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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Okamoto, K."

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Search Summary

This query matches 63 Structures.

Refinements

Structure Determination Methodology

experimental (63)

Scientific Name of Source Organism

	Rattus norvegicus (15)
	Bos taurus (14)
	Homo sapiens (12)
	Aeromonas sobria (3)
	Vibrio metschnikovii (3)
	Chaetoceros socialis f. radians RNA virus 01 (2)
	Giardia lamblia virus (2)
	Rosellinia necatrix megabirnavirus 1/W779 (2)
	Saccharomyces cerevisiae (2)
	Chaetoceros tenuissimus DNA virus type-II (1)

More...

Taxonomy

	Eukaryota (44)
	Riboviria (9)
	Bacteria (8)
	Varidnaviria (1)
	unclassified viruses (1)

Experimental Method

	X-RAY DIFFRACTION (51)
	ELECTRON MICROSCOPY (11)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (63)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (1)
	1.5 - 2.0 (21)
	2.0 - 2.5 (19)
	2.5 - 3.0 (11)
	3.0 - 3.5 (8)
	4.0 - 4.5 (1)

Release Date

	2000 - 2004 (5)
	2005 - 2009 (9)
	2010 - 2014 (9)
	2015 - 2019 (22)
	2020 - 2024 (17)
	2025 - 2029 (1)

Enzyme Classification Name

	Oxidoreductases (31)
	Transferases (6)
	Hydrolases (4)

Symmetry Type

	Cyclic (33)
	Asymmetric (21)
	Icosahedral (9)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (16)
	All alpha proteins (10)
	Alpha and beta proteins (a/b) (1)
	Artifacts (1)

AllSelected

1 to 25 of 63 Structures

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1FIQ \| pdb_00001fiq	Download File View File

CRYSTAL STRUCTURE OF XANTHINE OXIDASE FROM BOVINE MILK

Enroth, C., Eger, B.T., Okamoto, K., Nishino, T., Nishino, T., Pai, E.F.

(2000) Proc Natl Acad Sci U S A 97: 10723-10728

Released	2000-10-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bos taurus
Macromolecule	XANTHINE OXIDASE (protein)
Unique Ligands	FAD, FES, GOL, MOS, MTE, SAL

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1FO4 \| pdb_00001fo4	Download File View File

CRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE ISOLATED FROM BOVINE MILK

Enroth, C., Eger, B.T., Okamoto, K., Nishino, T., Nishino, T., Pai, E.F.

(2000) Proc Natl Acad Sci U S A 97: 10723-10728

Released	2000-10-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bos taurus
Macromolecule	XANTHINE DEHYDROGENASE (protein)
Unique Ligands	CA, FAD, FES, GOL, MOS, MTE, SAL

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1N5X \| pdb_00001n5x	Download File View File

Xanthine Dehydrogenase from Bovine Milk with Inhibitor TEI-6720 Bound

Okamoto, K., Eger, B.T., Nishino, T., Kondo, S., Pai, E.F., Nishino, T.

(2003) J Biological Chem 278: 1848-1855

Released	2003-03-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bos taurus
Macromolecule	Xanthine Dehydrogenase (protein)
Unique Ligands	FAD, FES, MOS, MTE, TEI

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1V97 \| pdb_00001v97	Download File View File

Crystal Structure of Bovine Milk Xanthine Dehydrogenase FYX-051 bound form

Okamoto, K., Matsumoto, K., Hille, R., Eger, B.T., Pai, E.F., Nishino, T.

(2004) Proc Natl Acad Sci U S A 101: 7931-7936

Released	2004-06-22
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase (protein)
Unique Ligands	ACY, CA, FAD, FES, FYX, GOL, MOS, MTE

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1VDV \| pdb_00001vdv	Download File View File

Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form

Fukunari, A., Okamoto, K., Nishino, T., Eger, B.T., Pai, E.F., Kamezawa, M., Yamada, I., Kato, N.

(2004) J Pharmacol Exp Ther 311: 519-528

Released	2004-12-21
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	ACY, CA, FAD, FES, GOL, MOS, MTE, YSH

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1WYG \| pdb_00001wyg	Download File View File

Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)

Nishino, T., Okamoto, K., Kawaguchi, Y., Hori, H., Matsumura, T., Eger, B.T., Pai, E.F., Nishino, T.

(2005) J Biological Chem 280: 24888-24894

Released	2005-05-31
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Rattus norvegicus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	ACY, CA, FAD, FES, PO4, SAL

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2E1Q \| pdb_00002e1q	Download File View File

Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val

Yamaguchi, Y., Matsumura, T., Ichida, K., Okamoto, K., Nishino, T.

(2007) J Biochem 141: 513-524

Released	2007-09-18
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	BCT, CA, FAD, FES, MOM, MTE, SAL

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2E3T \| pdb_00002e3t	Download File View File

Crystal structure of rat xanthine oxidoreductase mutant (W335A and F336L)

Asai, R., Nishino, T., Matsumura, T., Okamoto, K., Pai, E.F., Nishino, T.

(2007) J Biochem 141: 525-534

Released	2007-09-25
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Rattus norvegicus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	BCT, CA, FAD, FES, PO4, URC

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2MK4 \| pdb_00002mk4	Download File View File

Solution structure of ORF2

Miyakawa, T., Kobayashi, H., Tashiro, M., Yamanaka, H., Tanokura, M.

(2015) J Biological Chem 290: 11130-11143

Released	2015-03-25
Method	SOLUTION NMR
Organisms	Aeromonas sobria
Macromolecule	Open reading frame 2 (protein)

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2Z5B \| pdb_00002z5b	Download File View File

Crystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly

Yashiroda, H., Mizushima, T., Okamoto, K., Kameyama, T., Hayashi, H., Kishimoto, T., Kasahara, M., Kurimoto, E., Sakata, E., Suzuki, A., Hirano, Y., Murata, S., Kato, K., Yamane, T., Tanaka, K.

(2008) Nat Struct Mol Biol 15: 228-236

Released	2008-01-22
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Protein YPL144W (protein) Uncharacterized protein YLR021W (protein)

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2Z5C \| pdb_00002z5c	Download File View File

Crystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly

Yashiroda, H., Mizushima, T., Okamoto, K., Kameyama, T., Hayashi, H., Kishimoto, T., Kasahara, M., Kurimoto, E., Sakata, E., Suzuki, A., Hirano, Y., Murata, S., Kato, K., Yamane, T., Tanaka, K.

(2008) Nat Struct Mol Biol 15: 228-236

Released	2008-01-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Proteasome component PUP2 (protein) Protein YPL144W (protein) Uncharacterized protein YLR021W (protein)

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2Z5E \| pdb_00002z5e	Download File View File

Crystal Structure of Proteasome Assembling Chaperone 3

Okamoto, K., Kurimoto, E., Sakata, E., Suzuki, A., Yamane, T., Hirano, Y., Murata, S., Tanaka, K., Kato, K.

(2008) Nat Struct Mol Biol 15: 228-236

Released	2008-02-19
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Proteasome Assembling Chaperone 3 (protein)

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2Z9S \| pdb_00002z9s	Download File View File

Crystal Structure Analysis of rat HBP23/Peroxiredoxin I, Cys52Ser mutant

Matsumura, T., Okamoto, K., Nishino, T., Abe, Y.

(2008) J Biological Chem 283: 284-293

Released	2007-11-20
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Rattus norvegicus
Macromolecule	Peroxiredoxin-1 (protein)

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3AM9 \| pdb_00003am9	Download File View File

Complex of bovine xanthine dehydrogenase and trihydroxy FYX-051

Matsumoto, K., Okamoto, K., Ashizawa, N., Matsumura, T., Kusano, T., Nishino, T.

(2011) J Pharmacol Exp Ther 336: 95-103

Released	2010-11-03
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	BCT, CA, FAD, FES, FYO, GOL, MOS, MTE

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3AMZ \| pdb_00003amz	Download File View File

Bovine Xanthine Oxidoreductase urate bound form

Okamoto, K., Eger, B.T., Pai, E.F., Nishino, T.

(2010) J Am Chem Soc 132: 17080-17083

Released	2010-12-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	BCT, CA, FAD, FES, GOL, MOS, MTE, NAI, URC

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3AN1 \| pdb_00003an1	Download File View File

Crystal structure of rat D428A mutant, urate bound form

Okamoto, K., Kawaguchi, Y., Eger, B.T., Pai, E.F., Nishino, T.

(2010) J Am Chem Soc 132: 17080-17083

Released	2010-12-01
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Rattus norvegicus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	BCT, CA, FAD, FES, GOL, URC

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3AX7 \| pdb_00003ax7	Download File View File

Bovine Xanthine Oxidase, protease cleaved form

Ishikita, H., Eger, B.T., Pai, E.F., Okamoto, K., Nishino, T.

(2012) J Am Chem Soc 134: 999-1009

Released	2012-02-22
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	BCT, CA, FAD, FES, GOL, SAL, XAX

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3AX9 \| pdb_00003ax9	Download File View File

Bovine xanthine oxidase, protease cleaved form

Ishikita, H., Eger, B.T., Pai, E.F., Okamoto, K., Nishino, T.

(2012) J Am Chem Soc 134: 999-1009

Released	2012-02-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	BCT, CA, FAD, FES, GOL, SAL, XAX

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3BDJ \| pdb_00003bdj	Download File View File

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor

Eger, B.T., Okamoto, K., Nishino, T., Pai, E.F., Nishino, T.

(2008) Nucleosides Nucleotides Nucleic Acids 27: 888-893

Released	2008-11-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	141, CA, CO3, FAD, FES, GOL, MOW, MTE

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3HJR \| pdb_00003hjr	Download File View File

Crystal structure of serine protease of Aeromonas sobria

Utsunomiya, H., Tsuge, H., Kobayashi, H., Okamoto, K.

(2009) J Biological Chem 284: 27655-27663

Released	2009-06-02
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Aeromonas sobria
Macromolecule	Extracellular serine protease (protein)
Unique Ligands	CA

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3UNA \| pdb_00003una	Download File View File

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NAD Bound

Eger, B.T., Okamoto, K., Nishino, T., Pai, E.F.

(2012) J Am Chem Soc 134: 999-1009

Released	2012-05-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	CA, CO3, FAD, FES, GOL, MOS, MTE, NAD, SAL

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3UNC \| pdb_00003unc	Download File View File

Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution

Eger, B.T., Okamoto, K., Nishino, T., Pai, E.F.

(2012) J Am Chem Soc 134: 999-1009

Released	2012-05-09
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	CA, CO3, FAD, FES, GOL, MOS, MTE, SAL

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3UNI \| pdb_00003uni	Download File View File

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NADH Bound

Eger, B.T., Okamoto, K., Nishino, T., Pai, E.F.

(2012) J Am Chem Soc 134: 999-1009

Released	2012-05-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	CA, CO3, FAD, FES, GOL, MOS, MTE, NAI, SAL

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3VXW \| pdb_00003vxw	Download File View File

Crystal structure of Saccharomyces cerevisiae Atg8 complexed with Atg32 AIM

Noda, N.N., Inagaki, F.

(2012) J Biological Chem 287: 10631-10638

Released	2012-10-03
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Autophagy-related protein 8 (protein) Peptide from Autophagy-related protein 32 (protein)
Unique Ligands	SO4

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3WQB \| pdb_00003wqb	Download File View File

Crystal structure of aeromonas sobria serine protease (ASP) and the chaperone (ORF2) complex

Kobayashi, H., Yoshida, T., Miyakawa, T., Kato, R., Tashiro, M., Yamanaka, H., Tanokura, M., Tsuge, H.

(2015) J Biological Chem 290: 11130-11143

Released	2015-03-25
Method	X-RAY DIFFRACTION 1.41 Å
Organisms	Aeromonas sobria
Macromolecule	Extracellular serine protease (protein) Open reading frame 2 (protein)
Unique Ligands	CA

1 to 25 of 63 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

Symmetry Type

SCOP Classification

1FIQ | pdb_00001fiq

1FO4 | pdb_00001fo4

1N5X | pdb_00001n5x

1V97 | pdb_00001v97

1VDV | pdb_00001vdv

1WYG | pdb_00001wyg

2E1Q | pdb_00002e1q

2E3T | pdb_00002e3t

2MK4 | pdb_00002mk4

2Z5B | pdb_00002z5b

2Z5C | pdb_00002z5c

2Z5E | pdb_00002z5e

2Z9S | pdb_00002z9s

3AM9 | pdb_00003am9

3AMZ | pdb_00003amz

3AN1 | pdb_00003an1

3AX7 | pdb_00003ax7

3AX9 | pdb_00003ax9

3BDJ | pdb_00003bdj

3HJR | pdb_00003hjr

3UNA | pdb_00003una

3UNC | pdb_00003unc

3UNI | pdb_00003uni

3VXW | pdb_00003vxw

3WQB | pdb_00003wqb