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: Structure Author = "Akashi, S."

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 10 Structures.

Refinements

Structure Determination Methodology

experimental (10)

Scientific Name of Source Organism

	Homo sapiens (5)
	Bacillus subtilis (2)
	Geobacillus stearothermophilus (2)
	Enterococcus faecium (1)
	Oryza sativa Japonica Group (1)
	Rattus norvegicus (1)

Taxonomy

	Eukaryota (7)
	Bacteria (3)

Experimental Method

	X-RAY DIFFRACTION (9)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (10)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (2)
	2.0 - 2.5 (1)
	2.5 - 3.0 (3)
	3.0 - 3.5 (2)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (4)
	2015 - 2019 (1)
	2020 - 2024 (2)

Enzyme Classification Name

	Hydrolases (4)
	Transferases (3)
	Oxidoreductases (1)

Symmetry Type

	Cyclic (6)
	Asymmetric (4)

SCOP Classification

	All beta proteins (2)
	Alpha and beta proteins (a+b) (2)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 10 of 10 Structures

Page 1 of 1

Sort by

Explore in 3D

2ZP8 \| pdb_00002zp8	Download File View File

The Nature of the TRAP:Anti-TRAP complex

Watanabe, M., Heddle, J.G., Unzai, S., Akashi, S., Park, S.Y., Tame, J.R.H.

(2009) Proc Natl Acad Sci U S A 106: 2176-2181

Released	2009-02-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Bacillus subtilis Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein) Tryptophan RNA-binding attenuator protein-inhibitory protein (protein)
Unique Ligands	TRP, ZN

Explore in 3D

2ZP9 \| pdb_00002zp9	Download File View File

The Nature of the TRAP:Anti-TRAP complex

Watanabe, M., Heddle, J.G., Unzai, S., Akashi, S., Park, S.Y., Tame, J.R.H.

(2009) Proc Natl Acad Sci U S A 106: 2176-2181

Released	2009-02-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Bacillus subtilis Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein) Tryptophan RNA-binding attenuator protein-inhibitory protein (protein)
Unique Ligands	TRP, ZN

Explore in 3D

3A8R \| pdb_00003a8r	Download File View File

The structure of the N-terminal regulatory domain of a plant NADPH oxidase

Oda, T., Hashimoto, H., Kuwabara, N., Akashi, S., Hayashi, K., Kojima, C., Wong, H.L., Kawasaki, T., Shimamoto, K., Sato, M., Shimizu, T.

(2010) J Biological Chem 285: 1435-1445

Released	2009-10-27
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Oryza sativa Japonica Group
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	CA

Explore in 3D

3ABD \| pdb_00003abd	Download File View File

Structure of human REV7 in complex with a human REV3 fragment in a monoclinic crystal

Hara, K., Hashimoto, H., Murakumo, Y., Kobayashi, S., Kogame, T., Unzai, S., Akashi, S., Takeda, S., Shimizu, T., Sato, M.

(2010) J Biological Chem 285: 12299-12307

Released	2010-02-16
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase zeta catalytic subunit (protein) Mitotic spindle assembly checkpoint protein MAD2B (protein)

Explore in 3D

3ABE \| pdb_00003abe	Download File View File

Structure of human REV7 in complex with a human REV3 fragment in a tetragonal crystal

Hara, K., Hashimoto, H., Murakumo, Y., Kobayashi, S., Kogame, T., Unzai, S., Akashi, S., Takeda, S., Shimizu, T., Sato, M.

(2010) J Biological Chem 285: 12299-12307

Released	2010-02-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase zeta catalytic subunit (protein) Mitotic spindle assembly checkpoint protein MAD2B (protein)

Explore in 3D

3APM \| pdb_00003apm	Download File View File

Crystal structure of the human SNP PAD4 protein

Horikoshi, N., Tachiwana, H., Saito, K., Osakabe, A., Sato, M., Yamada, M., Akashi, S., Nishimura, Y., Kagawa, W., Kurumizaka, H.

(2011) Acta Crystallogr D Biol Crystallogr 67: 112-118

Released	2011-01-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)

Explore in 3D

3APN \| pdb_00003apn	Download File View File

Crystal structure of the human wild-type PAD4 protein

Horikoshi, N., Tachiwana, H., Saito, K., Osakabe, A., Sato, M., Yamada, M., Akashi, S., Nishimura, Y., Kagawa, W., Kurumizaka, H.

(2011) Acta Crystallogr D Biol Crystallogr 67: 112-118

Released	2011-01-26
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type-4 (protein)

Explore in 3D

3X1W \| pdb_00003x1w	Download File View File

Ras-related protein Rap1B with GDP

Noguchi, H., Ikegami, T., Akashi, S., Park, S.Y., Tame, J.R.H., Unzai, S.

(2015) Biochem Biophys Res Commun 462: 46-51

Released	2015-06-03
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Rattus norvegicus
Macromolecule	Ras-related protein Rap-1b (protein)
Unique Ligands	CD, GDP, MG

Explore in 3D

8XE7 \| pdb_00008xe7	Download File View File

Crystal structure of human Sirt2 without Sirt2-specific insertion

Konuma, T., Akashi, S.

(2024) Protein Sci 33: e4994-e4994

Released	2024-05-22
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacetylase sirtuin-2 (protein)
Unique Ligands	ZN

Explore in 3D

8XZ2 \| pdb_00008xz2	Download File View File

The structural model of a homodimeric D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria

Konuma, T., Takai, T., Tsuchiya, C., Nishida, M., Hashiba, M., Yamada, Y., Shirai, H., Motoda, Y., Nagadoi, A., Chikaishi, E., Akagi, K., Akashi, S., Yamazaki, T., Akutsu, H., Oe, A., Ikegami, T.

(2024) Protein Sci 33: e5002-e5002

Released	2024-05-22
Method	SOLUTION NMR
Organisms	Enterococcus faecium
Macromolecule	D-alanyl-D-alanine dipeptidase (protein)

1 to 10 of 10 Structures

Page 1 of 1

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.

2ZP8 | pdb_00002zp8

The Nature of the TRAP:Anti-TRAP complex

2ZP9 | pdb_00002zp9

The Nature of the TRAP:Anti-TRAP complex

3A8R | pdb_00003a8r

The structure of the N-terminal regulatory domain of a plant NADPH oxidase

3ABD | pdb_00003abd

Structure of human REV7 in complex with a human REV3 fragment in a monoclinic crystal

3ABE | pdb_00003abe

Structure of human REV7 in complex with a human REV3 fragment in a tetragonal crystal

3APM | pdb_00003apm

Crystal structure of the human SNP PAD4 protein

3APN | pdb_00003apn

Crystal structure of the human wild-type PAD4 protein

3X1W | pdb_00003x1w

Ras-related protein Rap1B with GDP

8XE7 | pdb_00008xe7

Crystal structure of human Sirt2 without Sirt2-specific insertion

8XZ2 | pdb_00008xz2

The structural model of a homodimeric D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria

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

Symmetry Type

SCOP Classification

2ZP8 | pdb_00002zp8

2ZP9 | pdb_00002zp9

3A8R | pdb_00003a8r

3ABD | pdb_00003abd

3ABE | pdb_00003abe

3APM | pdb_00003apm

3APN | pdb_00003apn

3X1W | pdb_00003x1w

8XE7 | pdb_00008xe7

8XZ2 | pdb_00008xz2