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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yoshida, H."

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Search Summary

This query matches 140 Structures.

Refinements

Structure Determination Methodology

experimental (140)

Scientific Name of Source Organism

	Stutzerimonas stutzeri (20)
	Homo sapiens (12)
	Pseudomonas cichorii (12)
	Mesorhizobium japonicum MAFF 303099 (10)
	Thermoactinomyces vulgaris (8)
	Staphylococcus equorum (7)
	Methylomonas sp. DH-1 (6)
	Acinetobacter sp. DL-28 (5)
	Escherichia coli K-12 (5)
	Cellulomonas parahominis (4)

More...

Taxonomy

	Bacteria (100)
	Eukaryota (31)
	Archaea (4)
	other sequences (4)
	Duplodnaviria (2)
	Riboviria (2)

Experimental Method

	X-RAY DIFFRACTION (136)
	SOLUTION NMR (3)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (140)
	RNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (82)
	2.0 - 2.5 (29)
	2.5 - 3.0 (16)
	3.0 - 3.5 (5)

Release Date

	1990 - 1994 (2)
	2005 - 2009 (26)
	2010 - 2014 (59)
	2015 - 2019 (28)
	2020 - 2024 (24)
	2025 - 2029 (1)

Enzyme Classification Name

	Isomerases (51)
	Oxidoreductases (25)
	Hydrolases (15)
	Transferases (7)
	Lyases (3)
	Ligases (1)

Membrane Protein Annotation

	OPM (1)
	PDBTM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (55)
	Cyclic (42)
	Dihedral (45)

SCOP Classification

	All beta proteins (22)
	Alpha and beta proteins (a+b) (7)
	Alpha and beta proteins (a/b) (13)
	All alpha proteins (4)
	Artifacts (2)
	Multi-domain proteins (alpha and beta) (1)
	Peptides (1)

AllSelected

1 to 25 of 140 Structures

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1RCK \| pdb_00001rck	Download File View File

THE THREE DIMENSIONAL STRUCTURE OF GUANINE-SPECIFIC RIBONUCLEASE F1 IN SOLUTION DETERMINED BY NMR SPECTROSCOPY AND DISTANCE GEOMETRY

Nakai, T., Yoshikawa, W., Nakamura, H., Yoshida, H.

(1992) Eur J Biochem 208: 41-51

Released	1994-11-30
Method	SOLUTION NMR
Organisms	Fusarium fujikuroi
Macromolecule	RIBONUCLEASE F1 (protein)

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1RCL \| pdb_00001rcl	Download File View File

THE THREE DIMENSIONAL STRUCTURE OF GUANINE-SPECIFIC RIBONUCLEASE F1 IN SOLUTION DETERMINED BY NMR SPECTROSCOPY AND DISTANCE GEOMETRY

Nakai, T., Yoshikawa, W., Nakamura, H., Yoshida, H.

(1992) Eur J Biochem 208: 41-51

Released	1994-11-30
Method	SOLUTION NMR
Organisms	Fusarium fujikuroi
Macromolecule	RIBONUCLEASE F1 (protein)

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2BA3 \| pdb_00002ba3	Download File View File

NMR Structure of NikA N-terminal Fragment

Yoshida, H., Furuya, N., Lin, Y.J., Guntert, P., Komano, T., Kainosho, M.

To be published

Released	2006-10-03
Method	SOLUTION NMR
Organisms	Plasmid R64
Macromolecule	NikA (protein)

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2D0F \| pdb_00002d0f	Download File View File

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N complexed with P2, a pullulan model oligosaccharide

Abe, A., Yoshida, H., Tonozuka, T., Sakano, Y., Kamitori, S.

(2005) FEBS J 272: 6145-6153

Released	2006-07-11
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Thermoactinomyces vulgaris
Macromolecule	alpha-amylase I (protein)
Unique Ligands	CA, MPD
Unique branched monosaccharides	BGC, GLC

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2D0G \| pdb_00002d0g	Download File View File

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P5, a pullulan model oligosaccharide

Abe, A., Yoshida, H., Tonozuka, T., Sakano, Y., Kamitori, S.

(2005) FEBS J 272: 6145-6153

Released	2006-07-11
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermoactinomyces vulgaris
Macromolecule	alpha-amylase I (protein)
Unique Ligands	BGC, CA, GLC, MPD
Unique branched monosaccharides	BGC, GLC

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2D0H \| pdb_00002d0h	Download File View File

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P2, a pullulan model oligosaccharide

Abe, A., Yoshida, H., Tonozuka, T., Sakano, Y., Kamitori, S.

(2005) FEBS J 272: 6145-6153

Released	2006-07-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermoactinomyces vulgaris
Macromolecule	alpha-amylase I (protein)
Unique Ligands	CA, MPD
Unique branched monosaccharides	GLC

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2D2O \| pdb_00002d2o	Download File View File

Structure of a complex of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with maltohexaose demonstrates the important role of aromatic residues at the reducing end of the substrate binding cleft

Ohtaki, A., Mizuno, M., Yoshida, H., Tonozuka, T., Sakano, Y., Kamitori, S.

(2006) Carbohydr Res 341: 1041-1046

Released	2006-08-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermoactinomyces vulgaris
Macromolecule	Neopullulanase 2 (protein)
Unique Ligands	CA
Unique branched monosaccharides	GLC

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2E6K \| pdb_00002e6k	Download File View File

X-ray structure of Thermus thermopilus HB8 TT0505

Yoshida, H., Kamitori, S., Agari, Y., Iino, H., Kanagawa, M., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-11-13
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Transketolase (protein)

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2ECE \| pdb_00002ece	Download File View File

X-ray structure of hypothetical selenium-binding protein from Sulfolobus tokodaii, ST0059

Yamada, M., Yoshida, H., Kuramitsu, S., Kamitori, S.

To be published

Released	2008-01-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	462aa long hypothetical selenium-binding protein (protein)

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2EIS \| pdb_00002eis	Download File View File

X-ray structure of acyl-CoA hydrolase-like protein, TT1379, from Thermus thermophilus HB8

Kamitori, S., Yoshida, H., Satoh, S., Iino, H., Ebihara, A., Chen, L., Fu, Z.-Q., Chrzas, J., Wang, B.-C., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-03-18
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Hypothetical protein TTHB207 (protein)
Unique Ligands	COA

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2HCV \| pdb_00002hcv	Download File View File

Crystal structure of L-rhamnose isomerase from Pseudomonas stutzeri with metal ion

Yoshida, H., Yamada, M., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 365: 1505-1516

Released	2006-12-19
Method	X-RAY DIFFRACTION 2 Å
Organisms	Stutzerimonas stutzeri
Macromolecule	L-rhamnose isomerase (protein)
Unique Ligands	ZN

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2I56 \| pdb_00002i56	Download File View File

Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose

Yoshida, H., Yamada, M., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 365: 1505-1516

Released	2006-12-19
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Stutzerimonas stutzeri
Macromolecule	L-rhamnose isomerase (protein)
Unique Ligands	RNS, ZN

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2I57 \| pdb_00002i57	Download File View File

Crystal Structure of L-Rhamnose Isomerase from Pseudomonas stutzeri in Complex with D-Allose

Yoshida, H., Yamada, M., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 365: 1505-1516

Released	2006-12-19
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Stutzerimonas stutzeri
Macromolecule	L-rhamnose isomerase (protein)
Unique Ligands	AOS, ZN

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2OHD \| pdb_00002ohd	Download File View File

Crystal structure of hypothetical molybdenum cofactor biosynthesis protein C from Sulfolobus tokodaii

Yoshida, H., Yamada, M., Kuramitsu, S., Kamitori, S.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 589-592

Released	2007-11-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	Probable molybdenum cofactor biosynthesis protein C (protein)

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2OU4 \| pdb_00002ou4	Download File View File

Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii

Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 374: 443-453

Released	2007-12-25
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pseudomonas cichorii
Macromolecule	D-tagatose 3-epimerase (protein)
Unique Ligands	MN

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2QUL \| pdb_00002qul	Download File View File

Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii at 1.79 A resolution

Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 374: 443-453

Released	2007-12-25
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Pseudomonas cichorii
Macromolecule	D-tagatose 3-epimerase (protein)
Unique Ligands	MN

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2QUM \| pdb_00002qum	Download File View File

Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii with D-tagatose

Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 374: 443-453

Released	2007-12-25
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Pseudomonas cichorii
Macromolecule	D-tagatose 3-epimerase (protein)
Unique Ligands	MN, TAG

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2QUN \| pdb_00002qun	Download File View File

Crystal Structure of D-tagatose 3-epimerase from Pseudomonas cichorii in Complex with D-fructose

Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 374: 443-453

Released	2007-12-25
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Pseudomonas cichorii
Macromolecule	D-tagatose 3-epimerase (protein)
Unique Ligands	FUD, MN

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2X1C \| pdb_00002x1c	Download File View File

The crystal structure of precursor acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum

Bokhove, M., Yoshida, H., Hensgens, C.M.H., van der Laan, J.M., Sutherland, J.D., Dijkstra, B.W.

(2010) Structure 18: 301

Released	2010-03-09
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Penicillium chrysogenum
Macromolecule	ACYL-COENZYME (protein)
Unique Ligands	CL, GOL, SO4

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2X1D \| pdb_00002x1d	Download File View File

The crystal structure of mature acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum

Bokhove, M., Yoshida, H., Hensgens, C.M.H., van der Laan, J.M., Sutherland, J.D., Dijkstra, B.W.

(2010) Structure 18: 301

Released	2010-03-09
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Penicillium chrysogenum
Macromolecule	ACYL-COENZYME (protein)
Unique Ligands	ACT, CL, D1D, GOL, PO4

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2X1E \| pdb_00002x1e	Download File View File

The crystal structure of mature acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum in complex 6- aminopenicillanic acid

Bokhove, M., Yoshida, H., Hensgens, C.M.H., van der Laan, J.M., Sutherland, J.D., Dijkstra, B.W.

(2010) Structure 18: 301

Released	2010-03-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Penicillium chrysogenum
Macromolecule	ACYL-COENZYME (protein)
Unique Ligands	CL, GOL, PO4, X1E

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2Z8G \| pdb_00002z8g	Download File View File

Aspergillus niger ATCC9642 isopullulanase complexed with isopanose

Mizuno, M., Koide, A., Yamamura, A., Akeboshi, H., Yoshida, H., Kamitori, S., Sakano, Y., Nishikawa, A., Tonozuka, T.

(2008) J Mol Biology 376: 210-220

Released	2007-12-18
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Aspergillus niger
Macromolecule	Isopullulanase (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BGC, GLC

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2ZKN \| pdb_00002zkn	Download File View File

X-ray structure of mutant galectin-1/lactose complex

Abe, A., Yoshida, H., Kamitori, S.

(2008) Glycobiology 18: 1065-1073

Released	2008-09-30
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Homo sapiens
Macromolecule	Galectin-1 (protein)
Unique branched monosaccharides	BGC, GAL

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2ZNL \| pdb_00002znl	Download File View File

Crystal structure of PA-PB1 complex form influenza virus RNA polymerase

Obayashi, E., Yoshida, H., Kawai, F., Shibayama, N., Kawaguchi, A., Nagata, K., Tame, J.R.H., Park, S.-Y.

(2008) Nature 454: 1127-1131

Released	2008-09-02
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Macromolecule	Polymerase acidic protein (protein) RNA-directed RNA polymerase catalytic subunit (protein)

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2ZYK \| pdb_00002zyk	Download File View File

Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin

Tonozuka, T., Sogawa, A., Yamada, M., Matsumoto, N., Yoshida, H., Kamitori, S., Ichikawa, K., Mizuno, M., Nishikawa, A., Sakano, Y.

(2007) FEBS J 274: 2109-2120

Released	2009-02-10
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermoactinomyces vulgaris
Macromolecule	Solute-binding protein (protein)
Unique branched monosaccharides	GLC

1 to 25 of 140 Structures

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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

1RCK | pdb_00001rck

1RCL | pdb_00001rcl

2BA3 | pdb_00002ba3

2D0F | pdb_00002d0f

2D0G | pdb_00002d0g

2D0H | pdb_00002d0h

2D2O | pdb_00002d2o

2E6K | pdb_00002e6k

2ECE | pdb_00002ece

2EIS | pdb_00002eis

2HCV | pdb_00002hcv

2I56 | pdb_00002i56

2I57 | pdb_00002i57

2OHD | pdb_00002ohd

2OU4 | pdb_00002ou4

2QUL | pdb_00002qul

2QUM | pdb_00002qum

2QUN | pdb_00002qun

2X1C | pdb_00002x1c

2X1D | pdb_00002x1d

2X1E | pdb_00002x1e

2Z8G | pdb_00002z8g

2ZKN | pdb_00002zkn

2ZNL | pdb_00002znl

2ZYK | pdb_00002zyk