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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nakasako, M."

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Search Summary

This query matches 88 Structures.

Refinements

Structure Determination Methodology

experimental (88)

Scientific Name of Source Organism

	Thermococcus profundus (35)
	Oryctolagus cuniculus (14)
	Homo sapiens (8)
	Aspergillus terreus (6)
	Bordetella bronchiseptica (4)
	Thermus thermophilus HB8 (4)
	Halobacterium salinarum (3)
	Mus musculus (3)
	Arabidopsis thaliana (2)
	Gallus gallus (2)

More...

Taxonomy

	Eukaryota (40)
	Archaea (38)
	Bacteria (10)

Experimental Method

	X-RAY DIFFRACTION (52)
	ELECTRON MICROSCOPY (34)
	SOLUTION NMR (2)

Polymer Entity Type

Protein (88)

Refinement Resolution (Å)

	1.0 - 1.5 (11)
	1.5 - 2.0 (10)
	2.0 - 2.5 (19)
	2.5 - 3.0 (31)
	3.0 - 3.5 (7)
	3.5 - 4.0 (7)
	> 4.5 (1)

Release Date

	1995 - 1999 (9)
	2000 - 2004 (17)
	2005 - 2009 (22)
	2010 - 2014 (5)
	2015 - 2019 (1)
	2020 - 2024 (34)

Enzyme Classification Name

	Oxidoreductases (39)
	Hydrolases (31)
	Translocases (16)
	Lyases (7)
	Isomerases (2)
	Transferases (2)

Membrane Protein Annotation

	PDBTM (18)
	MemProtMD (17)
	OPM (9)
	mpstruc (8)

Symmetry Type

	Asymmetric (69)
	Cyclic (12)
	Dihedral (8)

SCOP Classification

	Alpha and beta proteins (a/b) (26)
	Alpha and beta proteins (a+b) (28)
	All beta proteins (17)
	Membrane and cell surface proteins and peptides (16)
	Artifacts (2)

AllSelected

1 to 25 of 88 Structures

Page 1 of 4

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1BM1 \| pdb_00001bm1	Download File View File

CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE

Sato, H., Takeda, K., Tani, K., Hino, T., Okada, T., Nakasako, M., Kamiya, N., Kouyama, T.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1251-1256

Released	1999-04-27
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Halobacterium salinarum
Macromolecule	BACTERIORHODOPSIN (protein)
Unique Ligands	DPG, RET

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1DLF \| pdb_00001dlf	Download File View File

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25

Nakasako, M., Takahashi, H., Shimada, I., Arata, Y.

(1999) J Mol Biology 291: 117-134

Released	1999-07-26
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Mus musculus
Macromolecule	ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) (protein)
Unique Ligands	SO4

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1DZE \| pdb_00001dze	Download File View File

Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K

Takeda, K., Matsui, Y., Sato, H., Hino, T., Kanamori, E., Okumura, H., Yamane, T., Iizuka, T., Kamiya, N., Adachi, S., Kouyama, T.

(2004) J Mol Biology 341: 1023

Released	2000-08-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Halobacterium salinarum
Macromolecule	BACTERIORHODOPSIN (M INTERMEDIATE) (protein)
Unique Ligands	L1P, L2P, L3P, L4P, RET
Unique branched monosaccharides	GAL, GLC, MAN

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1EUZ \| pdb_00001euz	Download File View File

GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGATED STATE

Nakasako, M.

(2001) Biochemistry 40: 3069-3079

Released	2001-04-25
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Thermococcus profundus
Macromolecule	GLUTAMATE DEHYDROGENASE (protein)
Unique Ligands	SO4

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1IDP \| pdb_00001idp	Download File View File

Crystal structure of scytalone dehydratase F162A mutant in the unligated state

Nakasako, M., Motoyama, T., Yamaguchi, I.

(2002) Acta Crystallogr D Biol Crystallogr 58: 148-150

Released	2003-04-08
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Pyricularia grisea
Macromolecule	SCYTALONE DEHYDRATASE (protein)

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1IWO \| pdb_00001iwo	Download File View File

Crystal structure of the SR Ca2+-ATPase in the absence of Ca2+

Toyoshima, C., Nomura, H.

(2002) Nature 418: 605-611

Released	2002-08-14
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Oryctolagus cuniculus
Macromolecule	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (protein)
Unique Ligands	TG1

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1IWT \| pdb_00001iwt	Download File View File

Crystal Structure Analysis of Human lysozyme at 113K.

Joti, Y., Nakasako, M., Kidera, A., Go, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1421-1432

Released	2002-09-04
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)
Unique Ligands	CL

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1IWU \| pdb_00001iwu	Download File View File

Crystal Structure Analysis of Human lysozyme at 127K.

Joti, Y., Nakasako, M., Kidera, A., Go, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1421-1432

Released	2002-09-04
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)
Unique Ligands	CL

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1IWV \| pdb_00001iwv	Download File View File

Crystal Structure Analysis of Human lysozyme at 147K.

Joti, Y., Nakasako, M., Kidera, A., Go, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1421-1432

Released	2002-09-04
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)
Unique Ligands	CL

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1IWW \| pdb_00001iww	Download File View File

Crystal Structure Analysis of Human lysozyme at 152K.

Joti, Y., Nakasako, M., Kidera, A., Go, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1421-1432

Released	2002-09-04
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)
Unique Ligands	CL

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1IWX \| pdb_00001iwx	Download File View File

Crystal Structure Analysis of Human lysozyme at 161K.

Joti, Y., Nakasako, M., Kidera, A., Go, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1421-1432

Released	2002-09-04
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)
Unique Ligands	CL

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1IWY \| pdb_00001iwy	Download File View File

Crystal Structure Analysis of Human lysozyme at 170K.

Joti, Y., Nakasako, M., Kidera, A., Go, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1421-1432

Released	2002-09-04
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)
Unique Ligands	CL

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1IWZ \| pdb_00001iwz	Download File View File

Crystal Structure Analysis of Human lysozyme at 178K.

Joti, Y., Nakasako, M., Kidera, A., Go, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1421-1432

Released	2002-09-04
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Homo sapiens
Macromolecule	LYSOZYME C (protein)
Unique Ligands	CL

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1JWR \| pdb_00001jwr	Download File View File

Crystal structure of human lysozyme at 100 K

Higo, J., Nakasako, M.

(2002) J Comput Chem 23: 1323-1336

Released	2001-09-19
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	lysozyme (protein)

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1KJU \| pdb_00001kju	Download File View File

Ca2+-ATPase in the E2 State

Xu, C., Rice, W.J., He, W., Stokes, D.L.

(2002) J Mol Biology 316: 201-211

Released	2001-12-19
Method	ELECTRON MICROSCOPY 6 Å
Organisms	Oryctolagus cuniculus
Macromolecule	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1a (protein)

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1QM8 \| pdb_00001qm8	Download File View File

Structure of Bacteriorhodopsin at 100 K

Takeda, K., Matsui, Y., Sato, H., Hino, T., Kanamori, E., Okumura, H., Yamane, T., Kamiya, N., Kouyama, T.

(1998) J Mol Biology 283: 463

Released	2000-08-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Halobacterium salinarum
Macromolecule	BACTERIORHODOPSIN (protein)
Unique Ligands	L1P, L2P, L3P, L4P, RET
Unique branched monosaccharides	GAL, GLC, MAN

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1SU4 \| pdb_00001su4	Download File View File

Crystal structure of calcium ATPase with two bound calcium ions

Toyoshima, C., Nakasako, M., Nomura, H., Ogawa, H.

(2000) Nature 405: 647-655

Released	2004-05-04
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Oryctolagus cuniculus
Macromolecule	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (protein)
Unique Ligands	CA, NA

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1VFP \| pdb_00001vfp	Download File View File

Crystal structure of the SR CA2+-ATPase with bound AMPPCP

Toyoshima, C., Mizutani, T.

(2004) Nature 430: 529-535

Released	2004-07-06
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Oryctolagus cuniculus
Macromolecule	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (protein)
Unique Ligands	ACP, CA, MG

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1WN5 \| pdb_00001wn5	Download File View File

Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Cacodylic Acid

Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Kimura, M., Yamaguchi, I., Ueki, T.

(2007) J Biological Chem 282: 37103-37111

Released	2005-10-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aspergillus terreus
Macromolecule	Blasticidin-S deaminase (protein)
Unique Ligands	CAC, ZN

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1WN6 \| pdb_00001wn6	Download File View File

Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S

Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Kimura, M., Yamaguchi, I., Ueki, T.

(2007) J Biological Chem 282: 37103-37111

Released	2005-10-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aspergillus terreus
Macromolecule	Blasticidin-S deaminase (protein)
Unique Ligands	ARS, BST, ZN

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1WPG \| pdb_00001wpg	Download File View File

Crystal structure of the SR CA2+-ATPase with MGF4

Toyoshima, C., Nomura, H., Tsuda, T.

(2004) Nature 432: 361-368

Released	2004-10-05
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Oryctolagus cuniculus
Macromolecule	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (protein)
Unique Ligands	ADP, MF4, MG, NA, TG1