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: Citation Author = "Yabuki, T."

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 943 Structures.

Refinements

Structure Determination Methodology

experimental (943)

Scientific Name of Source Organism

	Homo sapiens (593)
	Mus musculus (209)
	Trypanosoma cruzi strain CL Brener (50)
	Arabidopsis thaliana (28)
	Sus scrofa (19)
	Ascaris suum (8)
	Trypanosoma brucei brucei (8)
	Thermus thermophilus HB8 (7)
	Trypanosoma brucei gambiense (6)
	Trypanosoma cruzi (6)

More...

Taxonomy

	Eukaryota (927)
	Bacteria (13)
	Eukaryota (eukaryotes) (4)
	other sequences (2)
	Archaea (1)

Experimental Method

	SOLUTION NMR (744)
	X-RAY DIFFRACTION (159)
	ELECTRON MICROSCOPY (40)

Polymer Entity Type

	Protein (941)
	DNA (3)
	RNA (3)

Refinement Resolution (Å)

	0.5 - 1.0 (3)
	1.0 - 1.5 (11)
	1.5 - 2.0 (46)
	2.0 - 2.5 (36)
	2.5 - 3.0 (42)
	3.0 - 3.5 (44)
	3.5 - 4.0 (6)
	4.0 - 4.5 (6)
	> 4.5 (5)

Release Date

	1990 - 1994 (3)
	1995 - 1999 (2)
	2000 - 2004 (198)
	2005 - 2009 (558)
	2010 - 2014 (84)
	2015 - 2019 (31)
	2020 - 2024 (67)

Enzyme Classification Name

	Oxidoreductases (102)
	Transferases (103)
	Hydrolases (66)
	Isomerases (15)
	Ligases (14)
	Translocases (14)
	Lyases (1)

Membrane Protein Annotation

	PDBTM (50)
	MemProtMD (45)
	OPM (27)
	mpstruc (15)

Symmetry Type

	Asymmetric (829)
	Cyclic (116)
	Dihedral (5)

SCOP Classification

	Artifacts (588)
	Alpha and beta proteins (a+b) (206)
	All beta proteins (177)
	Alpha and beta proteins (a/b) (86)
	All alpha proteins (136)
	Small proteins (98)
	Membrane and cell surface proteins and peptides (8)

AllSelected

1 to 25 of 943 Structures

Page 1 of 38

Sort by

Explore in 3D

1D8Z	Download File View File

SOLUTION STRUCTURE OF THE FIRST RNA-BINDING DOMAIN (RBD1) OF HU ANTIGEN C (HUC)

Inoue, M., Muto, Y., Sakamoto, H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) Nucleic Acids Res 28: 1743-1750

Released	2000-04-07
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	HU ANTIGEN C (protein)

Explore in 3D

1D9A	Download File View File

SOLUTION STRUCTURE OF THE SECOND RNA-BINDING DOMAIN (RBD2) OF HU ANTIGEN C (HUC)

Inoue, M., Muto, Y., Sakamoto, H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) Nucleic Acids Res 28: 1743-1750

Released	2000-04-07
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	HU ANTIGEN C (protein)

Explore in 3D

1FIY	Download File View File

THREE-DIMENSIONAL STRUCTURE OF PHOSPHOENOLPYRUVATE CARBOXYLASE FROM ESCHERICHIA COLI AT 2.8 A RESOLUTION

Kai, Y., Matsumura, H., Inoue, T., Terada, K., Nagara, Y., Yoshinaga, T., Kihara, A., Izui, K.

(1999) Proc Natl Acad Sci U S A 96: 823-828

Released	1999-02-09
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli K-12
Macromolecule	PHOSPHOENOLPYRUVATE CARBOXYLASE (protein)
Unique Ligands	ASP

Explore in 3D

1FNX	Download File View File

SOLUTION STRUCTURE OF THE HUC RBD1-RBD2 COMPLEXED WITH THE AU-RICH ELEMENT

Inoue, M., Hirao, M., Kasashima, K., Kim, I.-S., Kawai, G., Kigawa, T., Sakamoto, H., Muto, Y., Yokoyama, S.

(2000) To be published

Released	2003-06-24
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	HU ANTIGEN C (protein) AU-RICH RNA ELEMENT (nucleic acid)

Explore in 3D

1IUY	Download File View File

Solution structure of the cullin-3 homologue

Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2003-10-07
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	cullin-3 homologue (protein)

Explore in 3D

1IV0	Download File View File

Solution structure of the YqgF-family protein (N-terminal fragment)

Inoue, M., Kigawa, T., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2003-10-07
Method	SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	hypothetical protein (protein)

Explore in 3D

1IVO	Download File View File

Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains.

Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J.H., Saito, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) Cell 110: 775-787

Released	2002-10-16
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	Epidermal Growth Factor Receptor (protein) Epidermal growth factor (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

Explore in 3D

1IVZ	Download File View File

Solution structure of the SEA domain from murine hypothetical protein homologous to human mucin 16

Maeda, T., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biol Chem 279: 13174-13182

Released	2002-10-02
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	hypothetical protein 1110008I14RIK (protein)

Explore in 3D

1IXD	Download File View File

Solution structure of the CAP-GLY domain from human cylindromatosis tomour-suppressor CYLD

Saito, K., Koshiba, S., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Structure 12: 1719-1728

Released	2002-12-19
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Cylindromatosis tumour-suppressor CYLD (protein)

Explore in 3D

1J0F	Download File View File

Solution Structure of the SH3 Domain Binding Glutamic Acid-rich Protein Like 3

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

To be published

Released	2003-12-02
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	SH3 domain-binding glutamic acid-rich-like protein 3 (protein)

Explore in 3D

1J0G	Download File View File

Solution Structure of Mouse Hypothetical 9.1 kDa Protein, A Ubiquitin-like Fold

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

To be published

Released	2003-12-09
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Hypothetical Protein 1810045K17 (protein)

Explore in 3D

1J26	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 Biol

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

Explore in 3D

1J3T	Download File View File

Solution structure of the second SH3 domain of human intersectin 2 (KIAA1256)

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

To be published

Released	2004-06-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Intersectin 2 (protein)

Explore in 3D

1N27	Download File View File

Solution structure of the PWWP domain of mouse Hepatoma-derived growth factor, related protein 3

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

(2005) Protein Sci 14: 756-764

Released	2003-12-23
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Hepatoma-derived growth factor, related protein 3 (protein)

Explore in 3D

1PE6	Download File View File

REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION

Yamamoto, D., Matsumoto, K., Ohishi, H., Ishida, T., Inoue, M., Kitamura, K., Mizuno, H.

(1991) J Biol Chem 266: 14771-14777

Released	1993-04-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Carica papaya
Macromolecule	PAPAIN (protein)
Unique Ligands	E6C, MOH

Explore in 3D

1PIP	Download File View File

CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS

Yamamoto, A., Tomoo, K., Doi, M., Ohishi, H., Inoue, M., Ishida, T., Yamamoto, D., Tsuboi, S., Okamoto, H., Okada, Y.

(1992) Biochemistry 31: 11305-11309

Released	1993-10-31
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Carica papaya
Macromolecule	Papain (protein) SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE (protein)

Explore in 3D

1PPP	Download File View File

CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES

Ishida, T.

(1992) Biochem J 287: 797-803

Released	1994-01-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Carica papaya
Macromolecule	PAPAIN (protein)
Unique Ligands	E6C, MOH

Explore in 3D

1R79	Download File View File

Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta

Miyamoto, K., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-04-21
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Diacylglycerol kinase, delta (protein)
Unique Ligands	ZN

Explore in 3D

1UCV	Download File View File

Sterile alpha motif (SAM) domain of ephrin type-A receptor 8

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

To be published

Released	2004-05-11
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	EPHRIN TYPE-A RECEPTOR 8 (protein)

Explore in 3D

1UDL	Download File View File

The solution structure of the fifth SH3 domain of intersectin 2 (KIAA1256)

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

To be published

Released	2003-11-01
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	intersectin 2 (protein)

Explore in 3D

1UDM	Download File View File

Solution structure of Coactosin-like protein (Cofilin family) from Mus Musculus

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

(2009) Protein Sci 18: 2384-2392

Released	2004-05-18
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Coactosin-like protein (protein)

Explore in 3D

1UDX	Download File View File

Crystal structure of the conserved protein TT1381 from Thermus thermophilus HB8

Kukimoto-Niino, M., Shirouzu, M., Murayama, K., Inoue, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Mol Biol 337: 761-770

Released	2004-03-16
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Thermus thermophilus HB8
Macromolecule	the GTP-binding protein Obg (protein)
Unique Ligands	ACT, MPD

Explore in 3D

1UE9	Download File View File

Solution structure of the fourth SH3 domain of human intersectin 2 (KIAA1256)

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

To be published

Released	2003-11-09
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Intersectin 2 (protein)

Explore in 3D

1UEM	Download File View File

Solution Structure of the First Fibronectin Type III domain of human KIAA1568 Protein

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

To be published

Released	2003-11-19
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	KIAA1568 Protein (protein)

Explore in 3D

1UEN	Download File View File

Solution Structure of The Third Fibronectin III Domain of Human KIAA0343 Protein

Miyamoto, K., Kigawa, T., Hayashi, F., Inoue, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2003-11-19
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	KIAA0343 protein (protein)

1 to 25 of 943 Structures

Page 1 of 38

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