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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kumasaka, T."

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Search Summary

This query matches 162 Structures.

Refinements

Structure Determination Methodology

experimental (162)

Scientific Name of Source Organism

	Arthrobacter globiformis (35)
	Gallus gallus (16)
	Bos taurus (13)
	Homo sapiens (13)
	Bradyrhizobium sp. ORS 375 (9)
	Aspergillus terreus (6)
	Bacillus subtilis subsp. subtilis str. 168 (6)
	Photinus pyralis (5)
	Bacillus subtilis (4)
	Grifola frondosa (4)

More...

Taxonomy

	Bacteria (83)
	Eukaryota (71)
	Archaea (4)
	unclassified sequences (3)
	Eukaryota (eukaryotes) (1)
	Riboviria (1)

Experimental Method

	X-RAY DIFFRACTION (160)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (162)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (28)
	1.5 - 2.0 (89)
	2.0 - 2.5 (30)
	2.5 - 3.0 (11)
	3.0 - 3.5 (1)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (22)
	2005 - 2009 (21)
	2010 - 2014 (22)
	2015 - 2019 (51)
	2020 - 2024 (45)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (61)
	Oxidoreductases (55)
	Translocases (6)
	Transferases (9)
	Lyases (6)
	Isomerases (2)
	Ligases (1)

Membrane Protein Annotation

	PDBTM (8)
	MemProtMD (5)
	mpstruc (4)

Symmetry Type

	Asymmetric (82)
	Cyclic (69)
	Dihedral (14)

SCOP Classification

	Membrane and cell surface proteins and peptides (4)
	Alpha and beta proteins (a/b) (30)
	All beta proteins (24)
	Alpha and beta proteins (a+b) (26)
	All alpha proteins (10)
	Artifacts (8)
	Small proteins (5)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 162 Structures

Page 1 of 7

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1EE8 \| pdb_00001ee8	Download File View File

CRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8

Sugahara, M., Mikawa, T., Kumasaka, T., Yamamoto, M., Kato, R., Fukuyama, K., Inoue, Y., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) EMBO J 19: 3857-3869

Released	2001-01-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus HB8
Macromolecule	MUTM (FPG) PROTEIN (protein)
Unique Ligands	ZN

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1EH1 \| pdb_00001eh1	Download File View File

RIBOSOME RECYCLING FACTOR FROM THERMUS THERMOPHILUS

Toyoda, T., Tin, O.F., Ito, K., Fujiwara, T., Kumasaka, T., Yamamoto, M., Garber, M.B., Nakamura, Y.

(2000) RNA 6: 1432-1444

Released	2000-11-15
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermus thermophilus
Macromolecule	RIBOSOME RECYCLING FACTOR (protein)

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1ERZ \| pdb_00001erz	Download File View File

CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES

Nakai, T., Hasegawa, T., Yamashita, E., Yamamoto, M., Kumasaka, T., Ueki, T., Nanba, H., Ikenaka, Y., Takahashi, S., Sato, M., Tsukihara, T.

(2000) Structure 8: 729-737

Released	2001-04-06
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Agrobacterium sp. KNK712
Macromolecule	N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE (protein)

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1G12 \| pdb_00001g12	Download File View File

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Hori, T., Kumasaka, T., Yamamoto, M., Nonaka, T., Tanaka, N., Hashimoto, Y., Ueki, T., Takio, K.

(2001) Acta Crystallogr D Biol Crystallogr 57: 361-368

Released	2001-03-14
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Grifola frondosa
Macromolecule	PEPTIDYL-LYS METALLOENDOPEPTIDASE (protein)
Unique Ligands	MAN, ZN

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1GC0 \| pdb_00001gc0	Download File View File

CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA

Motoshima, H., Inagaki, K., Kumasaka, T., Furuichi, M., Inoue, H., Tamura, T., Esaki, N., Soda, K., Tanaka, N., Yamamoto, M., Tanaka, H.

(2000) J Biochem 128: 349-354

Released	2002-05-08
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Pseudomonas putida
Macromolecule	METHIONINE GAMMA-LYASE (protein)

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1GC2 \| pdb_00001gc2	Download File View File

CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA

Motoshima, H., Inagaki, K., Kumasaka, T., Furuichi, M., Inoue, H., Tamura, T., Esaki, N., Soda, K., Tanaka, N., Yamamoto, M., Tanaka, H.

(2000) J Biochem 128: 349-354

Released	2002-05-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	METHIONINE GAMMA-LYASE (protein)

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1GCJ \| pdb_00001gcj	Download File View File

N-TERMINAL FRAGMENT OF IMPORTIN-BETA

Lee, S.J., Imamoto, N., Sakai, H., Nakagawa, A., Kose, S., Koike, M., Yamamoto, M., Kumasaka, T., Yoneda, Y., Tsukihara, T.

(2000) J Mol Biology 302: 251-264

Released	2000-10-18
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mus musculus
Macromolecule	IMPORTIN BETA (protein)

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1GE5 \| pdb_00001ge5	Download File View File

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Hori, T., Kumasaka, T., Yamamoto, M., Nonaka, T., Tanaka, N., Hashimoto, Y., Ueki, T., Takio, K.

(2001) Acta Crystallogr D Biol Crystallogr 57: 361-368

Released	2001-03-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Grifola frondosa
Macromolecule	PEPTIDYL-LYS METALLOENDOPEPTIDASE (protein)
Unique Ligands	MAN, ZN

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1GE6 \| pdb_00001ge6	Download File View File

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Hori, T., Kumasaka, T., Yamamoto, M., Nonaka, T., Tanaka, N., Hashimoto, Y., Ueki, T., Takio, K.

(2001) Acta Crystallogr D Biol Crystallogr 57: 361-368

Released	2001-03-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Grifola frondosa
Macromolecule	PEPTIDYL-LYS METALLOENDOPEPTIDASE (protein)
Unique Ligands	MAN, ZN

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1GE7 \| pdb_00001ge7	Download File View File

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Hori, T., Kumasaka, T., Yamamoto, M., Nonaka, T., Tanaka, N., Hashimoto, Y., Ueki, T., Takio, K.

(2001) Acta Crystallogr D Biol Crystallogr 57: 361-368

Released	2001-03-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Grifola frondosa
Macromolecule	PEPTIDYL-LYS METALLOENDOPEPTIDASE (protein)
Unique Ligands	MAN, ZN

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1IO1 \| pdb_00001io1	Download File View File

CRYSTAL STRUCTURE OF F41 FRAGMENT OF FLAGELLIN

Samatey, F.A., Imada, K., Nagashima, S., Vondervisz, F., Kumasaka, T., Yamamoto, M., Namba, K.

(2001) Nature 410: 331-337

Released	2001-04-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	PHASE 1 FLAGELLIN (protein)

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1IOO \| pdb_00001ioo	Download File View File

CRYSTAL STRUCTURE OF NICOTIANA ALATA GEMETOPHYTIC SELF-INCOMPATIBILITY ASSOCIATED SF11-RNASE

Ida, K., Sato, M., Sakiyama, F., Norioka, S., Yamamoto, M., Kumasaka, T., Yamashita, E.

(2001) J Mol Biology 314: 103-112

Released	2002-05-08
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Nicotiana alata
Macromolecule	SF11-RNASE (protein)
Unique branched monosaccharides	BMA, MAN, NAG, XYP

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1K1W \| pdb_00001k1w	Download File View File

Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis

Imamura, H., Fushinobu, S., Kumasaka, T., Yamamoto, M., Jeon, B.S., Wakagi, T., Matsuzawa, H.

(2003) J Biological Chem 278: 19378-19386

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermococcus litoralis
Macromolecule	4-ALPHA-GLUCANOTRANSFERASE (protein)
Unique Ligands	CA, GLC, SO4

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1K1X \| pdb_00001k1x	Download File View File

Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis

Imamura, H., Fushinobu, S., Kumasaka, T., Yamamoto, M., Jeon, B.S., Wakagi, T., Matsuzawa, H.

(2003) J Biological Chem 278: 19378-19386

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermococcus litoralis
Macromolecule	4-ALPHA-GLUCANOTRANSFERASE (protein)
Unique Ligands	CA, TRS

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1K1Y \| pdb_00001k1y	Download File View File

Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose

Imamura, H., Fushinobu, S., Kumasaka, T., Yamamoto, M., Jeon, B.S., Wakagi, T., Matsuzawa, H.

(2003) J Biological Chem 278: 19378-19386

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermococcus litoralis
Macromolecule	4-ALPHA-GLUCANOTRANSFERASE (protein)
Unique Ligands	CA, TRS
Unique branched monosaccharides	AC1, GLC

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1UIR \| pdb_00001uir	Download File View File

Crystal Structure of Polyamine Aminopropyltransfease from Thermus thermophilus

Ganbe, T., Ohnuma, M., Sato, T., Kumasaka, T., Oshima, T., Tanaka, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2011) J Mol Biology 408: 971-986

Released	2003-08-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus
Macromolecule	Polyamine Aminopropyltransferase (protein)

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1UJ0 \| pdb_00001uj0	Download File View File

Crystal Structure of STAM2 SH3 domain in complex with a UBPY-derived peptide

Kaneko, T., Kumasaka, T., Ganbe, T., Sato, T., Miyazawa, K., Kitamura, N., Tanaka, N.

(2003) J Biological Chem 278: 48162-48168

Released	2003-12-23
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mus musculus
Macromolecule	deubiquitinating enzyme UBPY (protein) signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 (protein)
Unique Ligands	PO4

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1V3T \| pdb_00001v3t	Download File View File

Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase

Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 22615-22623

Released	2004-07-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Cavia porcellus
Macromolecule	leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase (protein)
Unique Ligands	NAP

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1V3U \| pdb_00001v3u	Download File View File

Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase in apo form

Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 22615-22623

Released	2004-07-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Cavia porcellus
Macromolecule	leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase (protein)
Unique Ligands	CL

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1V3V \| pdb_00001v3v	Download File View File

Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complexed with NADP and 15-oxo-PGE2

Hori, T., Yokomizo, T., Ago, H., Sugahara, M., Ueno, G., Yamamoto, M., Kumasaka, T., Shimizu, T., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 22615-22623

Released	2004-07-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Cavia porcellus
Macromolecule	leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase (protein)
Unique Ligands	5OP, CL, NAP

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1VBR \| pdb_00001vbr	Download File View File

Crystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose

Ihsanawati, Kumasaka, T., Kaneko, T., Nakamura, S., Tanaka, N.

(2005) Proteins 61: 999-1009

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermotoga maritima
Macromolecule	endo-1,4-beta-xylanase B (protein)
Unique Ligands	ACY
Unique branched monosaccharides	XYP, XYS

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1VBU \| pdb_00001vbu	Download File View File

Crystal structure of native xylanase 10B from Thermotoga maritima

Ihsanawati, Kumasaka, T., Kaneko, T., Nakamura, S., Tanaka, N.

(2005) Proteins 61: 999-1009

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermotoga maritima
Macromolecule	endo-1,4-beta-xylanase B (protein)
Unique Ligands	ACY, GOL, SO4