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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Oda, S."

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This query matches 8 Structures.

Refinements

Structure Determination Methodology

experimental (8)

Scientific Name of Source Organism

	Homo sapiens (5)
	Marburg virus - Musoke, Kenya, 1980 (1)
	Sudan ebolavirus - Uganda (2000) (1)
	Sudan virus - Boniface, Sudan,1976 (1)
	Tequatrovirus T4 (1)
	Vaccinia virus WR (1)

Taxonomy

	Eukaryota (4)
	Riboviria (2)
	Duplodnaviria (1)
	Eukaryota (eukaryotes) (1)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (7)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (7)
	DNA (1)

Refinement Resolution (Å)

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

Release Date

	2005 - 2009 (3)
	2010 - 2014 (2)
	2015 - 2019 (3)

Enzyme Classification Name

	Oxidoreductases (2)
	Hydrolases (2)
	Transferases (1)

Symmetry Type

	Asymmetric (4)
	Cyclic (3)

SCOP Classification

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

AllSelected

1 to 8 of 8 Structures

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2D0T \| pdb_00002d0t	Download File View File

Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase

Sugimoto, H., Oda, S., Otsuki, T., Hino, T., Yoshida, T., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) Proc Natl Acad Sci U S A 103: 2611-2616

Released	2006-01-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Indoleamine 2,3-dioxygenase (protein)
Unique Ligands	HEM, NHE, PIM

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2D0U \| pdb_00002d0u	Download File View File

Crystal structure of cyanide bound form of human indoleamine 2,3-dioxygenase

Sugimoto, H., Oda, S., Otsuki, T., Hino, T., Yoshida, T., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) Proc Natl Acad Sci U S A 103: 2611-2616

Released	2006-01-31
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Homo sapiens
Macromolecule	Indoleamine 2,3-dioxygenase (protein)
Unique Ligands	CYN, HEM, NHE

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2RT8 \| pdb_00002rt8	Download File View File

Structure of metallo-dna in solution

Yamaguchi, H., Sebera, J., Kondo, J., Oda, S., Komuro, T., Kawamura, T., Dairaku, T., Kondo, Y., Okamoto, I., Ono, A., Burda, J.V., Kojima, C., Sychrovsky, V., Tanaka, Y.

(2014) Nucleic Acids Res 42: 4094-4099

Released	2014-03-05
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPGPCPGPTPTPGPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPCPTPTPCPGPCPG)-3') (nucleic acid)
Unique Ligands	HG

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3JRV \| pdb_00003jrv	Download File View File

Structure of poxvirus K7 protein in complex with RNA helicase DDX3

Oda, S., Khan, R.A.

(2009) Structure 17: 1528-1537

Released	2009-11-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens Vaccinia virus WR
Macromolecule	ATP-dependent RNA helicase DDX3X (protein) Protein K7 (protein)

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3TSO \| pdb_00003tso	Download File View File

Structure of the cancer associated Rab25 protein in complex with FIP2

Oda, S., Lall, P.Y., McCaffrey, M.W., Khan, A.R.

To be published

Released	2012-09-19
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Rab11 family-interacting protein 2 (protein) Ras-related protein Rab-25 (protein)
Unique Ligands	GNP, GOL, MG, PO4

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5B0V \| pdb_00005b0v	Download File View File

Crystal Structure of Marburg virus VP40 Dimer

Oda, S., Bornholdt, Z.A., Abelson, D.M., Saphire, E.O.

(2015) J Virol 90: 1839-1848

Released	2016-01-20
Method	X-RAY DIFFRACTION 2.81 Å
Organisms	Marburg virus - Musoke, Kenya, 1980
Macromolecule	Matrix protein VP40 (protein)
Unique Ligands	EOH

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6OAF \| pdb_00006oaf	Download File View File

Sudan virus nucleoprotein core domain in complex with VP35 chaperoning peptide

Landeras-Bueno, S., Oda, S., Norris, M.J., Li Salie, Z., Ollmann Saphire, E.

(2019) mBio 10:

Released	2019-08-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Sudan ebolavirus - Uganda (2000) Sudan virus - Boniface, Sudan,1976
Macromolecule	Polymerase cofactor VP35,Nucleoprotein (protein)

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6QAJ \| pdb_00006qaj	Download File View File

Structure of the tripartite motif of KAP1/TRIM28

Stoll, G.A., Oda, S., Yu, M., Modis, Y.

(2019) Proc Natl Acad Sci U S A 116: 15042-15051

Released	2019-07-24
Method	X-RAY DIFFRACTION 2.901 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Endolysin,Transcription intermediary factor 1-beta (protein)
Unique Ligands	ZN

1 to 8 of 8 Structures

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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.

2D0T | pdb_00002d0t

Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase

2D0U | pdb_00002d0u

Crystal structure of cyanide bound form of human indoleamine 2,3-dioxygenase

2RT8 | pdb_00002rt8

Structure of metallo-dna in solution

3JRV | pdb_00003jrv

Structure of poxvirus K7 protein in complex with RNA helicase DDX3

3TSO | pdb_00003tso

Structure of the cancer associated Rab25 protein in complex with FIP2

5B0V | pdb_00005b0v

Crystal Structure of Marburg virus VP40 Dimer

6OAF | pdb_00006oaf

Sudan virus nucleoprotein core domain in complex with VP35 chaperoning peptide

6QAJ | pdb_00006qaj

Structure of the tripartite motif of KAP1/TRIM28

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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

2D0T | pdb_00002d0t

2D0U | pdb_00002d0u

2RT8 | pdb_00002rt8

3JRV | pdb_00003jrv

3TSO | pdb_00003tso

5B0V | pdb_00005b0v

6OAF | pdb_00006oaf

6QAJ | pdb_00006qaj