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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yohda, M."

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Search Summary

This query matches 86 Structures.

Refinements

Structure Determination Methodology

experimental (86)

Scientific Name of Source Organism

	Rhodococcus erythropolis (20)
	Bos taurus (13)
	Thiobacillus thioparus (8)
	Sulfurisphaera tokodaii str. 7 (6)
	Thermococcus sp. JCM 11816 (6)
	Corynebacterium sp. (4)
	Homo sapiens (4)
	Pyrococcus horikoshii OT3 (4)
	Photobacterium kishitanii (3)
	Rhodococcus sp. N-771 (2)

More...

Taxonomy

	Bacteria (43)
	Archaea (20)
	Eukaryota (20)
	Riboviria (2)

Experimental Method

	X-RAY DIFFRACTION (85)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (86)

Refinement Resolution (Å)

	1.0 - 1.5 (25)
	1.5 - 2.0 (31)
	2.0 - 2.5 (19)
	2.5 - 3.0 (5)
	3.0 - 3.5 (4)
	> 4.5 (2)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (8)
	2005 - 2009 (26)
	2010 - 2014 (29)
	2015 - 2019 (17)
	2020 - 2024 (4)
	2025 - 2029 (1)

Enzyme Classification Name

	Lyases (21)
	Hydrolases (14)
	Isomerases (7)
	Oxidoreductases (6)

Symmetry Type

	Asymmetric (43)
	Cyclic (33)
	Dihedral (20)
	Helical (2)
	Octahedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (16)
	Alpha and beta proteins (a+b) (26)
	All beta proteins (28)
	All alpha proteins (8)
	Small proteins (9)
	Artifacts (1)

AllSelected

1 to 25 of 86 Structures

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1IOK \| pdb_00001iok	Download File View File

CRYSTAL STRUCTURE OF CHAPERONIN-60 FROM PARACOCCUS DENITRIFICANS

Fukami, T.A., Yohda, M., Taguchi, H., Yoshida, M., Miki, K.

(2001) J Mol Biology 312: 501-509

Released	2001-10-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Paracoccus denitrificans
Macromolecule	CHAPERONIN 60 (protein)

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1IU9 \| pdb_00001iu9	Download File View File

Crystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3

Liu, L., Iwata, K., Yohda, M., Miki, K.

(2002) FEBS Lett 528: 114-118

Released	2003-09-09
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	aspartate racemase (protein)
Unique Ligands	CA

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1JFL \| pdb_00001jfl	Download File View File

CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA

Liu, L.J., Iwata, K., Kita, A., Kawarabayasi, Y., Yohda, M., Miki, K.

(2002) J Mol Biology 319: 479-489

Released	2002-06-05
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	ASPARTATE RACEMASE (protein)

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1Q2V \| pdb_00001q2v	Download File View File

Crystal structure of the chaperonin from Thermococcus strain KS-1 (nucleotide-free form)

Shomura, Y., Yoshida, T., Iizuka, R., Yohda, M., Maruyama, T., Miki, K.

(2004) J Mol Biology 335: 1265-1278

Released	2004-01-27
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermococcus sp. JCM 11816
Macromolecule	Thermosome alpha subunit (protein)
Unique Ligands	SO4

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1Q3Q \| pdb_00001q3q	Download File View File

Crystal structure of the chaperonin from Thermococcus strain KS-1 (two-point mutant complexed with AMP-PNP)

Shomura, Y., Yoshida, T., Iizuka, R., Maruyama, T., Yohda, M., Miki, K.

(2004) J Mol Biology 335: 1265-1278

Released	2004-01-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermococcus sp. JCM 11816
Macromolecule	Thermosome alpha subunit (protein)
Unique Ligands	ANP, MG

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1Q3R \| pdb_00001q3r	Download File View File

Crystal structure of the chaperonin from Thermococcus strain KS-1 (nucleotide-free form of single mutant)

Shomura, Y., Yoshida, T., Iizuka, R., Maruyama, T., Yohda, M., Miki, K.

(2004) J Mol Biology 335: 1265-1278

Released	2004-01-27
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Thermococcus sp. JCM 11816
Macromolecule	Thermosome alpha subunit (protein)
Unique Ligands	SO4

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1Q3S \| pdb_00001q3s	Download File View File

Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)

Shomura, Y., Yoshida, T., Iizuka, R., Maruyama, T., Yohda, M., Miki, K.

(2004) J Mol Biology 335: 1265-1278

Released	2004-01-27
Method	X-RAY DIFFRACTION 3 Å
Organisms	Thermococcus sp. JCM 11816
Macromolecule	Thermosome alpha subunit (protein)
Unique Ligands	ADP, MG

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1UE8 \| pdb_00001ue8	Download File View File

Crystal Structure of Thermophilic Cytochrome P450 from Sulfolobus tokodaii

Nakamura, N., Kamitori, S., Ohno, H.

(2004) J Inorg Biochem 98: 1194-1199

Released	2004-07-13
Method	X-RAY DIFFRACTION 3 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	367aa long hypothetical cytochrome P450 (protein)
Unique Ligands	CL, HEM

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1WOL \| pdb_00001wol	Download File View File

Crystal Structure of ST0689, an archaeal HEPN homologue

Arakawa, T., Akutsu, J., Yohda, M.

To be published

Released	2005-11-22
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	122aa long conserved hypothetical protein (protein)
Unique Ligands	TBU

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2AHJ \| pdb_00002ahj	Download File View File

NITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE

Nagashima, S., Nakasako, M., Dohmae, N., Tsujimura, M., Takio, K., Odaka, M., Yohda, M., Kamiya, N., Endo, I.

(1998) Nat Struct Biol 5: 347-351

Released	1999-01-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Rhodococcus erythropolis
Macromolecule	NITRILE HYDRATASE (protein)
Unique Ligands	DIO, FE, NO, SO4, ZN

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2DD4 \| pdb_00002dd4	Download File View File

Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme

Arakawa, T., Kawano, Y., Kataoka, S., Katayama, Y., Kamiya, N., Yohda, M., Odaka, M.

(2007) J Mol Biology 366: 1497-1509

Released	2007-01-30
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Thiobacillus thioparus
Macromolecule	Thiocyanate hydrolase alpha subunit (protein) Thiocyanate hydrolase beta subunit (protein) Thiocyanate hydrolase gamma subunit (protein)
Unique Ligands	FRU, TLA

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2DD5 \| pdb_00002dd5	Download File View File

Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus native holo-enzyme

Arakawa, T., Kawano, Y., Kataoka, S., Katayama, Y., Kamiya, N., Yohda, M., Odaka, M.

(2007) J Mol Biology 366: 1497-1509

Released	2007-01-30
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thiobacillus thioparus
Macromolecule	Thiocyanate hydrolase alpha subunit (protein) Thiocyanate hydrolase beta subunit (protein) Thiocyanate hydrolase gamma subunit (protein)
Unique Ligands	3CO, SO4

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2DX7 \| pdb_00002dx7	Download File View File

Crystal structure of Pyrococcus horikoshii OT3 aspartate racemase complex with citric acid

Ohtaki, A., Arakawa, T., Iizuka, R., Odaka, M., Yohda, M.

(2008) Proteins 70: 1167-1174

Released	2007-08-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	aspartate racemase (protein)
Unique Ligands	CIT

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2DXB \| pdb_00002dxb	Download File View File

Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers

Arakawa, T., Kawano, Y., Katayama, Y., Yohda, M., Odaka, M.

(2009) J Am Chem Soc 131: 14838-14843

Released	2007-08-28
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Thiobacillus thioparus
Macromolecule	Thiocyanate hydrolase subunit alpha (protein) Thiocyanate hydrolase subunit beta (protein) Thiocyanate hydrolase subunit gamma (protein)
Unique Ligands	3CO, PO4

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2DXC \| pdb_00002dxc	Download File View File

Recombinant thiocyanate hydrolase, fully-matured form

Arakawa, T., Kawano, Y., Katayama, Y., Yohda, M., Odaka, M.

(2009) J Am Chem Soc 131: 14838-14843

Released	2007-08-28
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thiobacillus thioparus
Macromolecule	Thiocyanate hydrolase subunit alpha (protein) Thiocyanate hydrolase subunit beta (protein) Thiocyanate hydrolase subunit gamma (protein)
Unique Ligands	3CO, TLA

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2ZCF \| pdb_00002zcf	Download File View File

Mutational study on Alpha-Gln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771

Takarada, H., Kawano, Y., Hashimoto, K., Nakayama, H., Ueda, S., Yohda, M., Kamiya, N., Dohmae, N., Maeda, M., Odaka, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) Biosci Biotechnol Biochem 70: 881-889

Released	2007-11-20
Method	X-RAY DIFFRACTION 1.43 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Nitrile hydratase subunit alpha (protein) Nitrile hydratase subunit beta (protein)
Unique Ligands	FE, MG

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2ZDI \| pdb_00002zdi	Download File View File

Crystal structure of Prefoldin from Pyrococcus horikoshii OT3

Kida, H., Miki, K.

(2008) J Mol Biology 376: 1130-1141

Released	2008-02-05
Method	X-RAY DIFFRACTION 3 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Prefoldin subunit alpha (protein) Prefoldin subunit beta (protein)
Unique Ligands	SO4

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2ZJX \| pdb_00002zjx	Download File View File

Bovine pancreatic trypsin inhibitor (BPTI) containing only the [5,55] disulfide bond

Islam, M.M., Sohya, S., Noguchi, K., Yohda, M., Kuroda, Y.

(2008) Proc Natl Acad Sci U S A 105: 15334-15339

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.09 Å
Organisms	Bos taurus
Macromolecule	Pancreatic trypsin inhibitor (protein)
Unique Ligands	SO4

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2ZPB \| pdb_00002zpb	Download File View File

nitrosylated Fe-type nitrile hydratase

Hashimoto, K., Suzuki, H., Taniguchi, K., Noguchi, T., Yohda, M., Odaka, M.

(2008) J Biological Chem 283: 36617-36623

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Nitrile hydratase subunit alpha (protein) Nitrile hydratase subunit beta (protein)
Unique Ligands	FE, MG, NO

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2ZPE \| pdb_00002zpe	Download File View File

nitrosylated Fe-type nitrile hydratase with tert-butylisonitrile

Hashimoto, K., Suzuki, H., Taniguchi, K., Noguchi, T., Yohda, M., Odaka, M.

(2008) J Biological Chem 283: 36617-36623

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Nitrile hydratase subunit alpha (protein) Nitrile hydratase subunit beta (protein)
Unique Ligands	FE, MG, NO, TB0

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2ZPF \| pdb_00002zpf	Download File View File

Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 18min at 293K

Hashimoto, K., Suzuki, H., Taniguchi, K., Noguchi, T., Yohda, M., Odaka, M.

(2008) J Biological Chem 283: 36617-36623

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.482 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Nitrile hydratase subunit alpha (protein) Nitrile hydratase subunit beta (protein)
Unique Ligands	FE, MG, NO, TB0

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2ZPG \| pdb_00002zpg	Download File View File

Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 120min at 293K

Hashimoto, K., Suzuki, H., Taniguchi, K., Noguchi, T., Yohda, M., Odaka, M.

(2008) J Biological Chem 283: 36617-36623

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.39 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Nitrile hydratase subunit alpha (protein) Nitrile hydratase subunit beta (protein)
Unique Ligands	FE, MG, TB0

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2ZPH \| pdb_00002zph	Download File View File

Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 340min at 293K

Hashimoto, K., Suzuki, H., Taniguchi, K., Noguchi, T., Yohda, M., Odaka, M.

(2008) J Biological Chem 283: 36617-36623

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.59 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Nitrile hydratase subunit alpha (protein) Nitrile hydratase subunit beta (protein)
Unique Ligands	FE, MG, TB0, TRS

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2ZPI \| pdb_00002zpi	Download File View File

Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 440min at 293K

Hashimoto, K., Suzuki, H., Taniguchi, K., Noguchi, T., Yohda, M., Odaka, M.

(2008) J Biological Chem 283: 36617-36623

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.491 Å
Organisms	Rhodococcus erythropolis
Macromolecule	Nitrile hydratase subunit alpha (protein) Nitrile hydratase subunit beta (protein)
Unique Ligands	FE, MG, TB0, TRS

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2ZQM \| pdb_00002zqm	Download File View File

Crystal structure of the prefoldin beta subunit from Thermococcus strain KS-1

Kida, H., Miki, K.

(2008) J Mol Biology 383: 465-474

Released	2008-08-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermococcus sp. JCM 11816
Macromolecule	Prefoldin beta subunit 1 (protein)
Unique Ligands	CIT, GOL

1 to 25 of 86 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

1IOK | pdb_00001iok

1IU9 | pdb_00001iu9

1JFL | pdb_00001jfl

1Q2V | pdb_00001q2v

1Q3Q | pdb_00001q3q

1Q3R | pdb_00001q3r

1Q3S | pdb_00001q3s

1UE8 | pdb_00001ue8

1WOL | pdb_00001wol

2AHJ | pdb_00002ahj

2DD4 | pdb_00002dd4

2DD5 | pdb_00002dd5

2DX7 | pdb_00002dx7

2DXB | pdb_00002dxb

2DXC | pdb_00002dxc

2ZCF | pdb_00002zcf

2ZDI | pdb_00002zdi

2ZJX | pdb_00002zjx

2ZPB | pdb_00002zpb

2ZPE | pdb_00002zpe

2ZPF | pdb_00002zpf

2ZPG | pdb_00002zpg

2ZPH | pdb_00002zph

2ZPI | pdb_00002zpi

2ZQM | pdb_00002zqm