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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yoneda, K."

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Search Summary

This query matches 70 Structures.

Refinements

Structure Determination Methodology

experimental (70)

Scientific Name of Source Organism

	Pyrobaculum calidifontis JCM 11548 (8)
	Gallus gallus (7)
	Pyrococcus horikoshii OT3 (5)
	Lentilactobacillus buchneri (4)
	Thermoplasma volcanium GSS1 (4)
	Bacillus smithii (3)
	Meretrix lusoria (3)
	Pyrobaculum aerophilum (3)
	Pyrobaculum aerophilum str. IM2 (3)
	Thermoplasma volcanium (3)

More...

Taxonomy

	Archaea (37)
	Bacteria (20)
	Eukaryota (14)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (70)

Polymer Entity Type

Protein (70)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (27)
	2.0 - 2.5 (32)
	2.5 - 3.0 (8)

Release Date

	2005 - 2009 (11)
	2010 - 2014 (26)
	2015 - 2019 (21)
	2020 - 2024 (12)

Enzyme Classification Name

	Oxidoreductases (31)
	Hydrolases (12)
	Isomerases (6)
	Transferases (5)
	Lyases (2)

Symmetry Type

	Cyclic (38)
	Asymmetric (23)
	Dihedral (15)

SCOP Classification

	Alpha and beta proteins (a/b) (21)
	Alpha and beta proteins (a+b) (8)
	Artifacts (5)
	All alpha proteins (5)

AllSelected

1 to 25 of 70 Structures

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1VCV \| pdb_00001vcv	Download File View File

Structure of 2-deoxyribose-5-phosphate aldolase from Pyrobaculum aerophilum

Sakuraba, H., Ohshima, T., Tsuge, H.

(2007) Appl Environ Microbiol 73: 7427-7434

Released	2005-08-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrobaculum aerophilum
Macromolecule	Probable deoxyribose-phosphate aldolase (protein)
Unique Ligands	ZN

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1WY6 \| pdb_00001wy6	Download File View File

Crystal Structure of Hypothetical Protein [ST1625p] from Hyperthermophilic Archaeon Sulfolobus tokodaii

Yoneda, K., Sakuraba, H., Tsuge, H., Katunuma, N., Kuramitsu, S., Kawabata, T., Ohshima, T.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 636-639

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	hypothetical protein ST1625 (protein)

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1WZU \| pdb_00001wzu	Download File View File

Crystal structure of quinolinate synthase (nadA)

Sakuraba, H.

(2005) J Biological Chem 280: 26645-26648

Released	2005-06-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Quinolinate synthetase A (protein)
Unique Ligands	MLT

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2DC1 \| pdb_00002dc1	Download File View File

Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus

Yoneda, K., Sakuraba, H., Tsuge, H., Ohshima, T.

(2007) FEBS J 274: 4315-4325

Released	2006-12-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	L-aspartate dehydrogenase (protein)
Unique Ligands	CIT, NAD

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2E5V \| pdb_00002e5v	Download File View File

Crystal structure of L-Aspartate Oxidase from hyperthermophilic archaeon Sulfolobus tokodaii

Yoneda, K., Sakuraba, H., Asai, I., Tsuge, H., Katunuma, N., Ohshima, T.

(2008) Biochim Biophys Acta 1784: 563-571

Released	2008-01-01
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	L-aspartate oxidase (protein)
Unique Ligands	CL, FAD

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2YVS \| pdb_00002yvs	Download File View File

Crystal structure of glycolate oxidase subunit GlcE from Thermus thermophilus HB8

Yoneda, K., Sakuraba, H., Kuramitsu, S., Ohshima, T.

To be published

Released	2008-04-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Glycolate oxidase subunit GlcE (protein)

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2YY7 \| pdb_00002yy7	Download File View File

Crystal structure of thermolabile L-threonine dehydrogenase from Flavobacterium frigidimaris KUC-1

Yoneda, K., Sakuraba, H., Oikawa, T., Muraoka, I., Ohshima, T.

(2010) FEBS J 277: 5124-5132

Released	2008-04-29
Method	X-RAY DIFFRACTION 2.061 Å
Organisms	Flavobacterium frigidimaris
Macromolecule	L-threonine dehydrogenase (protein)
Unique Ligands	GOL, MES, NAD, PE8

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2ZC0 \| pdb_00002zc0	Download File View File

Crystal structure of an archaeal alanine:glyoxylate aminotransferase

Sakuraba, H., Yoneda, K., Tsuge, H., Ohshima, T.

(2008) Acta Crystallogr D Biol Crystallogr 64: 696-699

Released	2008-06-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermococcus litoralis
Macromolecule	Alanine glyoxylate transaminase (protein)
Unique Ligands	IMD, PMP, ZN

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2ZPO \| pdb_00002zpo	Download File View File

Crystal Structure of Green Turtle Egg White Ribonuclease

Katekaew, S., Kakuta, Y., Torikata, T., Kimura, M., Yoneda, K., Araki, T.

To be published

Released	2008-08-19
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Chelonia mydas
Macromolecule	Ribonuclease (protein)
Unique Ligands	GOL, SO4

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2ZVR \| pdb_00002zvr	Download File View File

Crystal structure of a D-tagatose 3-epimerase-related protein from Thermotoga maritima

Sakuraba, H., Ohshima, T.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 199-203

Released	2009-03-10
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermotoga maritima
Macromolecule	Uncharacterized protein TM_0416 (protein)

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3A1N \| pdb_00003a1n	Download File View File

Crystal structure of L-Threonine dehydrogenase from Hyperthermophilic Archaeon Thermoplasma volcanium

Yoneda, K., Sakuraba, H., Ohshima, T.

(2012) J Biological Chem 287: 12966-12974

Released	2010-03-31
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Thermoplasma volcanium
Macromolecule	NDP-sugar epimerase (protein)
Unique Ligands	NAD

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3A4V \| pdb_00003a4v	Download File View File

Crystal structure of pyruvate bound L-Threonine dehydrogenase from Hyperthermophilic Archaeon Thermoplasma volcanium

Yoneda, K., Sakuraba, H., Ohshima, T.

(2012) J Biological Chem 287: 12966-12974

Released	2010-07-28
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Thermoplasma volcanium
Macromolecule	NDP-sugar epimerase (protein)
Unique Ligands	MPD, NAD, PYR

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3A9G \| pdb_00003a9g	Download File View File

Crystal Structure of PQQ-dependent sugar dehydrogenase apo-form

Sakuraba, H., Yokono, K., Yoneda, K., Ohshima, T.

(2010) Arch Biochem Biophys 502: 81-88

Released	2010-09-08
Method	X-RAY DIFFRACTION 2.39 Å
Organisms	Pyrobaculum aerophilum
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	CA
Unique branched monosaccharides	GLC

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3A9H \| pdb_00003a9h	Download File View File

Crystal Structure of PQQ-dependent sugar dehydrogenase holo-form

Sakuraba, H., Yokono, K., Yoneda, K., Ohshima, T.

(2010) Arch Biochem Biophys 502: 81-88

Released	2010-09-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pyrobaculum aerophilum
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	CA, PQQ
Unique branched monosaccharides	GLC

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3A9W \| pdb_00003a9w	Download File View File

Crystal structure of L-Threonine bound L-Threonine dehydrogenase (Y137F) from Hyperthermophilic Archaeon Thermoplasma volcanium

Yoneda, K., Sakuraba, H., Ohshima, T.

(2012) J Biological Chem 287: 12966-12974

Released	2010-11-10
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Thermoplasma volcanium
Macromolecule	NDP-sugar epimerase (protein)
Unique Ligands	MPD, MRD, NAD, THR

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3AB6 \| pdb_00003ab6	Download File View File

Crystal structure of NAG3 bound lysozyme from Meretrix lusoria

Yoneda, K., Kuwano, Y., Araki, T.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1202-1206

Released	2010-12-01
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Meretrix lusoria
Macromolecule	Lysozyme (protein)
Unique branched monosaccharides	NAG

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3ABI \| pdb_00003abi	Download File View File

Crystal Structure of L-Lysine Dehydrogenase from Hyperthermophilic Archaeon Pyrococcus horikoshii

Yoneda, K., Sakuraba, H., Fukuda, J., Ohshima, T.

(2010) J Biological Chem 285: 8444-8453

Released	2009-12-29
Method	X-RAY DIFFRACTION 2.44 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Putative uncharacterized protein PH1688 (protein)
Unique Ligands	NAD, SO4

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3AJR \| pdb_00003ajr	Download File View File

Crystal structure of L-3-Hydroxynorvaline bound L-Threonine dehydrogenase (Y137F) from Hyperthermophilic Archaeon Thermoplasma volcanium

Yoneda, K., Sakuraba, H., Ohshima, T.

(2012) J Biological Chem 287: 12966-12974

Released	2011-06-15
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Thermoplasma volcanium GSS1
Macromolecule	NDP-sugar epimerase (protein)
Unique Ligands	MPD, NAD, VAH

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3AW5 \| pdb_00003aw5	Download File View File

Structure of a multicopper oxidase from the hyperthermophilic archaeon Pyrobaculum aerophilum

Sakuraba, H., Ohshima, T., Yoneda, K.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 753-757

Released	2011-06-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrobaculum aerophilum str. IM2
Macromolecule	Multicopper oxidase (protein)
Unique Ligands	ACT, C2O, CU

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3AW9 \| pdb_00003aw9	Download File View File

Structure of UDP-galactose 4-epimerase mutant

Sakuraba, H., Kawai, T., Yoneda, K., Ohshima, T.

To be published

Released	2012-02-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pyrobaculum calidifontis JCM 11548
Macromolecule	NAD-dependent epimerase/dehydratase (protein)
Unique Ligands	GDU, NAD