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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, Y."

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Search Summary

This query matches 10 Structures.

Refinements

Structure Determination Methodology

experimental (10)

Scientific Name of Source Organism

	Aliarcobacter butzleri (4)
	Photobacterium phosphoreum (2)
	Aeropyrum pernix K1 (1)
	Mythimna separata (1)
	Triticum aestivum (1)
	unidentified tobacco necrosis virus (1)

Taxonomy

	Bacteria (6)
	Eukaryota (2)
	Archaea (1)
	Riboviria (1)

Experimental Method

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

Polymer Entity Type

Protein (10)

Refinement Resolution (Å)

	2.0 - 2.5 (3)
	2.5 - 3.0 (2)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (1)
	2005 - 2009 (2)
	2020 - 2024 (6)

Enzyme Classification Name

	Lyases (3)
	Transferases (1)

Membrane Protein Annotation

	PDBTM (4)
	MemProtMD (3)

Symmetry Type

	Cyclic (8)
	Asymmetric (1)
	Icosahedral (1)

SCOP Classification

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

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1 to 10 of 10 Structures

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1C8N \| pdb_00001c8n	Download File View File

TOBACCO NECROSIS VIRUS

Oda, Y., Fukuyama, K.

(2000) J Mol Biology 300: 153-169

Released	2000-08-30
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	unidentified tobacco necrosis virus
Macromolecule	COAT PROTEIN (protein)
Unique Ligands	CA

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1HSS \| pdb_00001hss	Download File View File

0.19 ALPHA-AMYLASE INHIBITOR FROM WHEAT

Oda, Y., Fukuyama, K.

(1997) Biochemistry 36: 13503-13511

Released	1998-07-01
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Triticum aestivum
Macromolecule	0.19 ALPHA-AMYLASE INHIBITOR (protein)

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1WKV \| pdb_00001wkv	Download File View File

Crystal structure of O-phosphoserine sulfhydrylase

Oda, Y., Mino, K., Ishikawa, K., Ataka, M.

(2005) J Mol Biology 351: 334-344

Released	2005-06-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Aeropyrum pernix K1
Macromolecule	cysteine synthase (protein)
Unique Ligands	ACT, PLP

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2RPS \| pdb_00002rps	Download File View File

Solution structure of a novel insect chemokine isolated from integument

Kamiya, M., Nakatogawa, S., Oda, Y., Kamijima, T., Aizawa, T., Demura, M., Hayakawa, Y., Kawano, K.

(2009) Curr Biol 19: 779-785

Released	2009-06-16
Method	SOLUTION NMR
Organisms	Mythimna separata
Macromolecule	Chemokine (protein)

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7ERU \| pdb_00007eru	Download File View File

Crystal structure of L-histidine decarboxylase (C57S mutant) from Photobacterium phosphoreum

Oda, Y., Nakata, K., Yamaguchi, H., Kashiwagi, T., Miyano, H., Mizukoshi, T.

(2022) J Biochem 171: 31-40

Released	2022-02-16
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Photobacterium phosphoreum
Macromolecule	Histidine decarboxylase (protein)

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7ERV \| pdb_00007erv	Download File View File

Crystal structure of L-histidine decarboxylase (C57S/C101V/C282V mutant) from Photobacterium phosphoreum

Oda, Y., Nakata, K., Yamaguchi, H., Kashiwagi, T., Miyano, H., Mizukoshi, T.

(2022) J Biochem 171: 31-40

Released	2022-02-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Photobacterium phosphoreum
Macromolecule	Histidine decarboxylase (protein)
Unique Ligands	IMD

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8H9X \| pdb_00008h9x	Download File View File

Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in sodium ion condition

Irie, K., Oda, Y.

(2023) Nat Commun 14: 4236-4236

Released	2023-07-26
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Aliarcobacter butzleri
Macromolecule	Ion transport protein (protein)
Unique Ligands	1N7, LMT, NA, PX4

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8H9Y \| pdb_00008h9y	Download File View File

Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in calcium ion condition

Irie, K., Oda, Y.

(2023) Nat Commun 14: 4236-4236

Released	2023-07-26
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Aliarcobacter butzleri
Macromolecule	Ion transport protein (protein)
Unique Ligands	1N7, CA, LMT, PX4

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8HA1 \| pdb_00008ha1	Download File View File

Crystal structure of voltage-gated sodium channel NavAb N49K/L176G mutant in sodium ion condition

Irie, K., Oda, Y.

(2023) Nat Commun 14: 4236-4236

Released	2023-07-26
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Aliarcobacter butzleri
Macromolecule	Ion transport protein (protein)
Unique Ligands	1N7, LMT, NA, PX4

Explore in 3D

8HA2 \| pdb_00008ha2	Download File View File

Crystal structure of voltage-gated sodium channel NavAb N49K/L176G mutant in calcium ion condition

Irie, K., Oda, Y.

(2023) Nat Commun 14: 4236-4236

Released	2023-07-26
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Aliarcobacter butzleri
Macromolecule	Ion transport protein (protein)
Unique Ligands	1N7, CA, LMT, PX4

1 to 10 of 10 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.

1C8N | pdb_00001c8n

TOBACCO NECROSIS VIRUS

1HSS | pdb_00001hss

0.19 ALPHA-AMYLASE INHIBITOR FROM WHEAT

1WKV | pdb_00001wkv

Crystal structure of O-phosphoserine sulfhydrylase

2RPS | pdb_00002rps

Solution structure of a novel insect chemokine isolated from integument

7ERU | pdb_00007eru

Crystal structure of L-histidine decarboxylase (C57S mutant) from Photobacterium phosphoreum

7ERV | pdb_00007erv

Crystal structure of L-histidine decarboxylase (C57S/C101V/C282V mutant) from Photobacterium phosphoreum

8H9X | pdb_00008h9x

Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in sodium ion condition

8H9Y | pdb_00008h9y

Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in calcium ion condition

8HA1 | pdb_00008ha1

Crystal structure of voltage-gated sodium channel NavAb N49K/L176G mutant in sodium ion condition

8HA2 | pdb_00008ha2

Crystal structure of voltage-gated sodium channel NavAb N49K/L176G mutant in calcium ion condition

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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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1C8N | pdb_00001c8n

1HSS | pdb_00001hss

1WKV | pdb_00001wkv

2RPS | pdb_00002rps

7ERU | pdb_00007eru

7ERV | pdb_00007erv

8H9X | pdb_00008h9x

8H9Y | pdb_00008h9y

8HA1 | pdb_00008ha1

8HA2 | pdb_00008ha2