., Shibata, N., Inoue, T., Miyake, C., Yokota, A., Kai, Y.

(1999) J Biological Chem 274: 15655-15661

Released	1999-09-27
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Galdieria partita
Macromolecule	PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE) (protein)
Unique Ligands	CAP, MG

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1BXU \| pdb_00001bxu	Download File View File

OXIDIZED PLASTOCYANIN FROM SYNECHOCOCCUS SP.

Inoue, T., Sugawara, H., Hamanaka, S., Tsukui, H., Suzuki, E., Kohzuma, T., Kai, Y.

(1999) Biochemistry 38: 6063-6069

Released	1999-06-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Synechococcus elongatus PCC 7942 = FACHB-805
Macromolecule	PLASTOCYANIN (protein)
Unique Ligands	CU

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1BXV \| pdb_00001bxv	Download File View File

REDUCED PLASTOCYANIN FROM SYNECHOCOCCUS SP.

Inoue, T., Sugawara, H., Hamanaka, S., Tsukui, H., Suzuki, E., Kohzuma, T., Kai, Y.

(1999) Biochemistry 38: 6063-6069

Released	1999-06-15
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Synechococcus elongatus PCC 7942 = FACHB-805
Macromolecule	PLASTOCYANIN (protein)
Unique Ligands	CU

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1BYO \| pdb_00001byo	Download File View File

WILD-TYPE PLASTOCYANIN FROM SILENE

Sugawara, H., Inoue, T., Li, C., Gotowda, M., Hibino, T., Takabe, T., Kai, Y.

(1999) J Biochem 125: 899-903

Released	1999-10-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Silene latifolia subsp. alba
Macromolecule	PROTEIN (PLASTOCYANIN) (protein)
Unique Ligands	CU

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1BYP \| pdb_00001byp	Download File View File

E43K,D44K DOUBLE MUTANT PLASTOCYANIN FROM SILENE

Sugawara, H., Inoue, T., Li, C., Gotowda, M., Hibino, T., Takabe, T., Kai, Y.

(1999) J Biochem 125: 899-903

Released	1999-10-19
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Silene latifolia subsp. alba
Macromolecule	PROTEIN (PLASTOCYANIN) (protein)
Unique Ligands	CU

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1C7K \| pdb_00001c7k	Download File View File

CRYSTAL STRUCTURE OF THE ZINC PROTEASE

Kurisu, G., Harada, S., Kai, Y.

(2000) J Inorg Biochem 82: 225-228

Released	2001-04-25
Method	X-RAY DIFFRACTION 1 Å
Organisms	Streptomyces caespitosus
Macromolecule	ZINC ENDOPROTEASE (protein)
Unique Ligands	CA, ZN

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1CUO \| pdb_00001cuo	Download File View File

CRYSTAL STRUCTURE ANALYSIS OF ISOMER-2 AZURIN FROM METHYLOMONAS J

Inoue, T., Nishio, N., Kai, Y., Suzuki, S., Kataoka, K.

(2003) J Mol Biology 333: 117-124

Released	2000-08-23
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Methylomonas sp. J
Macromolecule	PROTEIN (AZURIN ISO-2) (protein)
Unique Ligands	CU

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1FIY \| pdb_00001fiy	Download File View File

THREE-DIMENSIONAL STRUCTURE OF PHOSPHOENOLPYRUVATE CARBOXYLASE FROM ESCHERICHIA COLI AT 2.8 A RESOLUTION

Kai, Y., Matsumura, H., Inoue, T., Terada, K., Nagara, Y., Yoshinaga, T., Kihara, A., Izui, K.

(1999) Proc Natl Acad Sci U S A 96: 823-828

Released	1999-02-09
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli K-12
Macromolecule	PHOSPHOENOLPYRUVATE CARBOXYLASE (protein)
Unique Ligands	ASP

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1IR1 \| pdb_00001ir1	Download File View File

Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate

Mizohata, E., Matsumura, H., Okano, Y., Kumei, M., Takuma, H., Onodera, J., Kato, K., Shibata, N., Inoue, T., Yokota, A., Kai, Y.

(2002) J Mol Biology 316: 679-691

Released	2002-03-13
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Spinacia oleracea
Macromolecule	Large subunit of Rubisco (protein) Small subunit of Rubisco (protein)
Unique Ligands	CAP, MG

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1IR2 \| pdb_00001ir2	Download File View File

Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP)

Mizohata, E., Matsumura, H., Okano, Y., Kumei, M., Takuma, H., Onodera, J., Kato, K., Shibata, N., Inoue, T., Yokota, A., Kai, Y.

(2002) J Mol Biology 316: 679-691

Released	2002-03-20
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Large subunit of Rubisco (protein) Small subunit of Rubisco (protein)
Unique Ligands	CAP, GOL, MG

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1IWA \| pdb_00001iwa	Download File View File

RUBISCO FROM GALDIERIA PARTITA

Okano, Y., Mizohata, E., Xie, Y., Matsumura, H., Sugawara, H., Inoue, T., Yokota, A., Kai, Y.

(2002) FEBS Lett 527: 33-36

Released	2003-04-30
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Galdieria partita
Macromolecule	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (protein) ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (protein)
Unique Ligands	SO4

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1JQN \| pdb_00001jqn	Download File View File

Crystal structure of E.coli phosphoenolpyruvate carboxylase in complex with Mn2+ and DCDP

Matsumura, H., Kai, Y.

(2002) Structure 10: 1721-1730

Released	2003-01-14
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Escherichia coli
Macromolecule	phosphoenolpyruvate carboxylase (protein)
Unique Ligands	ASP, DCO, MN

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1JQO \| pdb_00001jqo	Download File View File

Crystal structure of C4-form phosphoenolpyruvate carboxylase from maize

Matsumura, H., Kai, Y.

(2002) Structure 10: 1721-1730

Released	2003-01-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Zea mays
Macromolecule	phosphoenolpyruvate carboxylase (protein)
Unique Ligands	SO4

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1KDI \| pdb_00001kdi	Download File View File

REDUCED FORM OF PLASTOCYANIN FROM DRYOPTERIS CRASSIRHIZOMA

Inoue, T., Gotowda, M., Hamada, K., Kohzuma, T., Yoshizaki, F., Sugimura, Y., Kai, Y.

(1999) J Biological Chem 274: 11817-11823

Released	1999-05-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Adiantum capillus-veneris
Macromolecule	PLASTOCYANIN (protein)
Unique Ligands	CU

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1KDJ \| pdb_00001kdj	Download File View File

OXIDIZED FORM OF PLASTOCYANIN FROM DRYOPTERIS CRASSIRHIZOMA

Inoue, T., Gotowda, M., Hamada, K., Kohzuma, T., Yoshizaki, F., Sugimura, Y., Kai, Y.

(1999) J Biological Chem 274: 11817-11823

Released	1999-05-11
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Adiantum capillus-veneris
Macromolecule	PLASTOCYANIN (protein)
Unique Ligands	CU

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1KUH \| pdb_00001kuh	Download File View File

ZINC PROTEASE FROM STREPTOMYCES CAESPITOSUS

Kurisu, G., Kinoshita, T., Sugimoto, A., Nagara, A., Kai, Y., Kasai, N., Harada, S.

(1997) J Biochem 121: 304-308

Released	1997-03-12
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces caespitosus
Macromolecule	ZINC PROTEASE (protein)
Unique Ligands	CA, ZN

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1MGT \| pdb_00001mgt	Download File View File

CRYSTAL STRUCTURE OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS KODAKARAENSIS STRAIN KOD1

Hashimoto, H., Inoue, T., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Kai, Y.

(1999) J Mol Biology 292: 707-716

Released	2000-01-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermococcus kodakarensis KOD1
Macromolecule	PROTEIN (O6-METHYLGUANINE-DNA METHYLTRANSFERASE) (protein)
Unique Ligands	SO4

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1PMY \| pdb_00001pmy	Download File View File

REFINED CRYSTAL STRUCTURE OF PSEUDOAZURIN FROM METHYLOBACTERIUM EXTORQUENS AM1 AT 1.5 ANGSTROMS RESOLUTION

Inoue, T., Kai, Y., Harada, S., Kasai, N., Ohshiro, Y., Suzuki, S., Kohzuma, T., Tobari, J.

(1994) Acta Crystallogr D Biol Crystallogr 50: 317-328

Released	1994-07-31
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Methylorubrum extorquens
Macromolecule	PSEUDOAZURIN (protein)
Unique Ligands	CU

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1QB4 \| pdb_00001qb4	Download File View File

CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE

Matsumura, H., Terada, M., Shirakata, S., Inoue, T., Yoshinaga, T., Izui, K., Kai, Y.

(1999) FEBS Lett 458: 93-96

Released	2002-05-01
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia coli
Macromolecule	PHOSPHOENOLPYRUVATE CARBOXYLASE (protein)
Unique Ligands	ASP, MN

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1RKR \| pdb_00001rkr	Download File View File

CRYSTAL STRUCTURE OF AZURIN-I FROM ALCALIGENES XYLOSOXIDANS NCIMB 11015

Li, C., Inoue, T., Gotowda, M., Suzuki, S., Yamaguchi, K., Kataoka, K., Kai, Y.

(1998) Acta Crystallogr D Biol Crystallogr 54: 347-354

Released	1998-05-20
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Achromobacter xylosoxidans
Macromolecule	AZURIN-I (protein)
Unique Ligands	CU

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1UAT \| pdb_00001uat	Download File View File

The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J

Inoue, T., Suzuki, S., Nisho, N., Yamaguchi, K., Kataoka, K., Tobari, J., Yong, X., Hamanaka, S., Matsumura, H., Kai, Y.

(2003) J Mol Biology 333: 117-124

Released	2004-03-30
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Methylomonas sp. J
Macromolecule	Azurin iso-2 (protein)
Unique Ligands	CU, SO4

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1V40 \| pdb_00001v40	Download File View File

First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase

Inoue, T., Okano, Y., Kado, Y., Aritake, K., Irikura, D., Uodome, N., Kinugasa, S., Okazaki, N., Matsumura, H., Kai, Y., Urade, Y.

(2004) J Biochem 135: 279-283

Released	2004-11-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Glutathione-requiring prostaglandin D synthase (protein)
Unique Ligands	GOL, GSH, MG, O16

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1WDD \| pdb_00001wdd	Download File View File

Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate

Mizohata, E., Matsumura, H., Ueno, T., Ishida, H., Inoue, T., Makino, A., Mae, T., Kai, Y.

(2012) J Mol Biology 422: 75-86

Released	2004-11-13
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Oryza sativa Japonica Group
Macromolecule	Ribulose bisphosphate carboxylase large chain (protein) Ribulose bisphosphate carboxylase small chain C (protein)
Unique Ligands	CAP, GOL, MG

1 to 25 of 44 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

1BQK | pdb_00001bqk

1BQR | pdb_00001bqr

1BWV | pdb_00001bwv

1BXU | pdb_00001bxu

1BXV | pdb_00001bxv

1BYO | pdb_00001byo

1BYP | pdb_00001byp

1C7K | pdb_00001c7k

1CUO | pdb_00001cuo

1FIY | pdb_00001fiy

1IR1 | pdb_00001ir1

1IR2 | pdb_00001ir2

1IWA | pdb_00001iwa

1JQN | pdb_00001jqn

1JQO | pdb_00001jqo

1KDI | pdb_00001kdi

1KDJ | pdb_00001kdj

1KUH | pdb_00001kuh

1MGT | pdb_00001mgt

1PMY | pdb_00001pmy

1QB4 | pdb_00001qb4

1RKR | pdb_00001rkr

1UAT | pdb_00001uat

1V40 | pdb_00001v40

1WDD | pdb_00001wdd