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

233,605 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: Citation Author = "Inoue, Y."

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 83 Structures.

Refinements

Structure Determination Methodology

experimental (83)

Scientific Name of Source Organism

	Homo sapiens (46)
	Thermus thermophilus (20)
	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (5)
	Thermus thermophilus HB8 (3)
	Bos taurus (2)
	Mus musculus (2)
	Thermochaetoides thermophila (2)
	Aquifex aeolicus (1)
	Cyanidioschyzon merolae strain 10D (1)
	Planomonospora sphaerica (1)

Taxonomy

	Eukaryota (53)
	Bacteria (30)

Experimental Method

	X-RAY DIFFRACTION (76)
	SOLUTION NMR (6)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (83)

Refinement Resolution (Å)

	0.5 - 1.0 (32)
	1.0 - 1.5 (9)
	1.5 - 2.0 (16)
	2.0 - 2.5 (10)
	2.5 - 3.0 (5)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)
	> 4.5 (1)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (20)
	2005 - 2009 (4)
	2010 - 2014 (3)
	2015 - 2019 (7)
	2020 - 2024 (47)

Enzyme Classification Name

	Hydrolases (18)
	Lyases (3)
	Transferases (2)
	Oxidoreductases (1)

Membrane Protein Annotation

	OPM (1)
	PDBTM (1)

Symmetry Type

	Asymmetric (63)
	Cyclic (17)
	Dihedral (3)
	Helical (2)

SCOP Classification

	Alpha and beta proteins (a+b) (16)
	All beta proteins (6)
	Alpha and beta proteins (a/b) (8)
	All alpha proteins (3)
	Artifacts (2)
	Small proteins (1)

AllSelected

1 to 25 of 83 Structures

Page 1 of 4

Sort by

Explore in 3D

1AB9 \| pdb_00001ab9	Download File View File

CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN

Sugio, S., Kashima, A., Inoue, Y., Maeda, I., Nose, T., Shimohigashi, Y.

(1998) Eur J Biochem 255: 12-23

Released	1997-08-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Bos taurus
Macromolecule	GAMMA-CHYMOTRYPSIN (protein) PENTAPEPTIDE (TPGVY) (protein)
Unique Ligands	SO4

Explore in 3D

1AFQ \| pdb_00001afq	Download File View File

CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED WITH A SYNTHETIC INHIBITOR

Sugio, S., Kashima, A., Inoue, Y., Maeda, I., Nose, T., Shimohigashi, Y.

(1998) Eur J Biochem 255: 12-23

Released	1997-09-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	BOVINE GAMMA-CHYMOTRYPSIN (protein)
Unique Ligands	0FG, SO4

Explore in 3D

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

Explore in 3D

1GD7 \| pdb_00001gd7	Download File View File

CRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RELATED CHAPERONE AND TRNA-BINDING ACTIVITIES.

Shibata, T., Inoue, Y., Vassylyev, D.G., Kawaguchi, S., Yokoyama, S., Muller, J., Linde, D., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) EMBO J 20: 562-569

Released	2001-09-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus
Macromolecule	CSAA PROTEIN (protein)

Explore in 3D

1IPA \| pdb_00001ipa	Download File View File

CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE

Nureki, O., Shirouzu, M., Hashimoto, K., Ishitani, R., Terada, T., Tamakoshi, M., Oshima, T., Chijimatsu, M., Takio, K., Vassylyev, D.G., Shibata, T., Inoue, Y., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Acta Crystallogr D Biol Crystallogr 58: 1129-1137

Released	2002-07-10
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus
Macromolecule	RNA 2'-O-RIBOSE METHYLTRANSFERASE (protein)

Explore in 3D

1IQR \| pdb_00001iqr	Download File View File

Crystal structure of DNA photolyase from Thermus thermophilus

Komori, H., Masui, R., Kuramitsu, S., Yokoyama, S., Shibata, T., Inoue, Y., Miki, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) Proc Natl Acad Sci U S A 98: 13560-13565

Released	2001-11-28
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus
Macromolecule	photolyase (protein)
Unique Ligands	FAD, PO4

Explore in 3D

1IQU \| pdb_00001iqu	Download File View File

Crystal structure of photolyase-thymine complex

Komori, H., Masui, R., Kuramitsu, S., Yokoyama, S., Shibata, T., Inoue, Y., Miki, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) Proc Natl Acad Sci U S A 98: 13560-13565

Released	2002-05-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	photolyase (protein)
Unique Ligands	FAD, PO4, TDR

Explore in 3D

1J1H \| pdb_00001j1h	Download File View File

Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus

Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., Kawai, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) FEBS Lett 535: 94-100

Released	2003-02-11
Method	SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	Small Protein B (protein)

Explore in 3D

1J26 \| pdb_00001j26	Download File View File

Solution structure of a putative peptidyl-tRNA hydrolase domain in a mouse hypothetical protein

Nameki, N., Kigawa, T., Koshiba, S., Kobayashi, N., Tochio, N., Inoue, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2010) J Mol Biology

Released	2004-06-01
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	immature colon carcinoma transcript 1 (protein)

Explore in 3D

1UI0 \| pdb_00001ui0	Download File View File

Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8

Hoseki, J., Okamoto, A., Masui, R., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) J Mol Biology 333: 515-526

Released	2003-10-14
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Thermus thermophilus
Macromolecule	Uracil-DNA Glycosylase (protein)
Unique Ligands	SF4, SO4, URA

Explore in 3D

1UI1 \| pdb_00001ui1	Download File View File

Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8

Hoseki, J., Okamoto, A., Masui, R., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) J Mol Biology 333: 515-526

Released	2003-10-14
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermus thermophilus
Macromolecule	Uracil-DNA Glycosylase (protein)
Unique Ligands	SF4

Explore in 3D

1V8I \| pdb_00001v8i	Download File View File

Crystal Structure Analysis of the ADP-ribose pyrophosphatase

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)

Explore in 3D

1V8L \| pdb_00001v8l	Download File View File

Structure Analysis of the ADP-ribose pyrophosphatase complexed with ADP-ribose

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	APR

Explore in 3D

1V8M \| pdb_00001v8m	Download File View File

Crystal structure analysis of ADP-ribose pyrophosphatase complexed with ADP-ribose and Gd

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	APR, GD

Explore in 3D

1V8N \| pdb_00001v8n	Download File View File

Crystal structure analysis of the ADP-ribose pyrophosphatase complexed with Zn

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	ZN

Explore in 3D

1V8R \| pdb_00001v8r	Download File View File

Crystal structure analysis of the ADP-ribose pyrophosphatase complexed with ADP-ribose and Zn

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2005-02-22
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	APR, ZN

Explore in 3D

1V8S \| pdb_00001v8s	Download File View File

Crystal structure analusis of the ADP-ribose pyrophosphatase complexed with AMP and Mg

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	AMP, MG

Explore in 3D

1V8T \| pdb_00001v8t	Download File View File

Crystal Structure analysis of the ADP-ribose pyrophosphatase complexed with ribose-5'-phosphate and Zn

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	R5P, ZN

Explore in 3D

1V8U \| pdb_00001v8u	Download File View File

Crystal structure analysis of the ADP-ribose pyrophosphatase of E82Q mutant with SO4 and Mg

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	MG, SO4

Explore in 3D

1V8V \| pdb_00001v8v	Download File View File

Crystal structure analysis of the ADP-ribose pyrophosphatase of E86Q mutant, complexed with ADP-ribose and Mg

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	APR, MG

Explore in 3D

1V8W \| pdb_00001v8w	Download File View File

Crystal structure analysis of the ADP-ribose pyrophosphatase of E82Q mutant, complexed with SO4 and Zn

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 1.66 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	SO4, ZN

Explore in 3D

1V8Y \| pdb_00001v8y	Download File View File

Crystal structure analysis of the ADP-ribose pyrophosphatase of E86Q mutant, complexed with ADP-ribose and Zn

Yoshiba, S., Ooga, T., Nakagawa, N., Shibata, T., Inoue, Y., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 37163-37174

Released	2004-10-19
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Thermus thermophilus
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	APR, ZN

Explore in 3D

1WOT \| pdb_00001wot	Download File View File

Structure of putative minimal nucleotidyltransferase

Suzuki, S., Hatanaka, H., Hondoh, T., Okumura, A., Kuroda, Y., Kuramitsu, S., Shibata, T., Inoue, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-09-07
Method	SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	PUTATIVE MINIMAL NUCLEOTIDYLTRANSFERASE (protein)

Explore in 3D

2D1Y \| pdb_00002d1y	Download File View File

Crystal structure of TT0321 from Thermus thermophilus HB8

Asada, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Chem Biol Interact 178: 117-126

Released	2006-03-02
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Thermus thermophilus
Macromolecule	hypothetical protein TT0321 (protein)
Unique Ligands	NAD

Explore in 3D

2EHD \| pdb_00002ehd	Download File View File

Crystal Structure Analysis of Oxidoreductase

Kamiya, N., Hikima, T., Ebihara, A., Inoue, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-03-11
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Oxidoreductase, short-chain dehydrogenase/reductase family (protein)
Unique Ligands	CO

1 to 25 of 83 Structures

Page 1 of 4

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.

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

1AB9 | pdb_00001ab9

1AFQ | pdb_00001afq

1EE8 | pdb_00001ee8

1GD7 | pdb_00001gd7

1IPA | pdb_00001ipa

1IQR | pdb_00001iqr

1IQU | pdb_00001iqu

1J1H | pdb_00001j1h

1J26 | pdb_00001j26

1UI0 | pdb_00001ui0

1UI1 | pdb_00001ui1

1V8I | pdb_00001v8i

1V8L | pdb_00001v8l

1V8M | pdb_00001v8m

1V8N | pdb_00001v8n

1V8R | pdb_00001v8r

1V8S | pdb_00001v8s

1V8T | pdb_00001v8t

1V8U | pdb_00001v8u

1V8V | pdb_00001v8v

1V8W | pdb_00001v8w

1V8Y | pdb_00001v8y

1WOT | pdb_00001wot

2D1Y | pdb_00002d1y

2EHD | pdb_00002ehd