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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Murakami, M."

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Search Summary

This query matches 17 Structures.

Refinements

Structure Determination Methodology

experimental (17)

Scientific Name of Source Organism

	Halobacterium salinarum (4)
	Todarodes pacificus (4)
	Sulfurisphaera tokodaii (2)
	Bos taurus (1)
	Halobacterium sp. AUS-2 (1)
	Hirudo medicinalis (1)
	Homo sapiens (1)
	Microcystis aeruginosa (1)
	Microcystis aeruginosa NIES-98 (1)
	Staphylococcus aureus (1)

More...

Taxonomy

	Archaea (9)
	Eukaryota (6)
	Bacteria (4)

Experimental Method

X-RAY DIFFRACTION (17)

Polymer Entity Type

Protein (17)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (6)
	2.5 - 3.0 (10)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (3)
	2005 - 2009 (8)
	2010 - 2014 (3)
	2015 - 2019 (1)

Enzyme Classification Name

	Hydrolases (3)
	Transferases (2)
	Lyases (3)
	Oxidoreductases (2)

Membrane Protein Annotation

	MemProtMD (9)
	PDBTM (9)
	OPM (3)
	mpstruc (2)

Symmetry Type

	Asymmetric (8)
	Cyclic (10)

SCOP Classification

	All alpha proteins (3)
	Membrane and cell surface proteins and peptides (5)
	All beta proteins (3)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 17 of 17 Structures

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1A2C \| pdb_00001a2c	Download File View File

Structure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-GREEN ALGA

Rios-Steiner, J.L., Murakami, M., Tulinsky, A.

(1998) J Am Chem Soc 120: 597

Released	1998-07-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Hirudo medicinalis Homo sapiens Microcystis aeruginosa
Macromolecule	Aeruginosin 298-A (protein) Hirudin variant-2 (protein) Thrombin heavy chain (protein) Thrombin light chain (protein)
Unique Ligands	NA

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1AQ7 \| pdb_00001aq7	Download File View File

TRYPSIN WITH INHIBITOR AERUGINOSIN 98-B

Sandler, B., Murakami, M., Clardy, J.

(1998) J Am Chem Soc 120: 595-596

Released	1998-02-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus Microcystis aeruginosa NIES-98
Macromolecule	AERUGINOSIN 98-B (protein) TRYPSIN (protein)

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1IXE \| pdb_00001ixe	Download File View File

Crystal structure of citrate synthase from Thermus thermophilus HB8

Murakami, M., Kanamori, E., Kawaguchi, S., Kuramitsu, S., Kouyama, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2015) Biophys Physicobiol 12: 47-56

Released	2003-07-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermus thermophilus
Macromolecule	citrate synthase (protein)
Unique Ligands	CIT, COA, GOL, SO4

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1IXF \| pdb_00001ixf	Download File View File

Crystal Structure of the K intermediate of bacteriorhodopsin

Matsui, Y., Sakai, K., Murakami, M., Shiro, Y., Adachi, S., Okumura, H., Kouyama, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 324: 469-481

Released	2002-12-18
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Halobacterium salinarum
Macromolecule	bacteriorhodopsin (protein)
Unique Ligands	L2P, L3P, RET
Unique branched monosaccharides	GAL, GLC, MAN

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1VGM \| pdb_00001vgm	Download File View File

Crystal Structure of an Isozyme of Citrate Synthase from Sulfolbus tokodaii strain7

Murakami, M., Ihara, K., Kouyama, T.

(2016) Biochem Res Int 2016: 7560919-7560919

Released	2005-06-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	378aa long hypothetical citrate synthase (protein)
Unique Ligands	GOL, SO4

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1VGO \| pdb_00001vgo	Download File View File

Crystal Structure of Archaerhodopsin-2

Yoshimura, K., Enami, N., Murakami, M., Okumura, H., Ihara, K., Kouyama, T.

(2006) J Mol Biology 358: 675-685

Released	2005-10-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Halobacterium sp. AUS-2
Macromolecule	Archaerhodopsin 2 (protein)
Unique Ligands	BNG, RET, SO4

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1VGP \| pdb_00001vgp	Download File View File

Crystal Structure of an Isozyme of Citrate Synthase from Sulfolbus tokodaii strain7

Murakami, M., Ihara, K., Kouyama, T.

(2016) Biochem Res Int 2016: 7560919-7560919

Released	2005-06-28
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	373aa long hypothetical citrate synthase (protein)

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1WCZ \| pdb_00001wcz	Download File View File

Crystal structure of an alkaline form of v8 protease from Staphylococcus aureus

Yamada, K., Ohta, M., Hasegawa, T., Torii, K., Murakami, M., Kouyama, K.

To be published

Released	2004-06-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Staphylococcus aureus
Macromolecule	Glutamyl endopeptidase (protein)
Unique Ligands	ZN

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1X0I \| pdb_00001x0i	Download File View File

Crystal Structure of the Acid Blue Form of Bacteriorhodopsin

Okumura, H., Murakami, M., Kouyama, T.

(2005) J Mol Biology 351: 481-495

Released	2005-08-02
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	L2P, L3P, RET, SO4

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1X0K \| pdb_00001x0k	Download File View File

Crystal Structure of Bacteriorhodopsin at pH 10

Okumura, H., Murakami, M., Kouyama, T.

(2005) J Mol Biology 351: 481-495

Released	2005-08-02
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	L2P, L3P, RET
Unique branched monosaccharides	GAL, GLC, MAN

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1X0S \| pdb_00001x0s	Download File View File

Crystal structure of the 13-cis isomer of bacteriorhodopsin

Nishikawa, T., Murakami, M., Kouyama, T.

(2005) J Mol Biology 352: 319-328

Released	2005-08-30
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	L2P, L3P, RET, SO4
Unique branched monosaccharides	GAL, GLC, MAN

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2DHT \| pdb_00002dht	Download File View File

Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7

Kondo, H., Murakami, M., Ihara, K., Suzuki, S., Kouyama, T.

To be published

Released	2007-03-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	409aa long hypothetical NADP-dependent isocitrate dehydrogenase (protein)

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2Z73 \| pdb_00002z73	Download File View File

Crystal structure of squid rhodopsin

Murakami, M., Kouyama, T.

(2008) Nature 453: 363-367

Released	2008-05-13
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Todarodes pacificus
Macromolecule	Rhodopsin (protein)
Unique Ligands	BOG, PC1, PLM, RET, SO4, TWT

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3ATQ \| pdb_00003atq	Download File View File

Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius

Sasaki, D., Fujihashi, M., Murakami, M., Yoshimura, T., Hemmi, H., Miki, K.

(2011) J Mol Biology 409: 543-557

Released	2011-05-04
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Sulfolobus acidocaldarius
Macromolecule	Conserved Archaeal protein (protein)
Unique Ligands	C14, FDA

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3AYM \| pdb_00003aym	Download File View File

Crystal structure of the batho intermediate of squid rhodopsin

Murakami, M., Kouyama, T.

(2011) J Mol Biology 413: 615-627

Released	2011-08-17
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Todarodes pacificus
Macromolecule	Rhodopsin (protein)
Unique Ligands	BOG, PC1, PLM, RET, SO4

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3AYN \| pdb_00003ayn	Download File View File

Crystal structure of squid isorhodopsin

Murakami, M., Kouyama, T.

(2011) J Mol Biology 413: 615-627

Released	2011-08-17
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Todarodes pacificus
Macromolecule	Rhodopsin (protein)
Unique Ligands	BOG, PC1, PLM, RET, SO4

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4WW3 \| pdb_00004ww3	Download File View File

Crystal structure of the lumi intermediate of squid rhodopsin

Murakami, M., Kouyama, T.

(2015) PLoS One 10: e0126970-e0126970

Released	2015-06-17
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Todarodes pacificus
Macromolecule	Rhodopsin (protein)
Unique Ligands	BOG, PC1, PLM, RET, SO4, TWT

1 to 17 of 17 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1A2C | pdb_00001a2c

Structure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-GREEN ALGA

1AQ7 | pdb_00001aq7

TRYPSIN WITH INHIBITOR AERUGINOSIN 98-B

1IXE | pdb_00001ixe

Crystal structure of citrate synthase from Thermus thermophilus HB8

1IXF | pdb_00001ixf

Crystal Structure of the K intermediate of bacteriorhodopsin

1VGM | pdb_00001vgm

Crystal Structure of an Isozyme of Citrate Synthase from Sulfolbus tokodaii strain7

1VGO | pdb_00001vgo

Crystal Structure of Archaerhodopsin-2

1VGP | pdb_00001vgp

Crystal Structure of an Isozyme of Citrate Synthase from Sulfolbus tokodaii strain7

1WCZ | pdb_00001wcz

Crystal structure of an alkaline form of v8 protease from Staphylococcus aureus

1X0I | pdb_00001x0i

Crystal Structure of the Acid Blue Form of Bacteriorhodopsin

1X0K | pdb_00001x0k

Crystal Structure of Bacteriorhodopsin at pH 10

1X0S | pdb_00001x0s

Crystal structure of the 13-cis isomer of bacteriorhodopsin

2DHT | pdb_00002dht

Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7

2Z73 | pdb_00002z73

Crystal structure of squid rhodopsin

3ATQ | pdb_00003atq

Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius

3AYM | pdb_00003aym

Crystal structure of the batho intermediate of squid rhodopsin

3AYN | pdb_00003ayn

Crystal structure of squid isorhodopsin

4WW3 | pdb_00004ww3

Crystal structure of the lumi intermediate of squid rhodopsin

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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

1A2C | pdb_00001a2c

1AQ7 | pdb_00001aq7

1IXE | pdb_00001ixe

1IXF | pdb_00001ixf

1VGM | pdb_00001vgm

1VGO | pdb_00001vgo

1VGP | pdb_00001vgp

1WCZ | pdb_00001wcz

1X0I | pdb_00001x0i

1X0K | pdb_00001x0k

1X0S | pdb_00001x0s

2DHT | pdb_00002dht

2Z73 | pdb_00002z73

3ATQ | pdb_00003atq

3AYM | pdb_00003aym

3AYN | pdb_00003ayn

4WW3 | pdb_00004ww3