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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Mizukoshi, T."

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Search Summary

This query matches 15 Structures.

Refinements

Structure Determination Methodology

experimental (15)

Scientific Name of Source Organism

	Homo sapiens (4)
	Bifidobacterium longum (2)
	Chromobacterium violaceum ATCC 12472 (2)
	Geobacillus stearothermophilus 10 (2)
	Photobacterium phosphoreum (2)
	Bifidobacterium longum subsp. longum F8 (1)
	Chryseobacterium proteolyticum (1)
	Streptomyces sp. X-119-6 (1)

Taxonomy

	Bacteria (11)
	Eukaryota (4)

Experimental Method

	X-RAY DIFFRACTION (11)
	ELECTRON MICROSCOPY (3)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (15)

Refinement Resolution (Å)

	1.5 - 2.0 (5)
	2.0 - 2.5 (2)
	2.5 - 3.0 (5)
	3.0 - 3.5 (2)

Release Date

	2010 - 2014 (1)
	2015 - 2019 (8)
	2020 - 2024 (6)

Enzyme Classification Name

	Lyases (5)
	Oxidoreductases (3)
	Hydrolases (1)

Symmetry Type

	Dihedral (6)
	Asymmetric (5)
	Cyclic (4)

SCOP Classification

	Alpha and beta proteins (a/b) (1)
	All beta proteins (4)
	Artifacts (4)

AllSelected

1 to 15 of 15 Structures

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2KSV \| pdb_00002ksv	Download File View File

The NMR structure of protein-glutaminase from Chryseobacterium proteolyticum

Kumeta, H., Miwa, N., Ogura, K., Kai, Y., Mizukoshi, T., Shimba, N., Suzuki, E., Inagaki, F.

(2010) J Biomol NMR 46: 251-255

Released	2010-02-16
Method	SOLUTION NMR
Organisms	Chryseobacterium proteolyticum
Macromolecule	Protein-glutaminase (protein)

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5D45 \| pdb_00005d45	Download File View File

Crystal Structure of FABP4 in complex with 3-(5-cyclopropyl-2,3-diphenyl-1H-indol-1-yl)propanoic acid

Tagami, U., Takahashi, K., Igarashi, S., Ejima, C., Yoshida, T., Takeshita, S., Miyanaga, W., Sugiki, M., Tokumasu, M., Hatanaka, T., Kashiwagi, T., Ishikawa, K., Miyano, H., Mizukoshi, T.

(2016) ACS Med Chem Lett 7: 435-439

Released	2016-06-22
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Fatty acid-binding protein, adipocyte (protein)
Unique Ligands	57P

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5D47 \| pdb_00005d47	Download File View File

Crystal Structure of FABP4 in complex with 3-[5-cyclopropyl-3-(3-methoxypyridin-4-yl)-2-phenyl-1H-indol-1-yl] propanoic acid

Tagami, U., Takahashi, K., Igarashi, S., Ejima, C., Yoshida, T., Takeshita, S., Miyanaga, W., Sugiki, M., Tokumasu, M., Hatanaka, T., Kashiwagi, T., Ishikawa, K., Miyano, H., Mizukoshi, T.

(2016) ACS Med Chem Lett 7: 435-439

Released	2016-06-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Fatty acid-binding protein, adipocyte (protein)
Unique Ligands	L19

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5D48 \| pdb_00005d48	Download File View File

Crystal Structure of FABP4 in complex with 3-{5-cyclopropyl-3-(3,5-dimethyl-1H-pyrazol-4-yl)-2-[3-(propan-2-yloxy) phenyl]-1H-indol-1-yl}propanoic acid

Tagami, U., Takahashi, K., Igarashi, S., Ejima, C., Yoshida, T., Takeshita, S., Miyanaga, W., Sugiki, M., Tokumasu, M., Hatanaka, T., Kashiwagi, T., Ishikawa, K., Miyano, H., Mizukoshi, T.

(2016) ACS Med Chem Lett 7: 435-439

Released	2016-06-22
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Homo sapiens
Macromolecule	Fatty acid-binding protein, adipocyte (protein)
Unique Ligands	L96, PO4

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5D4A \| pdb_00005d4a	Download File View File

Crystal Structure of FABP4 in complex with 3-(2-phenyl-1H-indol-1-yl)propanoic acid

Tagami, U., Takahashi, K., Igarashi, S., Ejima, C., Yoshida, T., Takeshita, S., Miyanaga, W., Sugiki, M., Tokumasu, M., Hatanaka, T., Kashiwagi, T., Ishikawa, K., Miyano, H., Mizukoshi, T.

(2016) ACS Med Chem Lett 7: 435-439

Released	2016-06-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Fatty acid-binding protein, adipocyte (protein)
Unique Ligands	57Q

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5ZBC \| pdb_00005zbc	Download File View File

Crystal structure of Se-Met tryptophan oxidase (C395A mutant) from Chromobacterium violaceum

Yamaguchi, H., Tatsumi, M., Takahashi, K., Tagami, U., Sugiki, M., Kashiwagi, T., Okazaki, S., Mizukoshi, T., Asano, Y.

(2018) J Biochem 164: 359-367

Released	2018-12-19
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Chromobacterium violaceum ATCC 12472
Macromolecule	Flavin-dependent L-tryptophan oxidase VioA (protein)
Unique Ligands	FAD

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5ZBD \| pdb_00005zbd	Download File View File

Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum

Yamaguchi, H., Tatsumi, M., Takahashi, K., Tagami, U., Sugiki, M., Kashiwagi, T., Okazaki, S., Mizukoshi, T., Asano, Y.

(2018) J Biochem 164: 359-367

Released	2018-12-19
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Chromobacterium violaceum ATCC 12472
Macromolecule	Flavin-dependent L-tryptophan oxidase VioA (protein)
Unique Ligands	FAD, TRP

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6ACF \| pdb_00006acf	Download File View File

structure of leucine dehydrogenase from Geobacillus stearothermophilus by cryo-EM

Yamaguchi, H., Kamegawa, A., Nakata, K., Kashiwagi, T., Mizukoshi, T., Fujiyoshi, Y., Tani, K.

(2019) J Struct Biol 205: 11-21

Released	2018-12-26
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Geobacillus stearothermophilus 10
Macromolecule	Leucine dehydrogenase (protein)

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6ACH \| pdb_00006ach	Download File View File

Structure of NAD+-bound leucine dehydrogenase from Geobacillus stearothermophilus by cryo-EM

Yamaguchi, H., Kamegawa, A., Nakata, K., Kashiwagi, T., Mizukoshi, T., Fujiyoshi, Y., Tani, K.

(2019) J Struct Biol 205: 11-21

Released	2018-12-26
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Geobacillus stearothermophilus 10
Macromolecule	Leucine dehydrogenase (protein)
Unique Ligands	NAD

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6LXV \| pdb_00006lxv	Download File View File

Cryo-EM structure of phosphoketolase from Bifidobacterium longum

Nakata, K., Miyazaki, N., Yamaguchi, H., Hirose, M., Miyano, H., Mizukoshi, T., Kashiwagi, T., Iwasaki, K.

(2022) J Struct Biol 214: 107842-107842

Released	2021-02-17
Method	ELECTRON MICROSCOPY 2.1 Å
Organisms	Bifidobacterium longum subsp. longum F8
Macromolecule	Phosphoketolase (protein)
Unique Ligands	CA, TPP

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7C8H \| pdb_00007c8h	Download File View File

Ambient temperature structure of Bifidobacterium longum phosphoketolase with thiamine diphosphate

Nakata, K., Kashiwagi, T., Nango, E., Miyano, H., Mizukoshi, T., Iwata, S.

(2023) Acta Crystallogr D Struct Biol 79: 290-303

Released	2021-06-02
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bifidobacterium longum
Macromolecule	Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (protein)
Unique Ligands	CA, LMR, MLA, SIN, TPP

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7C8I \| pdb_00007c8i	Download File View File

Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate

Nakata, K., Kashiwagi, T., Nango, E., Miyano, H., Mizukoshi, T., Iwata, S.

(2023) Acta Crystallogr D Struct Biol 79: 290-303

Released	2021-06-02
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bifidobacterium longum
Macromolecule	Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (protein)
Unique Ligands	CA, PEP, TPP

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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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8JPW \| pdb_00008jpw	Download File View File

Crystal Structure of Single-chain L-Glutamate Oxidase Mutant from Streptomyces sp. X-119-6

Yamaguchi, H., Takahashi, K., Tatsumi, M., Tagami, U., Mizukoshi, T., Miyano, H., Sugiki, M.

(2023) Enzyme Microb Technol 170: 110287-110287

Released	2023-08-09
Method	X-RAY DIFFRACTION 2.66 Å
Organisms	Streptomyces sp. X-119-6
Macromolecule	L-glutamate oxidase (protein)
Unique Ligands	AKG, FAD, ZN

1 to 15 of 15 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.

2KSV | pdb_00002ksv

The NMR structure of protein-glutaminase from Chryseobacterium proteolyticum

5D45 | pdb_00005d45

Crystal Structure of FABP4 in complex with 3-(5-cyclopropyl-2,3-diphenyl-1H-indol-1-yl)propanoic acid

5D47 | pdb_00005d47

Crystal Structure of FABP4 in complex with 3-[5-cyclopropyl-3-(3-methoxypyridin-4-yl)-2-phenyl-1H-indol-1-yl] propanoic acid

5D48 | pdb_00005d48

Crystal Structure of FABP4 in complex with 3-{5-cyclopropyl-3-(3,5-dimethyl-1H-pyrazol-4-yl)-2-[3-(propan-2-yloxy) phenyl]-1H-indol-1-yl}propanoic acid

5D4A | pdb_00005d4a

Crystal Structure of FABP4 in complex with 3-(2-phenyl-1H-indol-1-yl)propanoic acid

5ZBC | pdb_00005zbc

Crystal structure of Se-Met tryptophan oxidase (C395A mutant) from Chromobacterium violaceum

5ZBD | pdb_00005zbd

Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum

6ACF | pdb_00006acf

structure of leucine dehydrogenase from Geobacillus stearothermophilus by cryo-EM

6ACH | pdb_00006ach

Structure of NAD+-bound leucine dehydrogenase from Geobacillus stearothermophilus by cryo-EM

6LXV | pdb_00006lxv

Cryo-EM structure of phosphoketolase from Bifidobacterium longum

7C8H | pdb_00007c8h

Ambient temperature structure of Bifidobacterium longum phosphoketolase with thiamine diphosphate

7C8I | pdb_00007c8i

Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate

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

8JPW | pdb_00008jpw

Crystal Structure of Single-chain L-Glutamate Oxidase Mutant from Streptomyces sp. X-119-6

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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

2KSV | pdb_00002ksv

5D45 | pdb_00005d45

5D47 | pdb_00005d47

5D48 | pdb_00005d48

5D4A | pdb_00005d4a

5ZBC | pdb_00005zbc

5ZBD | pdb_00005zbd

6ACF | pdb_00006acf

6ACH | pdb_00006ach

6LXV | pdb_00006lxv

7C8H | pdb_00007c8h

7C8I | pdb_00007c8i

7ERU | pdb_00007eru

7ERV | pdb_00007erv

8JPW | pdb_00008jpw