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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Kato, T."

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Search Summary

This query matches 197 Structures.

Refinements

Structure Determination Methodology

experimental (197)

Scientific Name of Source Organism

	Homo sapiens (37)
	Thermus thermophilus HB8 (25)
	Mus musculus (22)
	Escherichia coli (18)
	synthetic construct (14)
	Candidatus Odinarchaeum yellowstonii (11)
	Thermococcus profundus (9)
	Salmonella enterica subsp. enterica serovar Typhimurium (7)
	Vibrio alginolyticus (7)
	Chlamydomonas reinhardtii (6)

More...

Taxonomy

	Bacteria (94)
	Eukaryota (79)
	Archaea (21)
	other sequences (14)
	Riboviria (13)
	Duplodnaviria (3)

Experimental Method

	ELECTRON MICROSCOPY (114)
	X-RAY DIFFRACTION (79)
	SOLUTION NMR (4)
	SOLID-STATE NMR (1)

Polymer Entity Type

	Protein (197)
	DNA (8)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (8)
	1.5 - 2.0 (12)
	2.0 - 2.5 (22)
	2.5 - 3.0 (43)
	3.0 - 3.5 (71)
	3.5 - 4.0 (26)
	4.0 - 4.5 (3)
	> 4.5 (8)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (5)
	2005 - 2009 (9)
	2010 - 2014 (9)
	2015 - 2019 (16)
	2020 - 2024 (142)
	2025 - 2029 (15)

Enzyme Classification Name

	Translocases (24)
	Hydrolases (34)
	Oxidoreductases (16)
	Isomerases (10)
	Transferases (6)

Membrane Protein Annotation

	PDBTM (57)
	mpstruc (38)
	OPM (27)
	MemProtMD (16)

Symmetry Type

	Asymmetric (143)
	Cyclic (39)
	Helical (7)
	Dihedral (4)
	Icosahedral (4)

SCOP Classification

	All beta proteins (5)
	Multi-domain proteins (alpha and beta) (5)
	Alpha and beta proteins (a+b) (7)
	All alpha proteins (3)
	Alpha and beta proteins (a/b) (5)

AllSelected

1 to 25 of 197 Structures

Page 1 of 8

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1IS1 \| pdb_00001is1	Download File View File

Crystal structure of ribosome recycling factor from Vibrio parahaemolyticus

Nakano, H., Yamaichi, Y., Uchiyama, S., Yoshida, T., Nishina, K., Kato, H., Ohkubo, T., Honda, T., Yamagata, Y., Kobayashi, Y.

(2003) J Biological Chem 278: 3427-3436

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Vibrio parahaemolyticus
Macromolecule	RIBOSOME RECYCLING FACTOR (protein)

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1RCH \| pdb_00001rch	Download File View File

SOLUTION NMR STRUCTURE OF RIBONUCLEASE HI FROM ESCHERICHIA COLI, 8 STRUCTURES

Yamazaki, T., Fujiwara, M., Kato, T., Yamasaki, K., Nagayama, K.

(2000) Biol Pharm Bull 23: 1147

Released	1997-02-12
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	RIBONUCLEASE HI (protein)

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1V79 \| pdb_00001v79	Download File View File

Crystal structures of adenosine deaminase complexed with potent inhibitors

Kinoshita, T.

(2004) J Med Chem 47: 2728-2731

Released	2004-12-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bos taurus
Macromolecule	Adenosine deaminase (protein)
Unique Ligands	FR7, ZN

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1V7A \| pdb_00001v7a	Download File View File

Crystal structures of adenosine deaminase complexed with potent inhibitors

Kinoshita, T.

(2004) J Med Chem 47: 2728-2731

Released	2004-12-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bos taurus
Macromolecule	adenosine deaminase (protein)
Unique Ligands	FRC, ZN

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1V7M \| pdb_00001v7m	Download File View File

Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab

Feese, M.D., Tamada, T., Kato, Y., Maeda, Y., Hirose, M., Matsukura, Y., Shigematsu, H., Kato, T., Miyazaki, H., Kuroki, R.

(2004) Proc Natl Acad Sci U S A 101: 1816-1821

Released	2004-03-02
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Monoclonal TN1 Fab Heavy Chain (protein) Monoclonal TN1 Fab Light Chain (protein) Thrombopoietin (protein)

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1V7N \| pdb_00001v7n	Download File View File

Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab

Feese, M.D., Tamada, T., Kato, Y., Maeda, Y., Hirose, M., Matsukura, Y., Shigematsu, H., Kato, T., Miyazaki, H., Kuroki, R.

(2004) Proc Natl Acad Sci U S A 101: 1816-1821

Released	2004-03-02
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Monoclonal TN1 Fab Heavy Chain (protein) Monoclonal TN1 Fab Light Chain (protein) Thrombopoietin (protein)

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1WUH \| pdb_00001wuh	Download File View File

Three-Dimensional Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

To be published

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.24 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, NFC, SF4

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1WUI \| pdb_00001wui	Download File View File

Ultra-High resolution Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

(2005) Structure 13: 1635-1642

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.04 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, MRD, NFC, SF4

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1WUJ \| pdb_00001wuj	Download File View File

Three-Dimensional Structure Of The Ni-B State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

(2005) Structure 13: 1635-1642

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, NFO, SF4

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1WUK \| pdb_00001wuk	Download File View File

High resolution Structure Of The Oxidized State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

(2005) Structure 13: 1635-1642

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MRD, NFO, SF4

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1WUL \| pdb_00001wul	Download File View File

High Resolution Structure Of The Reduced State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

(2005) Structure 13: 1635-1642

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, MRD, NFR, SF4

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1WXZ \| pdb_00001wxz	Download File View File

Crystal structure of adenosine deaminase ligated with a potent inhibitor

Kinoshita, T.

(2005) J Med Chem 48: 4750-4753

Released	2005-08-16
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bos taurus
Macromolecule	Adenosine deaminase (protein)
Unique Ligands	FRL, ZN

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2E1W \| pdb_00002e1w	Download File View File

Crystal structure of adenosine deaminase complexed with potent inhibitors

Kinoshita, T.

(2004) J Med Chem 47: 2728-2731

Released	2006-11-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bos taurus
Macromolecule	Adenosine deaminase (protein)
Unique Ligands	FR6, ZN

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2MME \| pdb_00002mme	Download File View File

Hybrid structure of the Shigella flexneri MxiH Type three secretion system needle

Demers, J.P., Habenstein, B., Loquet, A., Vasa, S.K., Becker, S., Baker, D., Lange, A., Sgourakis, N.G.

(2014) Nat Commun 5: 4976-4976

Released	2014-10-08
Method	SOLID-STATE NMR ELECTRON MICROSCOPY 7.7 Å
Organisms	Shigella flexneri
Macromolecule	MxiH (protein)

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2ZKH \| pdb_00002zkh	Download File View File

Human thrombopoietin neutralizing antibody TN1 FAB

Arai, S., Tamada, T., Honjo, E., Maeda, Y., Kuroki, R.

(2016) Protein Sci 25: 1786-1796

Released	2009-03-24
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Homo sapiens
Macromolecule	Monoclonal TN1 FAB heavy chain (protein) Monoclonal TN1 FAB light chain (protein)

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3A69 \| pdb_00003a69	Download File View File

Atomic model of the bacterial flagellar hook based on docking an X-ray derived structure and terminal two alpha-helices into an 7.1 angstrom resolution cryoEM map

Fujii, T., Kato, T., Namba, K.

(2009) Structure 17: 1485-1493

Released	2009-12-15
Method	ELECTRON MICROSCOPY 7.1 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Flagellar hook protein flgE (protein)

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3AJW \| pdb_00003ajw	Download File View File

Structure of FliJ, a soluble component of flagellar type III export apparatus

Imada, K., Ibuki, T., Minamino, T., Namba, K.

(2011) Nat Struct Mol Biol 18: 277-282

Released	2011-02-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Flagellar fliJ protein (protein)
Unique Ligands	HG

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3J0R \| pdb_00003j0r	Download File View File

Model of a type III secretion system needle based on a 7 Angstrom resolution cryoEM map

Fujii, T., Cheung, M., Blanco, A., Kato, T., Blocker, A.J., Namba, K.

(2012) Proc Natl Acad Sci U S A 109: 4461-4466

Released	2012-02-29
Method	ELECTRON MICROSCOPY 7.7 Å
Organisms	Shigella flexneri
Macromolecule	Protein mxiH (protein)

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3VXV \| pdb_00003vxv	Download File View File

Crystal structure of methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence

Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

(2013) J Biological Chem 288: 6351-6362

Released	2013-01-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	Methyl-CpG-binding domain protein 4 (protein) DNA (5'-D(GPTPCPAPCPTPAPCP(5CM)PGPGPAPCPA)-3') (nucleic acid) DNA (5'-D(GPTPCPTPGPGPTPAPGPTPGPAPCPT)-3') (nucleic acid)
Unique Ligands	ACT, EDO

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3VXX \| pdb_00003vxx	Download File View File

Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence

Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

(2013) J Biological Chem 288: 6351-6362

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.204 Å
Organisms	Mus musculus
Macromolecule	Methyl-CpG-binding domain protein 4 (protein) DNA (5'-D(GPTPCP(5CM)PGPGPTPAPGPTPGPAPCPT)-3') (nucleic acid) DNA (5'-D(GPTPCPAPCPTPAPCP(5CM)PGPGPAPCPA)-3') (nucleic acid)
Unique Ligands	ACT, EDO

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3VYB \| pdb_00003vyb	Download File View File

Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence

Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

(2013) J Biological Chem 288: 6351-6362

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus
Macromolecule	Methyl-CpG-binding domain protein 4 (protein) DNA (5'-D(GPTPCP(5HC)PGPGPTPAPGPTPGPAPCPT)-3') (nucleic acid) DNA (5'-D(GPTPCPAPCPTPAPCP(5CM)PGPGPAPCPA)-3') (nucleic acid)
Unique Ligands	ACT, EDO

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3VYQ \| pdb_00003vyq	Download File View File

Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1

Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

(2013) J Biological Chem 288: 6351-6362

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.525 Å
Organisms	Mus musculus
Macromolecule	Methyl-CpG-binding domain protein 4 (protein) DNA (5'-D(APCPAPTPCP(5CM)PGPGPTPGPA)-3') (nucleic acid) DNA (5'-D(TPCPAPCPTPGPGPAPTPGPT)-3') (nucleic acid)
Unique Ligands	EDO, ZN

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3WBN \| pdb_00003wbn	Download File View File

Crystal structure of MATE in complex with MaL6

Tanaka, Y., Ishitani, R., Nureki, O.

(2013) Nature 496: 247-251

Released	2013-06-12
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Pyrococcus furiosus DSM 3638
Macromolecule	MaL6 (protein) Putative uncharacterized protein (protein)
Unique Ligands	OLC