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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Tomoo, K."

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Search Summary

This query matches 30 Structures.

Refinements

Structure Determination Methodology

experimental (30)

Scientific Name of Source Organism

	Bos taurus (10)
	Homo sapiens (8)
	Mus musculus (7)
	Carica papaya (3)
	Streptomyces thermoviolaceus (2)
	synthetic construct (2)
	Thermus aquaticus (1)
	Vibrio vulnificus (1)

Taxonomy

	Eukaryota (24)
	Bacteria (4)
	other sequences (2)

Experimental Method

X-RAY DIFFRACTION (30)

Polymer Entity Type

	Protein (28)
	DNA (2)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.5 - 2.0 (14)
	2.0 - 2.5 (14)
	2.5 - 3.0 (1)

Release Date

	1990 - 1994 (3)
	1995 - 1999 (1)
	2000 - 2004 (4)
	2005 - 2009 (10)
	2010 - 2014 (5)
	2015 - 2019 (1)
	2020 - 2024 (6)

Enzyme Classification Name

	Hydrolases (13)
	Transferases (3)
	Ligases (2)

Symmetry Type

	Asymmetric (28)
	Cyclic (1)

SCOP Classification

	Alpha and beta proteins (a+b) (18)
	All beta proteins (1)
	Alpha and beta proteins (a/b) (1)
	Artifacts (1)

AllSelected

1 to 25 of 30 Structures

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1BTP \| pdb_00001btp	Download File View File

UNIQUE BINDING OF A NOVEL SYNTHETIC INHIBITOR, N-[3-[4-[4-(AMIDINOPHENOXY)-CARBONYL]PHENYL]-2-METHYL-2-PROPENOYL]-N-ALLYLGLYCINE METHANESULFONATE TO BOVINE TRYPSIN, REVEALED BY THE CRYSTAL STRUCTURE OF THE COMPLEX

Odagaki, Y., Nakai, H., Senokuchi, K., Kawamura, M., Hamanaka, N., Nakamura, M., Tomoo, K., Ishida, T.

(1995) Biochemistry 34: 12849-12853

Released	1996-01-29
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	BETA-TRYPSIN (protein)
Unique Ligands	CA

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1CWY \| pdb_00001cwy	Download File View File

CRYSTAL STRUCTURE OF AMYLOMALTASE FROM THERMUS AQUATICUS, A GLYCOSYLTRANSFERASE CATALYSING THE PRODUCTION OF LARGE CYCLIC GLUCANS

Przylas, I., Tomoo, K., Terada, Y., Takaha, T., Fuji, K., Saenger, W., Straeter, N.

(2000) J Mol Biology 296: 873-886

Released	2001-02-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus aquaticus
Macromolecule	AMYLOMALTASE (protein)

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1IPB \| pdb_00001ipb	Download File View File

CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GPPPA

Tomoo, K., Shen, X., Okabe, K., Nozoe, Y., Fukuhara, S., Morino, S., Ishida, T., Taniguchi, T., Hasegawa, H., Terashima, A., Sasaki, M., Katsuya, Y., Kitamura, K., Miyoshi, H., Ishikawa, M., Miura, K.

(2002) Biochem J 362: 539-544

Released	2002-05-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (protein)
Unique Ligands	GTA

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1IPC \| pdb_00001ipc	Download File View File

CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GTP

(2002) Biochem J 362: 539-544

Released	2002-05-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (protein)
Unique Ligands	MGP

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1PE6 \| pdb_00001pe6	Download File View File

REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION

Yamamoto, D., Matsumoto, K., Ohishi, H., Ishida, T., Inoue, M., Kitamura, K., Mizuno, H.

(1991) J Biological Chem 266: 14771-14777

Released	1993-04-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Carica papaya
Macromolecule	PAPAIN (protein)
Unique Ligands	E6C, MOH

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1PIP \| pdb_00001pip	Download File View File

CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS

Yamamoto, A., Tomoo, K., Doi, M., Ohishi, H., Inoue, M., Ishida, T., Yamamoto, D., Tsuboi, S., Okamoto, H., Okada, Y.

(1992) Biochemistry 31: 11305-11309

Released	1993-10-31
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Carica papaya
Macromolecule	Papain (protein) SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE (protein)

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1PPP \| pdb_00001ppp	Download File View File

CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES

Ishida, T.

(1992) Biochem J 287: 797-803

Released	1994-01-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Carica papaya
Macromolecule	PAPAIN (protein)
Unique Ligands	E6C, MOH

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1QDQ \| pdb_00001qdq	Download File View File

X-RAY CRYSTAL STRUCTURE OF BOVINE CATHEPSIN B-CA074 COMPLEX

Yamamoto, A.

(2000) J Biochem 127: 635-643

Released	2000-07-10
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Bos taurus
Macromolecule	CATHEPSIN B (protein)
Unique Ligands	074

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1VTU \| pdb_00001vtu	Download File View File

Structural characteristics of enantiomorphic DNA: Crystal analysis of racemates of the D(CGCGCG) duplex

Doi, M., Inoue, M., Tomoo, K., Ishida, T., Ueda, Y., Akagi, M., Urata, H.

(1993) J Am Chem Soc 115: 10432-10433

Released	2011-07-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	synthetic construct
Macromolecule	DNA (5'-D(CPGPCPGPCPG)-3') (nucleic acid)

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1WKW \| pdb_00001wkw	Download File View File

Crystal structure of the ternary complex of eIF4E-m7GpppA-4EBP1 peptide

Tomoo, K., Matsushita, Y., Fujisaki, H., Shen, X., Miyagawa, H., Kitamura, K., Miura, K., Ishida, T.

(2005) Biochim Biophys Acta 1753: 191-208

Released	2005-06-10
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Eukaryotic translation initiation factor 4E (protein) Eukaryotic translation initiation factor 4E binding protein 1 (protein)
Unique Ligands	GTA

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2DC6 \| pdb_00002dc6	Download File View File

X-ray crystal structure analysis of bovine spleen cathepsin B-CA073 complex

Watanabe, D.

To be published

Released	2006-01-24
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bos taurus
Macromolecule	cathepsin B (protein)
Unique Ligands	73V, GOL, PO4

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2DC7 \| pdb_00002dc7	Download File View File

X-ray crystal structure analysis of bovine spleen cathepsin B-CA042 complex

Watanabe, D.

To be published

Released	2006-01-24
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Bos taurus
Macromolecule	CATHEPSIN B (protein)
Unique Ligands	042, GOL, PO4

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2DC8 \| pdb_00002dc8	Download File View File

X-ray crystal structure analysis of bovine spleen cathepsin B-CA059 complex

Watanabe, D.

To be published

Released	2006-01-24
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Bos taurus
Macromolecule	CATHEPSIN B (protein)
Unique Ligands	59A, GOL, PO4

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2DC9 \| pdb_00002dc9	Download File View File

X-ray crystal structure analysis of bovine spleen cathepsin B-CA074Me complex

Watanabe, D.

To be published

Released	2006-01-24
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Bos taurus
Macromolecule	CATHEPSIN B (protein)
Unique Ligands	74M, GOL, PO4

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2DCA \| pdb_00002dca	Download File View File

X-ray crystal structure analysis of bovine spleen cathepsin B-CA075 complex

Watanabe, D.

To be published

Released	2006-01-24
Method	X-RAY DIFFRACTION 2.11 Å
Organisms	Bos taurus
Macromolecule	CATHEPSIN B (protein)
Unique Ligands	75V, GOL, PO4

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2DCB \| pdb_00002dcb	Download File View File

X-ray crystal structure analysis of bovine spleen cathepsin B-CA076 complex

Watanabe, D.

To be published

Released	2006-01-24
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Bos taurus
Macromolecule	CATHEPSIN B (protein)
Unique Ligands	76V, GOL, PO4

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2DCC \| pdb_00002dcc	Download File View File

X-ray crystal structure analysis of bovine spleen cathepsin B-CA077 complex

Watanabe, D.

To be published

Released	2006-01-24
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Bos taurus
Macromolecule	CATHEPSIN B (protein)
Unique Ligands	77B, GOL, PO4

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2DCD \| pdb_00002dcd	Download File View File

X-ray crystal structure analysis of bovine spleen cathepsin B-CA078 complex

Watanabe, D.

To be published

Released	2006-01-24
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bos taurus
Macromolecule	CATHEPSIN B (protein)
Unique Ligands	78A, GOL, PO4

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2ZEQ \| pdb_00002zeq	Download File View File

Crystal structure of ubiquitin-like domain of murine Parkin

Tomoo, K.

(2008) Biochim Biophys Acta 1784: 1059-1067

Released	2008-08-19
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Mus musculus
Macromolecule	E3 ubiquitin-protein ligase parkin (protein)

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3AM7 \| pdb_00003am7	Download File View File

Crystal structure of the ternary complex of eIF4E-M7GTP-4EBP2 peptide

Tomoo, K., Fukuyo, A., In, Y., Ishida, T.

(2011) J Pept Sci 17: 650-657

Released	2011-08-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Eukaryotic translation initiation factor 4E (protein) Eukaryotic translation initiation factor 4E-binding protein 2 (protein)
Unique Ligands	MGP

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3B1L \| pdb_00003b1l	Download File View File

Crystal Structure of parkin ubiquitin-like domain R33Q mutant

Tomoo, K., Ikemiya, A., Amami, Y., In, Y., Ishida, T.

To be published

Released	2012-07-04
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Mus musculus
Macromolecule	E3 ubiquitin-protein ligase parkin (protein)

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3VXB \| pdb_00003vxb	Download File View File

Crystal Structure of BxlE from Streptomyces thermoviolaceus OPC-520

Tomoo, K., Ishida, T., Miyamoto, K., Tsujibo, H.

To be published

Released	2013-09-18
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Streptomyces thermoviolaceus
Macromolecule	Putative sugar-binding lipoprotein (protein)
Unique Ligands	GOL

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3VXC \| pdb_00003vxc	Download File View File

Crystal Structure of Xylobiose-BxlE complex from Streptomyces thermoviolaceus OPC-520

Tomoo, K., Ishida, T., Miyamoto, K., Tsujibo, H.

To be published

Released	2013-09-18
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Streptomyces thermoviolaceus
Macromolecule	Putative sugar-binding lipoprotein (protein)
Unique branched monosaccharides	XYP

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5JZQ \| pdb_00005jzq	Download File View File

Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals massive presence of multiple conformations

Drozdzal, P., Gilski, M., Jaskolski, M.

(2016) Acta Crystallogr D Struct Biol 72: 1203-1211

Released	2016-11-09
Method	X-RAY DIFFRACTION 0.78 Å
Organisms	synthetic construct
Macromolecule	DNA (5'-D(CPGPCPGPCPG)-3') (nucleic acid)
Unique Ligands	MG

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6LRA \| pdb_00006lra	Download File View File

The complex structure of PHF core domain peptide of tau and antibody's Fab domain.

Tomohiro, T., Kouki, S., Tomohiro, S., Takahiro, T., Katsushiro, M., Yasuko, I., Katsuhiko, M., Taizo, T., Toshimitsu, I., Koji, T.

(2020) FEBS Lett

Released	2020-08-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Fab Heavy Chain (protein) Fab Light Chain (protein) VQIINK (protein)

1 to 25 of 30 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

1BTP | pdb_00001btp

1CWY | pdb_00001cwy

1IPB | pdb_00001ipb

1IPC | pdb_00001ipc

1PE6 | pdb_00001pe6

1PIP | pdb_00001pip

1PPP | pdb_00001ppp

1QDQ | pdb_00001qdq

1VTU | pdb_00001vtu

1WKW | pdb_00001wkw

2DC6 | pdb_00002dc6

2DC7 | pdb_00002dc7

2DC8 | pdb_00002dc8

2DC9 | pdb_00002dc9

2DCA | pdb_00002dca

2DCB | pdb_00002dcb

2DCC | pdb_00002dcc

2DCD | pdb_00002dcd

2ZEQ | pdb_00002zeq

3AM7 | pdb_00003am7

3B1L | pdb_00003b1l

3VXB | pdb_00003vxb

3VXC | pdb_00003vxc

5JZQ | pdb_00005jzq

6LRA | pdb_00006lra