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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kato, Y."

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Search Summary

This query matches 46 Structures.

Refinements

Structure Determination Methodology

experimental (46)

Scientific Name of Source Organism

	Homo sapiens (16)
	Mus musculus (6)
	Aquifex aeolicus VF5 (5)
	Rattus norvegicus (4)
	Rhodococcus erythropolis (4)
	Burkholderia sp. (2)
	Dioscoreophyllum cumminsii (2)
	Dokdonia eikasta (2)
	Saccharolobus solfataricus (2)
	Aspergillus nidulans (1)

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Taxonomy

	Eukaryota (26)
	Bacteria (20)
	Archaea (3)
	Eukaryota (eukaryotes) (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (40)
	SOLUTION NMR (5)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (46)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (15)
	2.0 - 2.5 (9)
	2.5 - 3.0 (8)
	3.0 - 3.5 (6)
	4.0 - 4.5 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (9)
	2005 - 2009 (8)
	2010 - 2014 (3)
	2015 - 2019 (16)
	2020 - 2024 (9)

Enzyme Classification Name

	Hydrolases (10)
	Lyases (5)
	Oxidoreductases (5)
	Isomerases (3)
	Transferases (1)

Membrane Protein Annotation

	MemProtMD (2)
	PDBTM (2)
	mpstruc (2)
	OPM (1)

Symmetry Type

	Asymmetric (29)
	Cyclic (20)

SCOP Classification

	All beta proteins (11)
	Alpha and beta proteins (a+b) (7)
	All alpha proteins (5)
	Artifacts (5)
	Alpha and beta proteins (a/b) (4)
	Membrane and cell surface proteins and peptides (2)
	Small proteins (2)

AllSelected

1 to 25 of 46 Structures

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1EH9 \| pdb_00001eh9	Download File View File

CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS GLYCOSYLTREHALOSE TREHALOHYDROLASE

Feese, M.D., Kato, Y., Tamada, T., Kato, M., Komeda, T., Kobayashi, K., Kuroki, R.

(2000) J Mol Biology 301: 451-464

Released	2001-02-19
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharolobus solfataricus
Macromolecule	GLYCOSYLTREHALOSE TREHALOHYDROLASE (protein)

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1EHA \| pdb_00001eha	Download File View File

CRYSTAL STRUCTURE OF GLYCOSYLTREHALOSE TREHALOHYDROLASE FROM SULFOLOBUS SOLFATARICUS

Feese, M.D., Kato, Y., Tamada, T., Kato, M., Komeda, T., Kobayashi, K., Kuroki, R.

(2000) J Mol Biology 301: 451-464

Released	2001-02-19
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharolobus solfataricus
Macromolecule	GLYCOSYLTREHALOSE TREHALOHYDROLASE (protein)

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1GIF \| pdb_00001gif	Download File View File

HUMAN GLYCOSYLATION-INHIBITING FACTOR

Kato, Y., Kuroki, R.

(1996) Proc Natl Acad Sci U S A 93: 3007-3010

Released	1997-03-12
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	GLYCOSYLATION-INHIBITING FACTOR (protein)

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1IUQ \| pdb_00001iuq	Download File View File

The 1.55 A Crystal Structure of Glycerol-3-Phosphate Acyltransferase

Tamada, T., Feese, M.D., Kato, Y., Kuroki, R.

(2004) Acta Crystallogr D Biol Crystallogr 60: 13-21

Released	2003-10-07
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Cucurbita moschata
Macromolecule	Glycerol-3-Phosphate Acyltransferase (protein)
Unique Ligands	GOL, SO4

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1IV7 \| pdb_00001iv7	Download File View File

Crystal Structure of Single Chain Monellin

Tamada, T., Kato, Y., Kuroki, R.

To be published

Released	2003-10-07
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Dioscoreophyllum cumminsii
Macromolecule	Monellin (protein)

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1IV9 \| pdb_00001iv9	Download File View File

Crystal Structure of Single Chain Monellin

Tamada, T., Kato, Y., Kuroki, R.

To be published

Released	2003-10-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Dioscoreophyllum cumminsii
Macromolecule	Monellin (protein)

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1KKO \| pdb_00001kko	Download File View File

CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMMONIA LYASE

Levy, C.W., Buckley, P.A., Sedelnikova, S., Kato, Y., Asano, Y., Rice, D.W., Baker, P.J.

(2002) Structure 10: 105-113

Released	2002-01-30
Method	X-RAY DIFFRACTION 1.33 Å
Organisms	Citrobacter amalonaticus
Macromolecule	3-METHYLASPARTATE AMMONIA-LYASE (protein)
Unique Ligands	SO4

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1LF8 \| pdb_00001lf8	Download File View File

Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide

Kato, Y., Misra, S., Puertollano, R., Hurley, J.H., Bonifacino, J.S.

(2002) Nat Struct Biol 9: 532-536

Released	2002-06-26
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA3 (protein) Cation-independent mannose-6-phosphate receptor (protein)

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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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1X25 \| pdb_00001x25	Download File View File

Crystal Structure of a Member of YjgF Family from Sulfolobus Tokodaii (ST0811)

Miyakawa, T., Lee, W.C., Hatano, K., Kato, Y., Sawano, Y., Miyazono, K., Nagata, K., Tanokura, M.

(2006) Proteins 62: 557-561

Released	2006-02-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	Hypothetical UPF0076 protein ST0811 (protein)

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1ZR7 \| pdb_00001zr7	Download File View File

Solution structure of the first WW domain of FBP11

Kato, Y., Hino, Y., Tanokura, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) Proteins 63: 227-234

Released	2006-05-30
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	huntingtin-interacting protein HYPA/FBP11 (protein)

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2DYF \| pdb_00002dyf	Download File View File

Solution structure of the first WW domain of FBP11 / HYPA (FBP11 WW1) complexed with a PL (PPLP) motif peptide ligand

Kato, Y., Miyakawa, T., Kurita, J., Tanokura, M.

To be published

Released	2006-10-24
Method	SOLUTION NMR
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	Huntingtin-interacting protein HYPA/FBP11 (protein) PL (PPLP) motif peptide from Myosin tail region-interacting protein MTI1 (protein)

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2JV4 \| pdb_00002jv4	Download File View File

Structure Characterisation of PINA WW Domain and Comparison with other Group IV WW Domains, PIN1 and ESS1

Ng, C.A., Kato, Y., Tanokura, M., Brownlee, R.T.C.

(2008) Biochim Biophys Acta 1784: 1208-1214

Released	2007-10-16
Method	SOLUTION NMR
Organisms	Aspergillus nidulans
Macromolecule	Peptidyl-prolyl cis/trans isomerase (protein)

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2RR7 \| pdb_00002rr7	Download File View File

Microtubule Binding Domain of DYNEIN-C

Kato, Y., Yagi, T., Ohki, S., Burgess, S., Honda, S., Kamiya, R., Tanokura, M.

(2014) Structure 22: 1628-1638

Released	2011-06-08
Method	SOLUTION NMR
Organisms	Chlamydomonas reinhardtii
Macromolecule	Dynein heavy chain 9 (protein)

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2RVD \| pdb_00002rvd	Download File View File

NMR STRUCTURE of A MUTANT OF CHIGNOLIN, CLN025

Kato, Y., Ishimura, M., Honda, S.

(2008) J Am Chem Soc 130: 15327-15331

Released	2015-08-12
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	CLN025 (protein)

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3A15 \| pdb_00003a15	Download File View File

Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (OxdRE)

Sawai, H., Sugimoto, H., Kato, Y., Asano, Y., Shiro, Y., Aono, S.

(2009) J Biological Chem 284: 32089-32096

Released	2009-09-08
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Aldoxime dehydratase (protein)
Unique Ligands	HEM

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3A16 \| pdb_00003a16	Download File View File

Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Propionaldoxime

Sawai, H., Sugimoto, H., Kato, Y., Asano, Y., Shiro, Y., Aono, S.

(2009) J Biological Chem 284: 32089-32096

Released	2009-09-08
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Aldoxime dehydratase (protein)
Unique Ligands	HEM, MG, PXO

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3A17 \| pdb_00003a17	Download File View File

Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (Co-crystal)

Sawai, H., Sugimoto, H., Kato, Y., Asano, Y., Shiro, Y., Aono, S.

(2009) J Biological Chem 284: 32089-32096

Released	2009-09-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Aldoxime dehydratase (protein)
Unique Ligands	BXO, HEM

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3A18 \| pdb_00003a18	Download File View File

Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (soaked crystal)

Sawai, H., Sugimoto, H., Kato, Y., Asano, Y., Shiro, Y., Aono, S.

(2009) J Biological Chem 284: 32089-32096

Released	2009-09-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Aldoxime dehydratase (protein)
Unique Ligands	BXO, HEM

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3WSR \| pdb_00003wsr	Download File View File

Crystal structure of CLEC-2 in complex with O-glycosylated podoplanin

Nagae, M., Morita-Matsumoto, K., Kato, M., Kato-Kaneko, M., Kato, Y., Yamaguchi, Y.

(2014) Structure 22: 1711-1721

Released	2014-10-22
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Homo sapiens
Macromolecule	C-type lectin domain family 1 member B (protein) Peptide from Podoplanin (protein)
Unique branched monosaccharides	A2G, GAL, SIA

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3WWK \| pdb_00003wwk	Download File View File

Crystal structure of CLEC-2 in complex with rhodocytin

Nagae, M., Morita-Matsumoto, K., Kato, M., Kato-Kaneko, M., Kato, Y., Yamaguchi, Y.

(2014) Structure 22: 1711-1721

Released	2014-10-22
Method	X-RAY DIFFRACTION 2.98 Å
Organisms	Calloselasma rhodostoma Homo sapiens
Macromolecule	C-type lectin domain family 1 member B (protein) Snaclec rhodocytin subunit alpha (protein) Snaclec rhodocytin subunit beta (protein)

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3X3B \| pdb_00003x3b	Download File View File

Crystal structure of the light-driven sodium pump KR2 in acidic state

Kato, H.E., Inoue, K., Abe-Yoshizumi, R., Kato, Y., Ono, H., Konno, M., Ishizuka, T., Hoque, M.R., Hososhima, S., Kunitomo, H., Ito, J., Yoshizawa, S., Yamashita, K., Takemoto, M., Nishizawa, T., Taniguchi, R., Kogure, K., Maturana, A.D., Iino, Y., Yawo, H., Ishitani, R., Kandori, H., Nureki, O.

(2015) Nature 521: 48-53

Released	2015-04-08
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	OLA, PEG, RET

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3X3C \| pdb_00003x3c	Download File View File

Crystal structure of the light-driven sodium pump KR2 in neutral state

(2015) Nature 521: 48-53

Released	2015-04-08
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	OLA, RET

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5GIR \| pdb_00005gir	Download File View File

Crystal structure of a Fab fragment with its ligand peptide

Kitago, Y., Kaneko, K.K., Ogasawara, S., Kato, Y., Takagi, J.

(2016) Biochem Biophys Res Commun 478: 1274-1279

Released	2016-09-14
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Heavy chain of Fab fragment (protein) LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP (protein) Light chain of Fab fragment (protein)
Unique Ligands	EDO, SO4

1 to 25 of 46 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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1EH9 | pdb_00001eh9

1EHA | pdb_00001eha

1GIF | pdb_00001gif

1IUQ | pdb_00001iuq

1IV7 | pdb_00001iv7

1IV9 | pdb_00001iv9

1KKO | pdb_00001kko

1LF8 | pdb_00001lf8

1V7M | pdb_00001v7m

1V7N | pdb_00001v7n

1X25 | pdb_00001x25

1ZR7 | pdb_00001zr7

2DYF | pdb_00002dyf

2JV4 | pdb_00002jv4

2RR7 | pdb_00002rr7

2RVD | pdb_00002rvd

3A15 | pdb_00003a15

3A16 | pdb_00003a16

3A17 | pdb_00003a17

3A18 | pdb_00003a18

3WSR | pdb_00003wsr

3WWK | pdb_00003wwk

3X3B | pdb_00003x3b

3X3C | pdb_00003x3c

5GIR | pdb_00005gir