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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Wakagi, T."

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Search Summary

This query matches 131 Structures.

Refinements

Structure Determination Methodology

experimental (131)

Scientific Name of Source Organism

	Pseudomonas fluorescens (11)
	Sulfurisphaera tokodaii str. 7 (10)
	Bifidobacterium longum (9)
	Bifidobacterium breve (8)
	Aspergillus aculeatus (7)
	Aspergillus luchuensis (7)
	Halalkalibacterium halodurans C-125 (7)
	Thermococcus litoralis (7)
	Bifidobacterium bifidum JCM 1254 (6)
	Bifidobacterium longum subsp. longum JCM 1217 (6)

More...

Taxonomy

	Bacteria (90)
	Archaea (23)
	Eukaryota (18)

Experimental Method

	X-RAY DIFFRACTION (130)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (131)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (56)
	2.0 - 2.5 (60)
	2.5 - 3.0 (11)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (37)
	2005 - 2009 (35)
	2010 - 2014 (41)
	2015 - 2019 (8)
	2020 - 2024 (8)

Enzyme Classification Name

	Hydrolases (64)
	Transferases (27)
	Lyases (17)
	Oxidoreductases (12)
	Isomerases (3)

Symmetry Type

	Cyclic (87)
	Asymmetric (52)
	Dihedral (7)
	Octahedral (2)

SCOP Classification

	Alpha and beta proteins (a+b) (13)
	All beta proteins (29)
	Alpha and beta proteins (a/b) (23)
	All alpha proteins (22)
	Artifacts (5)
	Multi-domain proteins (alpha and beta) (3)

AllSelected

1 to 25 of 131 Structures

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1BK1 \| pdb_00001bk1	Download File View File

ENDO-1,4-BETA-XYLANASE C

Fushinobu, S., Ito, K., Konno, M., Wakagi, T., Matsuzawa, H.

(1998) Protein Eng 11: 1121-1128

Released	1999-01-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Aspergillus luchuensis
Macromolecule	ENDO-1,4-B-XYLANASE C (protein)

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1EZ4 \| pdb_00001ez4	Download File View File

CRYSTAL STRUCTURE OF NON-ALLOSTERIC L-LACTATE DEHYDROGENASE FROM LACTOBACILLUS PENTOSUS AT 2.3 ANGSTROM RESOLUTION

Uchikoba, H., Fushinobu, S., Wakagi, T., Konno, M., Taguchi, H., Matsuzawa, H.

(2002) Proteins 46: 206-214

Released	2001-12-28
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Lactiplantibacillus pentosus
Macromolecule	LACTATE DEHYDROGENASE (protein)
Unique Ligands	NAD

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1GC5 \| pdb_00001gc5	Download File View File

CRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERMOCOCCUS LITORALIS

Ito, S., Fushinobu, S., Yoshioka, I., Koga, S., Matsuzawa, H., Wakagi, T.

(2001) Structure 9: 205-214

Released	2001-07-25
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermococcus litoralis
Macromolecule	ADP-DEPENDENT GLUCOKINASE (protein)
Unique Ligands	ADP

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1IRE \| pdb_00001ire	Download File View File

Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila

Miyanaga, A., Fushinobu, S., Ito, K., Wakagi, T.

(2001) Biochem Biophys Res Commun 288: 1169-1174

Released	2002-10-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudonocardia thermophila
Macromolecule	Nitrile Hydratase (protein)
Unique Ligands	CO

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1IUN \| pdb_00001iun	Download File View File

meta-Cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) S103A mutant hexagonal

Fushinobu, S., Saku, T., Hidaka, M., Jun, S.-Y., Nojiri, H., Yamane, H., Shoun, H., Omori, T., Wakagi, T.

(2002) Protein Sci 11: 2184-2195

Released	2002-09-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Pseudomonas fluorescens
Macromolecule	meta-Cleavage product hydrolase (protein)
Unique Ligands	ACT

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1IUO \| pdb_00001iuo	Download File View File

meta-Cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) S103A mutant complexed with acetates

Fushinobu, S., Saku, T., Hidaka, M., Jun, S.-Y., Nojiri, H., Yamane, H., Shoun, H., Omori, T., Wakagi, T.

(2002) Protein Sci 11: 2184-2195

Released	2002-09-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas fluorescens
Macromolecule	meta-Cleavage product hydrolase (protein)
Unique Ligands	ACT

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1IUP \| pdb_00001iup	Download File View File

meta-Cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) S103A mutant complexed with isobutyrates

Fushinobu, S., Saku, T., Hidaka, M., Jun, S.-Y., Nojiri, H., Yamane, H., Shoun, H., Omori, T., Wakagi, T.

(2002) Protein Sci 11: 2184-2195

Released	2002-09-18
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Pseudomonas fluorescens
Macromolecule	meta-Cleavage product hydrolase (protein)
Unique Ligands	ALQ

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1IYO \| pdb_00001iyo	Download File View File

Toho-1 beta-Lactamase In Complex With Cefotaxime

Shimamura, T., Ibuka, A., Fushinobu, S., Wakagi, T., Ishiguro, M., Ishii, Y., Matsuzawa, H.

(2002) J Biological Chem 277: 46601-46608

Released	2002-12-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	Toho-1 beta-lactamase (protein)
Unique Ligands	CEF, SO4

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1IYP \| pdb_00001iyp	Download File View File

Toho-1 beta-Lactamase In Complex With Cephalothin

Shimamura, T., Ibuka, A., Fushinobu, S., Wakagi, T., Ishiguro, M., Ishii, Y., Matsuzawa, H.

(2002) J Biological Chem 277: 46601-46608

Released	2002-12-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	Toho-1 beta-lactamase (protein)
Unique Ligands	CEP, SO4

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1IYQ \| pdb_00001iyq	Download File View File

Toho-1 beta-Lactamase In Complex With Benzylpenicillin

Shimamura, T., Ibuka, A., Fushinobu, S., Wakagi, T., Ishiguro, M., Ishii, Y., Matsuzawa, H.

(2002) J Biological Chem 277: 46601-46608

Released	2002-12-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	Toho-1 beta-lactamase (protein)
Unique Ligands	PNM, SO4

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1J1I \| pdb_00001j1i	Download File View File

Crystal structure of a His-tagged Serine Hydrolase Involved in the Carbazole Degradation (CarC enzyme)

Habe, H., Morii, K., Fushinobu, S., Nam, J.W., Ayabe, Y., Yoshida, T., Wakagi, T., Yamane, H., Nojiri, H., Omori, T.

(2003) Biochem Biophys Res Commun 303: 631-639

Released	2003-06-17
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Janthinobacterium
Macromolecule	meta cleavage compound hydrolase (protein)

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1J30 \| pdb_00001j30	Download File View File

The crystal structure of sulerythrin, a rubrerythrin-like protein from a strictly aerobic and thermoacidiphilic archaeon

Fushinobu, S., Shoun, H., Wakagi, T.

(2003) Biochemistry 42: 11707-11715

Released	2003-10-14
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	144aa long hypothetical rubrerythrin (protein)
Unique Ligands	FE, OXY, ZN

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1J3P \| pdb_00001j3p	Download File View File

Crystal structure of Thermococcus litoralis phosphoglucose isomerase

Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

To be published

Released	2004-02-24
Method	X-RAY DIFFRACTION 2.02 Å
Organisms	Thermococcus litoralis
Macromolecule	Phosphoglucose Isomerase (protein)
Unique Ligands	FE

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1J3Q \| pdb_00001j3q	Download File View File

Crystal structure of Thermococcus litoralis phosphogrucose isomerase soaked with FeSO4

Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

To be published

Released	2004-02-24
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Thermococcus litoralis
Macromolecule	Phosphoglucose Isomerase (protein)
Unique Ligands	FE

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1J3R \| pdb_00001j3r	Download File View File

Crystal structure of Thermococcus litoralis phosphogrucose isomerase complexed with gluconate-6-phosphate

Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

To be published

Released	2004-02-24
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Thermococcus litoralis
Macromolecule	Phosphoglucose Isomerase (protein)
Unique Ligands	6PG, FE

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1K1W \| pdb_00001k1w	Download File View File

Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis

Imamura, H., Fushinobu, S., Kumasaka, T., Yamamoto, M., Jeon, B.S., Wakagi, T., Matsuzawa, H.

(2003) J Biological Chem 278: 19378-19386

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermococcus litoralis
Macromolecule	4-ALPHA-GLUCANOTRANSFERASE (protein)
Unique Ligands	CA, GLC, SO4

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1K1X \| pdb_00001k1x	Download File View File

Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis

Imamura, H., Fushinobu, S., Kumasaka, T., Yamamoto, M., Jeon, B.S., Wakagi, T., Matsuzawa, H.

(2003) J Biological Chem 278: 19378-19386

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermococcus litoralis
Macromolecule	4-ALPHA-GLUCANOTRANSFERASE (protein)
Unique Ligands	CA, TRS

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1K1Y \| pdb_00001k1y	Download File View File

Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose

Imamura, H., Fushinobu, S., Kumasaka, T., Yamamoto, M., Jeon, B.S., Wakagi, T., Matsuzawa, H.

(2003) J Biological Chem 278: 19378-19386

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermococcus litoralis
Macromolecule	4-ALPHA-GLUCANOTRANSFERASE (protein)
Unique Ligands	CA, TRS
Unique branched monosaccharides	AC1, GLC

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1KFA \| pdb_00001kfa	Download File View File

Crystal structure of Fab fragment complexed with gibberellin A4

Murata, T., Fushinobu, S., Nakajima, M., Asami, O., Sassa, T., Wakagi, T., Yamaguchi, I.

(2002) Biochem Biophys Res Commun 293: 489-496

Released	2002-09-11
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mus musculus
Macromolecule	monoclonal antibody heavy chain (protein) monoclonal antibody light chain (protein)
Unique Ligands	GA4

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1KWG \| pdb_00001kwg	Download File View File

Crystal structure of Thermus thermophilus A4 beta-galactosidase

Hidaka, M., Fushinobu, S., Ohtsu, N., Motoshima, H., Matsuzawa, H., Shoun, H., Wakagi, T.

(2002) J Mol Biology 322: 79-91

Released	2002-09-18
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Thermus thermophilus
Macromolecule	BETA-GALACTOSIDASE (protein)
Unique Ligands	ACT, CL, MPD, ZN

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1KWK \| pdb_00001kwk	Download File View File

Crystal structure of Thermus thermophilus A4 beta-galactosidase in complex with galactose

Hidaka, M., Fushinobu, S., Ohtsu, N., Motoshima, H., Matsuzawa, H., Shoun, H., Wakagi, T.

(2002) J Mol Biology 322: 79-91

Released	2002-10-02
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	BETA-GALACTOSIDASE (protein)
Unique Ligands	ACT, CL, GAL, MPD, ZN

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1UA4 \| pdb_00001ua4	Download File View File

Crystal Structure of an ADP-dependent Glucokinase from Pyrococcus furiosus

Ito, S., Jeong, J.J., Yoshioka, I., Koga, S., Fushinobu, S., Shoun, H., Wakagi, T.

(2003) J Mol Biology 331: 871-883

Released	2004-02-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pyrococcus furiosus
Macromolecule	ADP-dependent glucokinase (protein)
Unique Ligands	AMP, BGC, GLC

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1UGP \| pdb_00001ugp	Download File View File

Crystal structure of Co-type nitrile hydratase complexed with n-butyric acid

Miyanaga, A., Fushinobu, S., Ito, K., Shoun, H., Wakagi, T.

(2004) Eur J Biochem 271: 429-438

Released	2004-06-17
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Pseudonocardia thermophila
Macromolecule	Cobalt-containing nitrile hydratase subunit alpha (protein) Cobalt-containing nitrile hydratase subunit beta (protein)
Unique Ligands	BUA, CO

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1UGQ \| pdb_00001ugq	Download File View File

Crystal structure of apoenzyme of Co-type nitrile hydratase

Miyanaga, A., Fushinobu, S., Ito, K., Shoun, H., Wakagi, T.

(2004) Eur J Biochem 271: 429-438

Released	2004-06-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudonocardia thermophila
Macromolecule	Nitrile Hydratase alpha subunit (protein) Nitrile Hydratase beta subunit (protein)

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1UGR \| pdb_00001ugr	Download File View File

Crystal structure of aT109S mutant of Co-type nitrile hydratase

Miyanaga, A., Fushinobu, S., Ito, K., Shoun, H., Wakagi, T.

(2004) Eur J Biochem 271: 429-438

Released	2004-06-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudonocardia thermophila
Macromolecule	Nitrile Hydratase alpha subunit (protein) Nitrile Hydratase beta subunit (protein)
Unique Ligands	CO

1 to 25 of 131 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

Symmetry Type

SCOP Classification

1BK1 | pdb_00001bk1

1EZ4 | pdb_00001ez4

1GC5 | pdb_00001gc5

1IRE | pdb_00001ire

1IUN | pdb_00001iun

1IUO | pdb_00001iuo

1IUP | pdb_00001iup

1IYO | pdb_00001iyo

1IYP | pdb_00001iyp

1IYQ | pdb_00001iyq

1J1I | pdb_00001j1i

1J30 | pdb_00001j30

1J3P | pdb_00001j3p

1J3Q | pdb_00001j3q

1J3R | pdb_00001j3r

1K1W | pdb_00001k1w

1K1X | pdb_00001k1x

1K1Y | pdb_00001k1y

1KFA | pdb_00001kfa

1KWG | pdb_00001kwg

1KWK | pdb_00001kwk

1UA4 | pdb_00001ua4

1UGP | pdb_00001ugp

1UGQ | pdb_00001ugq

1UGR | pdb_00001ugr