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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yoshida, M."

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Search Summary

This query matches 342 Structures.

Refinements

Structure Determination Methodology

experimental (342)

Scientific Name of Source Organism

	Homo sapiens (227)
	Mus musculus (43)
	Coprinopsis cinerea (11)
	Thermus thermophilus (10)
	Bacillus sp. PS3 (7)
	Thermus thermophilus HB8 (7)
	Arabidopsis thaliana (6)
	Azotobacter vinelandii (4)
	Rhizobium sp. MTP-10005 (4)
	Streptomyces avermitilis MA-4680 = NBRC 14893 (4)

More...

Taxonomy

	Eukaryota (299)
	Bacteria (42)
	other sequences (2)
	Duplodnaviria (1)

Experimental Method

	SOLUTION NMR (157)
	X-RAY DIFFRACTION (144)
	ELECTRON MICROSCOPY (40)
	SOLID-STATE NMR (1)

Polymer Entity Type

	Protein (341)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (16)
	1.5 - 2.0 (61)
	2.0 - 2.5 (40)
	2.5 - 3.0 (34)
	3.0 - 3.5 (24)
	3.5 - 4.0 (8)
	4.0 - 4.5 (1)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (9)
	2000 - 2004 (49)
	2005 - 2009 (128)
	2010 - 2014 (23)
	2015 - 2019 (56)
	2020 - 2024 (68)
	2025 - 2029 (8)

Enzyme Classification Name

	Transferases (109)
	Hydrolases (51)
	Oxidoreductases (14)
	Lyases (4)
	Ligases (5)
	Translocases (4)
	Isomerases (2)

Membrane Protein Annotation

	OPM (6)
	PDBTM (3)
	mpstruc (2)
	MemProtMD (1)

Symmetry Type

	Asymmetric (290)
	Cyclic (46)
	Dihedral (7)
	Helical (6)

SCOP Classification

	Artifacts (123)
	Alpha and beta proteins (a/b) (38)
	Alpha and beta proteins (a+b) (64)
	All beta proteins (71)
	All alpha proteins (38)
	Small proteins (8)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 25 of 342 Structures

Page 1 of 14

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1BHI \| pdb_00001bhi	Download File View File

STRUCTURE OF TRANSACTIVATION DOMAIN OF CRE-BP1/ATF-2, NMR, 20 STRUCTURES

Nagadoi, A., Nakazawa, K., Uda, H., Maekawa, T., Ishii, S., Nishimura, Y.

(1999) J Mol Biology 287: 593-607

Released	1999-06-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	CRE-BP1 (protein)

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1CP8 \| pdb_00001cp8	Download File View File

NMR STRUCTURE OF DNA (5'-D(TTGGCCAA)2-3') COMPLEXED WITH NOVEL ANTITUMOR DRUG UCH9

Katahira, R., Katahira, M., Yamashita, Y., Ogawa, H., Kyogoku, Y., Yoshida, M.

(1998) Nucleic Acids Res 26: 744-755

Released	1999-07-01
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(PTPTPGPGPCPCPAPA)-3') (nucleic acid)
Unique Ligands	DDA, DXA, MG
Unique branched monosaccharides	DDA, DDL, DRI

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1E79 \| pdb_00001e79	Download File View File

Bovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide)

Gibbons, C., Montgomery, M.G., Leslie, A.G.W., Walker, J.E.

(2000) Nat Struct Biol 7: 1055

Released	2000-11-03
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bos taurus
Macromolecule	ATP SYNTHASE ALPHA CHAIN HEART ISOFORM (protein) ATP SYNTHASE BETA CHAIN (protein) ATP SYNTHASE DELTA CHAIN (protein) ATP SYNTHASE EPSILON CHAIN (protein) ATP SYNTHASE GAMMA CHAIN (protein)
Unique Ligands	ADP, ATP, DCW, GOL, MG, SO4

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1IDM \| pdb_00001idm	Download File View File

3-ISOPROPYLMALATE DEHYDROGENASE, LOOP-DELETED CHIMERA

Sakurai, M., Ohzeki, M., Moriyama, H., Sato, M., Tanaka, N.

(1996) Acta Crystallogr D Biol Crystallogr 52: 124-128

Released	1995-09-15
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	3-ISOPROPYLMALATE DEHYDROGENASE (protein)

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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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1IPD \| pdb_00001ipd	Download File View File

THREE-DIMENSIONAL STRUCTURE OF A HIGHLY THERMOSTABLE ENZYME, 3-ISOPROPYLMALATE DEHYDROGENASE OF THERMUS THERMOPHILUS AT 2.2 ANGSTROMS RESOLUTION

Imada, K., Sato, M., Tanaka, N., Katsube, Y., Matsuura, Y., Oshima, T.

(1991) J Mol Biology 222: 725-738

Released	1993-10-31
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	3-ISOPROPYLMALATE DEHYDROGENASE (protein)
Unique Ligands	SO4

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1IVZ \| pdb_00001ivz	Download File View File

Solution structure of the SEA domain from murine hypothetical protein homologous to human mucin 16

Maeda, T., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Biological Chem 279: 13174-13182

Released	2002-10-02
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	hypothetical protein 1110008I14RIK (protein)

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1IXZ \| pdb_00001ixz	Download File View File

Crystal structure of the FtsH ATPase domain from Thermus thermophilus

Niwa, H., Tsuchiya, D., Makyio, H., Yoshida, M., Morikawa, K.

(2002) Structure 10: 1415-1423

Released	2002-11-06
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	ATP-dependent metalloprotease FtsH (protein)
Unique Ligands	HG, SO4

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1IY0 \| pdb_00001iy0	Download File View File

Crystal structure of the FtsH ATPase domain with AMP-PNP from Thermus thermophilus

Niwa, H., Tsuchiya, D., Makyio, H., Yoshida, M., Morikawa, K.

(2002) Structure 10: 1415-1423

Released	2002-11-06
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Thermus thermophilus
Macromolecule	ATP-dependent metalloprotease FtsH (protein)
Unique Ligands	ANP

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1IY1 \| pdb_00001iy1	Download File View File

Crystal structure of the FtsH ATPase domain with ADP from Thermus thermophilus

Niwa, H., Tsuchiya, D., Makyio, H., Yoshida, M., Morikawa, K.

(2002) Structure 10: 1415-1423

Released	2002-11-06
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermus thermophilus
Macromolecule	ATP-dependent metalloprotease FtsH (protein)
Unique Ligands	ADP

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1IY2 \| pdb_00001iy2	Download File View File

Crystal structure of the FtsH ATPase domain from Thermus thermophilus

Niwa, H., Tsuchiya, D., Makyio, H., Yoshida, M., Morikawa, K.

(2002) Structure 10: 1415-1423

Released	2002-11-06
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Thermus thermophilus
Macromolecule	ATP-dependent metalloprotease FtsH (protein)
Unique Ligands	SO4

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1IYG \| pdb_00001iyg	Download File View File

Solution structure of RSGI RUH-001, a Fis1p-like and CGI-135 homologous domain from a mouse cDNA

Ohashi, W., Hirota, H., Yamazaki, T., Koshiba, S., Hamada, T., Yoshida, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2003-02-14
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Hypothetical protein (2010003O14) (protein)

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1J3C \| pdb_00001j3c	Download File View File

Solution structure of the C-terminal domain of the HMGB2

Kurita, J., Shimahara, H., Yoshida, M., Tate, S.

To be published

Released	2004-05-25
Method	SOLUTION NMR
Organisms	Sus scrofa
Macromolecule	High mobility group protein 2 (protein)

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1J3D \| pdb_00001j3d	Download File View File

Solution structure of the C-terminal domain of the HMGB2

Kurita, J., Shimahara, H., Yoshida, M., Tate, S.

To be published

Released	2004-05-25
Method	SOLUTION NMR
Organisms	Sus scrofa
Macromolecule	High mobility group protein 2 (protein)

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1J3X \| pdb_00001j3x	Download File View File

Solution structure of the N-terminal domain of the HMGB2

Kurita, J., Shimahara, H., Yoshida, M., Tate, S.

To be published

Released	2004-06-29
Method	SOLUTION NMR
Organisms	Sus scrofa
Macromolecule	High mobility group protein 2 (protein)

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1L5H \| pdb_00001l5h	Download File View File

FeMo-cofactor Deficient Nitrogenase MoFe Protein

Schmid, B., Ribbe, M.W., Einsle, O., Yoshida, M., Thomas, L.M., Dean, D.R., Rees, D.C., Burgess, B.K.

(2002) Science 296: 352-356

Released	2002-04-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Azotobacter vinelandii
Macromolecule	nitrogenase molybdenum-iron protein alpha chain (protein) nitrogenase molybdenum-iron protein beta chain (protein)
Unique Ligands	CA, CLF

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1M1N \| pdb_00001m1n	Download File View File

Nitrogenase MoFe protein from Azotobacter vinelandii

Einsle, O., Tezcan, F.A., Andrade, S.L.A., Schmid, B., Yoshida, M., Howard, J.B., Rees, D.C.

(2002) Science 297: 1696-1700

Released	2002-09-11
Method	X-RAY DIFFRACTION 1.16 Å
Organisms	Azotobacter vinelandii
Macromolecule	Nitrogenase molybdenum-iron protein alpha chain (protein) Nitrogenase molybdenum-iron protein beta chain (protein)
Unique Ligands	CA, CFN, CLF, HCA

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1M1Y \| pdb_00001m1y	Download File View File

Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein

Schmid, B., Einsle, O., Chiu, H.J., Willing, A., Yoshida, M., Howard, J.B., Rees, D.C.

(2002) Biochemistry 41: 15557-15565

Released	2003-02-11
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Azotobacter vinelandii
Macromolecule	Nitrogenase molybdenum-iron protein alpha chain (protein) Nitrogenase molybdenum-iron protein beta chain (protein) nitrogenase IRON protein 1 (protein)
Unique Ligands	CA, CFM, CLF, HCA, SF4

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1M34 \| pdb_00001m34	Download File View File

Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP-Tetrafluoroaluminate

Schmid, B., Einsle, O., Chiu, H.-J., Willing, A., Yoshida, M., Howard, J.B., Rees, D.C.

(2002) Biochemistry 41: 15557-15565

Released	2003-02-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Azotobacter vinelandii
Macromolecule	Nitrogenase Iron Protein 1 (protein) Nitrogenase Molybdenum-Iron Protein alpha chain (protein) Nitrogenase Molybdenum-Iron Protein beta chain (protein)
Unique Ligands	ADP, ALF, CA, CFM, CLF, HCA, MG, SF4