RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

232,059 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Structure Author = "Kato, R."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 136 Structures.

Refinements

Structure Determination Methodology

experimental (136)

Scientific Name of Source Organism

	Homo sapiens (81)
	Mus musculus (20)
	Saccharomyces cerevisiae (6)
	Bos taurus (5)
	Canis lupus familiaris (5)
	Bifidobacterium bifidum (4)
	Aspergillus oryzae RIB40 (3)
	Cyclocybe cylindracea (3)
	Rheum palmatum (3)
	Synechococcus sp. (3)

More...

Taxonomy

	Eukaryota (124)
	Bacteria (12)
	Eukaryota (eukaryotes) (3)

Experimental Method

X-RAY DIFFRACTION (136)

Polymer Entity Type

Protein (136)

Refinement Resolution (Å)

	1.0 - 1.5 (16)
	1.5 - 2.0 (56)
	2.0 - 2.5 (28)
	2.5 - 3.0 (25)
	3.0 - 3.5 (10)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (14)
	2005 - 2009 (71)
	2010 - 2014 (32)
	2015 - 2019 (16)
	2020 - 2024 (3)

Enzyme Classification Name

	Hydrolases (35)
	Transferases (23)
	Ligases (1)
	Isomerases (1)
	Lyases (1)

Membrane Protein Annotation

	MemProtMD (1)
	OPM (1)
	PDBTM (1)

Symmetry Type

	Asymmetric (102)
	Cyclic (41)
	Octahedral (1)

SCOP Classification

	All beta proteins (44)
	Alpha and beta proteins (a/b) (20)
	Artifacts (23)
	Alpha and beta proteins (a+b) (16)
	All alpha proteins (11)
	Coiled coil proteins (1)
	Small proteins (1)

AllSelected

1 to 25 of 136 Structures

Page 1 of 6

Sort by

Explore in 3D

1D2M	Download File View File

UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME

Nakagawa, N., Sugahara, M., Masui, R., Kato, R., Fukuyama, K., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1999) J Biochem 126: 986-990

Released	2000-03-22
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus HB8
Macromolecule	EXCINUCLEASE ABC SUBUNIT B (protein)
Unique Ligands	BOG, SO4

Explore in 3D

1EE8	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

Explore in 3D

1IU1	Download File View File

Crystal structure of human gamma1-adaptin ear domain

Nogi, T., Shiba, Y., Kawasaki, M., Shiba, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Takatsu, H., Nakayama, K., Wakatsuki, S.

(2002) Nat Struct Biol 9: 527-531

Released	2002-07-10
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	gamma1-adaptin (protein)

Explore in 3D

1J2J	Download File View File

Crystal structure of GGA1 GAT N-terminal region in complex with ARF1 GTP form

Shiba, T., Kawasaki, M., Takatsu, H., Nogi, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Nakayama, K., Wakatsuki, S.

(2003) Nat Struct Biol 10: 386-393

Released	2003-05-06
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	ADP-ribosylation factor 1 (protein) ADP-ribosylation factor binding protein GGA1 (protein)
Unique Ligands	GTP, IOD, MG

Explore in 3D

1JWF	Download File View File

Crystal Structure of human GGA1 VHS domain.

Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T., Nakayama, K., Wakatsuki, S.

(2002) Nature 415: 937-941

Released	2002-03-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA1 (protein)

Explore in 3D

1JWG	Download File View File

VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide

Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T., Nakayama, K., Wakatsuki, S.

(2002) Nature 415: 937-941

Released	2002-03-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA1 (protein) Cation-independent mannose-6-phosphate receptor (protein)
Unique Ligands	IOD

Explore in 3D

1O3X	Download File View File

Crystal structure of human GGA1 GAT domain

Shiba, T., Kawasaki, M., Takatsu, H., Nogi, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Nakayama, K., Wakatsuki, S.

(2003) Nat Struct Biol 10: 386-393

Released	2003-05-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA1 (protein)

Explore in 3D

1O3Y	Download File View File

Crystal structure of mouse ARF1 (delta17-Q71L), GTP form

Shiba, T., Kawasaki, M., Takatsu, H., Nogi, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Nakayama, K., Wakatsuki, S.

(2003) Nat Struct Biol 10: 386-393

Released	2003-05-20
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Mus musculus
Macromolecule	ADP-ribosylation factor 1 (protein)
Unique Ligands	GTP, MG

Explore in 3D

1SNT	Download File View File

Structure of the human cytosolic sialidase Neu2

Chavas, L.M.G., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Kato, R., Monti, E., Wakatsuki, S.

(2005) J Biol Chem 280: 469-475

Released	2004-11-02
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	Sialidase 2 (protein)

Explore in 3D

1SO7	Download File View File

Maltose-induced structure of the human cytolsolic sialidase Neu2

Chavas, L.M.G., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Kato, R., Monti, E., Wakatsuki, S.

(2005) J Biol Chem 280: 469-475

Released	2004-11-02
Method	X-RAY DIFFRACTION 1.49 Å
Organisms	Homo sapiens
Macromolecule	Sialidase 2 (protein)
Unique Ligands	CL

Explore in 3D

1V82	Download File View File

Crystal structure of human GlcAT-P apo form

Kakuda, S., Shiba, T., Ishiguro, M., Tagawa, H., Oka, S., Kajihara, Y., Kawasaki, T., Wakatsuki, S., Kato, R.

(2004) J Biol Chem 279: 22693-22703

Released	2004-05-25
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (protein)
Unique Ligands	TLA

Explore in 3D

1V83	Download File View File

Crystal structure of human GlcAT-P in complex with Udp and Mn2+

Kakuda, S., Shiba, T., Ishiguro, M., Tagawa, H., Oka, S., Kajihara, Y., Kawasaki, T., Wakatsuki, S., Kato, R.

(2004) J Biol Chem 279: 22693-22703

Released	2004-05-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (protein)
Unique Ligands	MN, TLA, UDP

Explore in 3D

1V84	Download File View File

Crystal structure of human GlcAT-P in complex with N-acetyllactosamine, Udp, and Mn2+

Kakuda, S., Shiba, T., Ishiguro, M., Tagawa, H., Oka, S., Kajihara, Y., Kawasaki, T., Wakatsuki, S., Kato, R.

(2004) J Biol Chem 279: 22693-22703

Released	2004-05-25
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Homo sapiens
Macromolecule	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (protein)
Unique Ligands	MN, TLA, UDP
Unique branched monosaccharides	GAL, NAG, NDG

Explore in 3D

1VCU	Download File View File

Structure of the human cytosolic sialidase Neu2 in complex with the inhibitor DANA

Chavas, L.M.G., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Kato, R., Monti, E., Wakatsuki, S.

(2005) J Biol Chem 280: 469-475

Released	2004-11-02
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	Sialidase 2 (protein)
Unique Ligands	DAN, EPE

Explore in 3D

1WR6	Download File View File

Crystal structure of GGA3 GAT domain in complex with ubiquitin

Kawasaki, M., Shiba, T., Shiba, Y., Yamaguchi, Y., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.

(2005) Genes Cells 10: 639-654

Released	2005-06-28
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA3 (protein) ubiquitin (protein)

Explore in 3D

1WRD	Download File View File

Crystal structure of Tom1 GAT domain in complex with ubiquitin

Akutsu, M., Kawasaki, M., Katoh, Y., Shiba, T., Yamaguchi, Y., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.

(2005) FEBS Lett 579: 5385-5391

Released	2005-10-11
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	Target of Myb protein 1 (protein) Ubiquitin (protein)

Explore in 3D

1WRM	Download File View File

Crystal structure of JSP-1

Yokota, T., Kashima, A., Kato, R., Sugio, S.

(2006) Proteins 66: 272-278

Released	2005-10-22
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	dual specificity phosphatase 22 (protein)
Unique Ligands	MES

Explore in 3D

2A6V	Download File View File

Crystal structure of Emp46p carbohydrate recognition domain (CRD), potassium-bound form

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biol Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.52 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp46p (protein)
Unique Ligands	EDO, K

Explore in 3D

2A6W	Download File View File

Crystal structure of Emp46p carbohydrate recognition domain (CRD), metal-free form

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biol Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp46p (protein)

Explore in 3D

2A6X	Download File View File

Crystal structure of Emp46p carbohydrate recognition domain (CRD), Y131F mutant

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Biol Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp46p (protein)
Unique Ligands	EDO, K

Explore in 3D

2A6Y	Download File View File

Crystal structure of Emp47p carbohydrate recognition domain (CRD), tetragonal crystal form

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biol Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.42 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp47p (form1) (protein)
Unique Ligands	SO4

Explore in 3D

2A6Z	Download File View File

Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 1

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biol Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp47p (form2) (protein)

Explore in 3D

2A71	Download File View File

Crystal structure of Emp47p carbohydrate recognition domain (CRD), orthorhombic crystal form

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biol Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp47p (protein)

Explore in 3D

2D0J	Download File View File

Crystal Structure of Human GlcAT-S Apo Form

Shiba, T., Kakuda, S., Ishiguro, M., Oka, S., Kawasaki, T., Wakatsuki, S., Kato, R.

To be published

Released	2006-07-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 (protein)

Explore in 3D

2D3G	Download File View File

Double sided ubiquitin binding of Hrs-UIM

Hirano, S., Kawasaki, M., Kato, R., Wakatsuki, S.

(2006) Nat Struct Mol Biol 13: 272-277

Released	2005-12-20
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	ubiquitin (protein) ubiquitin interacting motif from hepatocyte growth factor-regulated tyrosine kinase substrate (protein)

1 to 25 of 136 Structures

Page 1 of 6

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

All questions and comments will receive a response in a timely manner.

Use this form for questions about RCSB.org and RCSB PDB services.
Please attach a screenshot when reporting an issue, if possible.
To update/release your in-progress structure depositions:
access the OneDep Communication panel
For questions/corrections to specific PDB entries, including citation updates:
email deposit-help@mail.wwpdb.org

First Name

Last Name

Subject

Question, Comment, Feedback or Other

Attach File(s)
Use CTRL or Shift keys to select more than one file ( files max)

I agree to the Help Desk Privacy Policy

Optional: To help us learn more about our users, what is your:

Institution Type

Role

Main Research Interest

Thank you for providing your feedback! Someone will be in touch with you shortly. This window will automatically close in 5 seconds.

Apologies, our feedback server is currently unavailable and we are troubleshooting the issue. In the meantime, please copy and paste the below information into an email addressed to info@rcsb.org

Prepare Data

Validate Data

Deposit Data

Help and Resources

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