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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nakamura, T."

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Search Summary

This query matches 227 Structures.

Refinements

Structure Determination Methodology

experimental (227)

Scientific Name of Source Organism

	Homo sapiens (91)
	Aeropyrum pernix K1 (31)
	Escherichia coli (17)
	Mus musculus (17)
	Clostridium botulinum (11)
	Pyrococcus horikoshii OT3 (9)
	Human immunodeficiency virus 1 (7)
	Escherichia coli K-12 (6)
	Pyrococcus furiosus (6)
	Pyrococcus furiosus DSM 3638 (6)

More...

Taxonomy

	Eukaryota (115)
	Archaea (57)
	Bacteria (48)
	Riboviria (9)

Experimental Method

	X-RAY DIFFRACTION (213)
	ELECTRON MICROSCOPY (8)
	SOLUTION NMR (6)

Polymer Entity Type

	Protein (227)
	DNA (19)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (31)
	1.5 - 2.0 (105)
	2.0 - 2.5 (51)
	2.5 - 3.0 (31)
	3.0 - 3.5 (3)

Release Date

	2000 - 2004 (3)
	2005 - 2009 (39)
	2010 - 2014 (61)
	2015 - 2019 (44)
	2020 - 2024 (80)

Enzyme Classification Name

	Hydrolases (59)
	Oxidoreductases (39)
	Transferases (30)
	Lyases (10)

Membrane Protein Annotation

	PDBTM (3)
	MemProtMD (1)

Symmetry Type

	Asymmetric (127)
	Cyclic (65)
	Dihedral (46)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a/b) (36)
	All beta proteins (52)
	Alpha and beta proteins (a+b) (26)
	Artifacts (16)
	All alpha proteins (6)
	Small proteins (4)

AllSelected

1 to 25 of 227 Structures

Page 1 of 10

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1IRE \| pdb_00001ire	Download File View File

Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila

Miyanaga, A., Fushinobu, S., Ito, K., Wakagi, T.

(2001) Biochem Biophys Res Commun 288: 1169-1174

Released	2002-10-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudonocardia thermophila
Macromolecule	Nitrile Hydratase (protein)
Unique Ligands	CO

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1K36 \| pdb_00001k36	Download File View File

NMR Structure of human Epiregulin

Sato, K., Miura, K., Tada, M., Aizawa, T., Miyamoto, K., Kawano, K.

(2003) FEBS Lett 553: 232-238

Released	2003-09-30
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Epiregulin (protein)

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1K37 \| pdb_00001k37	Download File View File

NMR Structure of human Epiregulin

Sato, K., Miura, K., Tada, M., Aizawa, T., Miyamoto, K., Kawano, K.

(2003) FEBS Lett 553: 232-238

Released	2003-09-30
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Epiregulin (protein)

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1X0R \| pdb_00001x0r	Download File View File

Thioredoxin Peroxidase from Aeropyrum pernix K1

Nakamura, T., Yamamoto, T., Inoue, T., Matsumura, H., Kobayashi, A., Hagihara, Y., Uegaki, K., Ataka, M., Kai, Y., Ishikawa, K.

(2006) Proteins 62: 822-826

Released	2005-12-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable peroxiredoxin (protein)
Unique Ligands	EDO

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2CWR \| pdb_00002cwr	Download File View File

Crystal structure of chitin biding domain of chitinase from Pyrococcus furiosus

Uegaki, K., Nakamura, T., Ishikawa, K., Matsumura, H.

(2008) J Mol Biology 381: 670-680

Released	2006-07-11
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Pyrococcus furiosus
Macromolecule	chitinase (protein)

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2CZN \| pdb_00002czn	Download File View File

Solution structure of the chitin-binding domain of hyperthermophilic chitinase from pyrococcus furiosus

Uegaki, T., Ikegami, T., Nakamura, T., Hagihara, Y., Mine, S., Inoue, T., Matsumura, H., Ataka, M., Ishikawa, K.

(2008) J Mol Biology 381: 670-680

Released	2006-07-18
Method	SOLUTION NMR
Organisms	Pyrococcus furiosus
Macromolecule	chitinase (protein)

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2D5R \| pdb_00002d5r	Download File View File

Crystal Structure of a Tob-hCaf1 Complex

Horiuchi, M., Suzuki, N.N., Muroya, N., Takahasi, K., Nishida, M., Yoshida, Y., Ikematsu, N., Nakamura, T., Kawamura-Tsuzuku, J., Yamamoto, T., Inagaki, F.

(2009) J Biological Chem 284: 13244-13255

Released	2006-12-12
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	CCR4-NOT transcription complex subunit 7 (protein) Tob1 protein (protein)

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2D6K \| pdb_00002d6k	Download File View File

Crystal structure of mouse galectin-9 N-terminal CRD (crystal form 1)

Nagae, M., Nishi, N., Nakamura, T., Murata, T., Wakatsuki, S., Kato, R.

(2006) J Biological Chem 281: 35884-35893

Released	2006-09-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mus musculus
Macromolecule	lectin, galactose binding, soluble 9 (protein)

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2D6L \| pdb_00002d6l	Download File View File

Crystal structure of mouse galectin-9 N-terminal CRD (crystal form 2)

Nagae, M., Nishi, N., Nakamura, T., Wakatsuki, S., Kato, R.

(2006) J Biological Chem 281: 35884-35893

Released	2006-09-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mus musculus
Macromolecule	lectin, galactose binding, soluble 9 (protein)

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2D6M \| pdb_00002d6m	Download File View File

Crystal structure of mouse galectin-9 N-terminal CRD in complex with lactose

Nagae, M., Nishi, N., Nakamura, T., Wakatsuki, S., Kato, R.

(2006) J Biological Chem 281: 35884-35893

Released	2006-09-26
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mus musculus
Macromolecule	lectin, galactose binding, soluble 9 (protein)
Unique branched monosaccharides	GAL, GLC

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2D6N \| pdb_00002d6n	Download File View File

Crystal structure of mouse galectin-9 N-terminal CRD in complex with N-acetyllactosamine

Nagae, M., Nishi, N., Nakamura, T., Murata, T., Wakatsuki, S., Kato, R.

(2006) J Biological Chem 281: 35884-35893

Released	2006-09-26
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	lectin, galactose binding, soluble 9 (protein)
Unique branched monosaccharides	GAL, NAG

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2D6O \| pdb_00002d6o	Download File View File

Crystal structure of mouse galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer

Nagae, M., Nishi, N., Nakamura, T., Murata, T., Wakatsuki, S., Kato, R.

(2006) J Biological Chem 281: 35884-35893

Released	2006-09-26
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Mus musculus
Macromolecule	lectin, galactose binding, soluble 9 (protein)
Unique Ligands	GOL
Unique branched monosaccharides	GAL, NAG

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2D6P \| pdb_00002d6p	Download File View File

Crystal structure of mouse galectin-9 N-terminal CRD in complex with T-antigen

Nagae, M., Nishi, N., Nakamura, T., Murata, T., Wakatsuki, S., Kato, R.

(2006) J Biological Chem 281: 35884-35893

Released	2006-09-26
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mus musculus
Macromolecule	lectin, galactose binding, soluble 9 (protein)
Unique branched monosaccharides	GAL, NGA

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2DFV \| pdb_00002dfv	Download File View File

Hyperthermophilic threonine dehydrogenase from Pyrococcus horikoshii

Ishikawa, K., Higashi, N., Nakamura, T., Matsuura, T., Nakagawa, A.

(2007) J Mol Biology 366: 857-867

Released	2007-01-16
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Probable L-threonine 3-dehydrogenase (protein)
Unique Ligands	NAD, SO4, ZN

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2DSK \| pdb_00002dsk	Download File View File

Crystal structure of catalytic domain of hyperthermophilic chitinase from Pyrococcus furiosus

Nakamura, T., Mine, S., Hagihara, Y., Ishikawa, K., Uegaki, K.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 7-11

Released	2007-02-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Pyrococcus furiosus
Macromolecule	chitinase (protein)
Unique Ligands	GOL, SO4

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2E2G \| pdb_00002e2g	Download File View File

Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (pre-oxidation form)

Nakamura, T., Yamamoto, T., Abe, M., Matsumura, H., Hagihara, Y., Goto, T., Yamaguchi, T., Inoue, T.

(2008) Proc Natl Acad Sci U S A 105: 6238-6242

Released	2007-11-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable peroxiredoxin (protein)

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2E2M \| pdb_00002e2m	Download File View File

Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)

Nakamura, T., Yamamoto, T., Abe, M., Matsumura, H., Hagihara, Y., Goto, T., Yamaguchi, T., Inoue, T.

(2008) Proc Natl Acad Sci U S A 105: 6238-6242

Released	2007-11-20
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable peroxiredoxin (protein)

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2E7A \| pdb_00002e7a	Download File View File

TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity

Mukai, Y., Yamagata, Y., Tsutsumi, Y.

(2008) J Biological Chem 283: 998-1007

Released	2007-11-13
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Tumor necrosis factor (protein)

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2NVL \| pdb_00002nvl	Download File View File

Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfonic acid form)

Nakamura, T., Yamamoto, T., Abe, M., Matsumura, H., Hagihara, Y., Goto, T., Yamaguchi, T., Inoue, T.

(2008) Proc Natl Acad Sci U S A 105: 6238-6242

Released	2007-11-20
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Aeropyrum pernix K1
Macromolecule	Probable peroxiredoxin (protein)

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2RTS \| pdb_00002rts	Download File View File

Chitin binding domain1

Uegaki, K.

(2014) J Biochem 155: 115-122

Released	2014-04-23
Method	SOLUTION NMR
Organisms	Pyrococcus furiosus DSM 3638
Macromolecule	chitinase (protein)

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2Z3Q \| pdb_00002z3q	Download File View File

Crystal structure of the IL-15/IL-15Ra complex

Chirifu, M., Yamagata, Y., Davis, S.J., Ikemizu, S.

(2007) Nat Immunol 8: 1001-1007

Released	2007-09-04
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-15 (protein) Interleukin-15 receptor alpha chain (protein)

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2Z3R \| pdb_00002z3r	Download File View File

Crystal structure of the IL-15/IL-15Ra complex

Chirifu, M., Yamagata, Y., Davis, S.J., Ikemizu, S.

(2007) Nat Immunol 8: 1001-1007

Released	2007-09-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-15 (protein) Interleukin-15 receptor alpha chain (protein)
Unique Ligands	GOL