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 = "Oda, M."

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 53 Structures.

Refinements

Structure Determination Methodology

experimental (53)

Scientific Name of Source Organism

	Saccharomonospora viridis (18)
	Homo sapiens (8)
	Clostridium perfringens (7)
	Mus musculus (7)
	Oryctolagus cuniculus (7)
	synthetic construct (5)
	Bacillus cereus (4)
	Gallus gallus (2)
	Bacillus subtilis (1)
	Cellulosimicrobium cellulans (1)

Taxonomy

	Bacteria (31)
	Eukaryota (24)
	other sequences (5)

Experimental Method

	X-RAY DIFFRACTION (51)
	SOLUTION NMR (2)

Polymer Entity Type

Protein (53)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (20)
	1.5 - 2.0 (16)
	2.0 - 2.5 (10)
	2.5 - 3.0 (4)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (1)
	2005 - 2009 (6)
	2010 - 2014 (11)
	2015 - 2019 (10)
	2020 - 2024 (23)

Enzyme Classification Name

	Hydrolases (26)
	Transferases (6)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (51)
	Cyclic (1)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (14)
	Alpha and beta proteins (a/b) (18)
	Artifacts (10)
	All beta proteins (3)
	All alpha proteins (2)

AllSelected

1 to 25 of 53 Structures

Page 1 of 3

Sort by

Explore in 3D

1IDY	Download File View File

STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE

Furukawa, K., Oda, M., Nakamura, H.

(1996) Proc Natl Acad Sci U S A 93: 13583-13588

Released	1996-12-23
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3 (protein)

Explore in 3D

1IDZ	Download File View File

STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, 20 STRUCTURES

Furukawa, K., Oda, M., Nakamura, H.

(1996) Proc Natl Acad Sci U S A 93: 13583-13588

Released	1996-12-23
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3 (protein)

Explore in 3D

1VEA	Download File View File

Crystal Structure of HutP, an RNA binding antitermination protein

Kumarevel, T.S., Fujimoto, Z., Karthe, P., Oda, M., Mizuno, H., Kumar, P.K.R.

(2004) Structure 12: 1269-1280

Released	2004-07-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bacillus subtilis
Macromolecule	Hut operon positive regulatory protein (protein)
Unique Ligands	HBN

Explore in 3D

2DDR	Download File View File

Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion

Ago, H., Oda, M., Takahashi, M., Tsuge, H., Ochi, S., Katunuma, N., Miyano, M., Sakurai, J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Biol Chem 281: 16157-16167

Released	2006-05-02
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Bacillus cereus
Macromolecule	Sphingomyelin phosphodiesterase (protein)
Unique Ligands	CA

Explore in 3D

2DDS	Download File View File

Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion

Ago, H., Oda, M., Takahashi, M., Tsuge, H., Ochi, S., Katunuma, N., Miyano, M., Sakurai, J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Biol Chem 281: 16157-16167

Released	2006-05-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bacillus cereus
Macromolecule	Sphingomyelin phosphodiesterase (protein)
Unique Ligands	CO

Explore in 3D

2DDT	Download File View File

Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion

Ago, H., Oda, M., Tsuge, H., Katunuma, N., Miyano, M., Sakurai, J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Biol Chem 281: 16157-16167

Released	2006-05-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bacillus cereus
Macromolecule	Sphingomyelin phosphodiesterase (protein)
Unique Ligands	MES, MG, SO4

Explore in 3D

2DTM	Download File View File

Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies

Oda, M., Ito, N., Tsumuraya, T., Suzuki, K., Fujii, I.

(2007) J Mol Biol 369: 198-209

Released	2007-05-29
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Mus musculus
Macromolecule	IMMUNOGLOBULIN 6D9 (protein)

Explore in 3D

2UYR	Download File View File

Crystal structure of Bacillus cereus sphingomyelinase mutant :N57A

Oda, M., Tsuge, H., Sakurai, J.

To be published

Released	2008-05-27
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bacillus cereus
Macromolecule	SPHINGOMYELINASE C (protein)
Unique Ligands	MG

Explore in 3D

3ATG	Download File View File

endo-1,3-beta-glucanase from Cellulosimicrobium cellulans

Tanabe, Y., Pang, Z., Oda, M., Mikami, B.

(2018) Biochim Biophys Acta 1866: 415-425

Released	2012-01-18
Method	X-RAY DIFFRACTION 1.66 Å
Organisms	Cellulosimicrobium cellulans
Macromolecule	GLUCANASE (protein)
Unique Ligands	CA, GOL, PO4

Explore in 3D

3BUZ	Download File View File

Crystal structure of ia-bTAD-actin complex

Tsuge, H., Nagahama, M., Oda, M., Iwamoto, S., Utsunomiya, H., Marquez, V.E., Katunuma, N., Nishizawa, M., Sakurai, J.

(2008) Proc Natl Acad Sci U S A 105: 7399-7404

Released	2008-05-13
Method	X-RAY DIFFRACTION 2.81 Å
Organisms	Clostridium perfringens Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) Iota toxin component Ia (protein)
Unique Ligands	ATP, CA, LAR, TAD

Explore in 3D

3WA4	Download File View File

Grb2 SH2 domain/CD28-derived peptide complex

Higo, K., Oda, M., Ito, N.

(2013) PLoS One 8: e74482-e74482

Released	2014-02-26
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Homo sapiens
Macromolecule	Growth factor receptor-bound protein 2 (protein) T-cell-specific surface glycoprotein CD28 (protein)
Unique Ligands	ACY, CD

Explore in 3D

4GY2	Download File View File

Crystal structure of apo-Ia-actin complex

Tsurumura, T., Oda, M., Nagahama, M., Tsuge, H.

(2013) Proc Natl Acad Sci U S A 110: 4267-4272

Released	2013-02-20
Method	X-RAY DIFFRACTION 2.71 Å
Organisms	Clostridium perfringens Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) Iota toxin component Ia (protein)
Unique Ligands	ATP, CA, LAR, PO4

Explore in 3D

4H03	Download File View File

Crystal structure of NAD+-Ia-actin complex

Tsurumura, T., Oda, M., Nagahama, M., Tsuge, H.

(2013) Proc Natl Acad Sci U S A 110: 4267-4272

Released	2013-02-20
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Clostridium perfringens Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) Iota toxin component Ia (protein)
Unique Ligands	ATP, CA, EDO, LAR, NAD, PO4

Explore in 3D

4H0T	Download File View File

Crystal structure of Ia-ADPR-actin complex

Tsurumura, T., Oda, M., Nagahama, M., Tsuge, H.

(2013) Proc Natl Acad Sci U S A 110: 4267-4272

Released	2013-02-20
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Clostridium perfringens Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) Iota toxin component Ia (protein)
Unique Ligands	AR6, ATP, CA, EDO, LAR, PO4

Explore in 3D

4H0V	Download File View File

Crystal structure of NAD+-Ia(E378S)-actin complex

Tsurumura, T., Oda, M., Nagahama, M., Tsuge, H.

(2013) Proc Natl Acad Sci U S A 110: 4267-4272

Released	2013-02-20
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Clostridium perfringens Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) Iota toxin component Ia (protein)
Unique Ligands	ATP, CA, EDO, LAR, NAD, PO4

Explore in 3D

4H0X	Download File View File

Crystal structure of NAD+-Ia(E380A)-actin complex

Tsurumura, T., Oda, M., Nagahama, M., Tsuge, H.

(2013) Proc Natl Acad Sci U S A 110: 4267-4272

Released	2013-02-20
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Clostridium perfringens Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) Iota toxin component Ia (protein)
Unique Ligands	ATP, CA, EDO, LAR, NAD, PO4

Explore in 3D

4H0Y	Download File View File

Crystal structure of NAD+-Ia(E380S)-actin complex

Tsurumura, T., Oda, M., Nagahama, M., Tsuge, H.

(2013) Proc Natl Acad Sci U S A 110: 4267-4272

Released	2013-02-20
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Clostridium perfringens Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) Iota toxin component Ia (protein)
Unique Ligands	ATP, CA, EDO, LAR, NAD, PO4

Explore in 3D

4WFI	Download File View File

Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-free state

Miyakawa, T., Mizushima, H., Ohtsuka, J., Oda, M., Kawai, F., Tanokura, M.

(2015) Appl Microbiol Biotechnol 99: 4297-4307

Released	2014-12-24
Method	X-RAY DIFFRACTION 1.446 Å
Organisms	Saccharomonospora viridis
Macromolecule	Cutinase (protein)

Explore in 3D

4WFJ	Download File View File

Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 1.75 angstrom resolution

Miyakawa, T., Mizushima, H., Ohtsuka, J., Oda, M., Kawai, F., Tanokura, M.

(2015) Appl Microbiol Biotechnol 99: 4297-4307

Released	2014-12-24
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Saccharomonospora viridis
Macromolecule	Cutinase (protein)
Unique Ligands	CA, CL

Explore in 3D

4WFK	Download File View File

Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 2.35 angstrom resolution

Miyakawa, T., Mizushima, H., Ohtsuka, J., Oda, M., Kawai, F., Tanokura, M.

(2015) Appl Microbiol Biotechnol 99: 4297-4307

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Saccharomonospora viridis
Macromolecule	Cutinase (protein)
Unique Ligands	CA, CL

Explore in 3D

5AUL	Download File View File

PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex

Inaba, S., Numoto, N., Morii, H., Ikura, T., Oda, M., Ito, N.

(2017) J Biol Chem 292: 1052-1060

Released	2016-05-25
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase regulatory subunit alpha (protein) T-cell-specific surface glycoprotein CD28 (protein)
Unique Ligands	GOL

Explore in 3D

5GJH	Download File View File

Gads SH2 domain/CD28-derived peptide complex

Inaba, S., Numoto, N., Morii, H., Ogawa, S., Ikura, T., Abe, R., Ito, N., Oda, M.

(2017) J Biol Chem 292: 1052-1060

Released	2016-12-14
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Homo sapiens
Macromolecule	GRB2-related adapter protein 2 (protein) T-cell-specific surface glycoprotein CD28 (protein)

Explore in 3D

5GJI	Download File View File

PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex

Inaba, S., Numoto, N., Morii, H., Ogawa, S., Ikura, T., Abe, R., Ito, N., Oda, M.

(2017) J Biol Chem 292: 1052-1060

Released	2016-12-14
Method	X-RAY DIFFRACTION 0.9 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase regulatory subunit alpha (protein) T-cell-specific surface glycoprotein CD28 (protein)
Unique Ligands	GOL, SO4

Explore in 3D

5ZNO	Download File View File

Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S/ mutant in Ca(2+)-bound state

Numoto, N., Inaba, S., Yamagami, Y., Kamiya, N., Bekker, G.J., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M.

(2018) Biochemistry 57: 5289-5300

Released	2018-09-12
Method	X-RAY DIFFRACTION 1.60264346898 Å
Organisms	Saccharomonospora viridis
Macromolecule	Alpha/beta hydrolase family protein (protein)
Unique Ligands	CA, GOL

Explore in 3D

5ZRQ	Download File View File

Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state

Numoto, N., Kamiya, N., Bekker, G.J., Yamagami, Y., Inaba, S., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M.

(2018) Biochemistry 57: 5289-5300

Released	2018-09-12
Method	X-RAY DIFFRACTION 1.12 Å
Organisms	Saccharomonospora viridis
Macromolecule	Alpha/beta hydrolase family protein (protein)
Unique Ligands	CA, GOL, SO4, ZN

1 to 25 of 53 Structures

Page 1 of 3

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