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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kimura, M."

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Search Summary

This query matches 65 Structures.

Refinements

Structure Determination Methodology

experimental (65)

Scientific Name of Source Organism

	Mus musculus (8)
	Pyrococcus horikoshii (8)
	Pyrococcus horikoshii OT3 (8)
	Momordica charantia (7)
	Aspergillus terreus (6)
	Homo sapiens (6)
	Nicotiana glutinosa (4)
	Oryza sativa Japonica Group (3)
	Autographa californica nucleopolyhedrovirus (2)
	Bombyx mori (2)

More...

Taxonomy

	Eukaryota (37)
	Archaea (18)
	Bacteria (6)
	Viruses incertae sedis (2)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (65)

Polymer Entity Type

	Protein (65)
	RNA (2)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (29)
	2.0 - 2.5 (23)
	2.5 - 3.0 (4)
	3.0 - 3.5 (2)
	3.5 - 4.0 (2)

Release Date

	2000 - 2004 (16)
	2005 - 2009 (32)
	2010 - 2014 (13)
	2015 - 2019 (4)

Enzyme Classification Name

	Hydrolases (29)
	Transferases (19)
	Lyases (10)

Symmetry Type

	Asymmetric (44)
	Cyclic (18)
	Dihedral (10)

SCOP Classification

	Alpha and beta proteins (a/b) (23)
	Alpha and beta proteins (a+b) (18)
	All alpha proteins (5)
	All beta proteins (2)
	Artifacts (4)

AllSelected

1 to 25 of 65 Structures

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1IQ4 \| pdb_00001iq4	Download File View File

5S-RRNA BINDING RIBOSOMAL PROTEIN L5 FROM BACILLUS STEAROTHERMOPHILUS

Nakashima, T., Yao, M., Kawamura, S., Iwasaki, K., Kimura, M., Tanaka, I.

(2001) RNA 7: 692-701

Released	2001-06-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	50S RIBOSOMAL PROTEIN L5 (protein)

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1IQV \| pdb_00001iqv	Download File View File

Crystal Structure Analysis of the archaebacterial ribosomal protein S7

Hosaka, H., Yao, M., Kimura, M., Tanaka, I.

(2001) J Biochem 130: 695-701

Released	2001-08-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pyrococcus horikoshii
Macromolecule	RIBOSOMAL PROTEIN S7 (protein)

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1IYB \| pdb_00001iyb	Download File View File

Crystal Structure of the Nicotiana glutinosa Ribonuclease NW

Kawano, S., Kakuta, Y., Kimura, M.

(2002) Biochemistry 41: 15195-15202

Released	2003-08-05
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Nicotiana glutinosa
Macromolecule	Ribonuclease (protein)
Unique Ligands	5GP

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1IZ6 \| pdb_00001iz6	Download File View File

Crystal Structure of Translation Initiation Factor 5A from Pyrococcus Horikoshii

Yao, M., Ohsawa, A., Kikukawa, S., Tanaka, I., Kimura, M.

(2003) J Biochem 133: 75-81

Released	2003-01-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Initiation Factor 5A (protein)

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1J1F \| pdb_00001j1f	Download File View File

Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP

Numata, T., Suzuki, A., Kakuta, Y., Kimura, K., Yao, M., Tanaka, I., Yoshida, Y., Ueda, T., Kimura, M.

(2003) Biochemistry 42: 5270-5278

Released	2003-05-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Momordica charantia
Macromolecule	RIBONUCLEASE MC1 (protein)
Unique Ligands	5GP

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1J1G \| pdb_00001j1g	Download File View File

Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP

Numata, T., Suzuki, A., Kakuta, Y., Kimura, K., Yao, M., Tanaka, I., Yoshida, Y., Ueda, T., Kimura, M.

(2003) Biochemistry 42: 5270-5278

Released	2003-05-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Momordica charantia
Macromolecule	Ribonuclease MC1 (protein)
Unique Ligands	5GP

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1J3A \| pdb_00001j3a	Download File View File

Crystal structure of ribosomal protein L13 from Pyrococcus horikoshii

Nakashima, T., Tanaka, M., Kazama, T., Kawamura, S., Kimura, M., Yao, M., Tanaka, I.

To be published

Released	2003-02-04
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Pyrococcus horikoshii
Macromolecule	50S ribosomal protein L13P (protein)

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1UAX \| pdb_00001uax	Download File View File

Crystal structure of the ribonuclease H2 from Pyrococcus horikoshii OT3

Hata, T., Numata, T., Kakuta, Y., Kimura, M.

To be published

Released	2004-06-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Ribonuclease HII (protein)

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1UCA \| pdb_00001uca	Download File View File

Crystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 2'-UMP

Suzuki, A., Yao, M., Tanaka, I., Numata, T., Kikukawa, S., Yamasaki, N., Kimura, M.

(2000) Biochem Biophys Res Commun 275: 572-576

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Momordica charantia
Macromolecule	Ribonuclease MC (protein)
Unique Ligands	U2P

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1UCC \| pdb_00001ucc	Download File View File

Crystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 3'-UMP.

Suzuki, A., Yao, M., Tanaka, I., Numata, T., Kikukawa, S., Yamasaki, N., Kimura, M.

(2000) Biochem Biophys Res Commun 275: 572-576

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Momordica charantia
Macromolecule	Ribonuclease MC (protein)
Unique Ligands	U3P

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1UCD \| pdb_00001ucd	Download File View File

Crystal structure of Ribonuclease MC1 from bitter gourd seeds complexed with 5'-UMP

Suzuki, A., Numata, T., Yao, M., Kimura, M., Tanaka, I.

To be published

Released	2004-05-18
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Momordica charantia
Macromolecule	Ribonuclease MC (protein)
Unique Ligands	U5P, URA

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1UCG \| pdb_00001ucg	Download File View File

Crystal structure of Ribonuclease MC1 N71T mutant

Suzuki, A., Numata, T., Yao, M., Tanaka, I., Kimura, M.

(2003) Biochemistry 42: 5270-5278

Released	2003-04-29
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Momordica charantia
Macromolecule	Ribonuclease MC (protein)
Unique Ligands	MN

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1V76 \| pdb_00001v76	Download File View File

Crystal Structure of Archaeal Ribonuclease P Protein Ph1771p from Pyrococcus horikoshii OT3

Numata, T., Kakuta, Y., Kimura, M.

(2004) RNA 10: 1423-1432

Released	2004-10-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus horikoshii
Macromolecule	RNase P protein Ph1771p (protein)
Unique Ligands	SO4

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1V77 \| pdb_00001v77	Download File View File

Crystal structure of the PH1877 protein

Takagi, H., Numata, T., Kakuta, Y., Kimura, M.

(2004) Biochem Biophys Res Commun 319: 787-794

Released	2004-08-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pyrococcus horikoshii
Macromolecule	hypothetical protein PH1877 (protein)

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1V9H \| pdb_00001v9h	Download File View File

Crystal structure of the RNase MC1 mutant Y101A in complex with 5'-UMP

Kimura, K., Numata, T., Kakuta, Y., Kimura, M.

(2004) Biosci Biotechnol Biochem 68: 1748-1757

Released	2004-10-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Momordica charantia
Macromolecule	Ribonuclease MC (protein)
Unique Ligands	SO4, U5P

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1VB5 \| pdb_00001vb5	Download File View File

Crystal Structure Analysis of the Pyrococcus horikoshii OT3 translation initiation factor eIF-2B

Kakuta, Y., Tahara, M., Maetani, S., Kimura, M.

(2004) Biochem Biophys Res Commun 319: 725-732

Released	2004-12-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	translation initiation factor eIF-2B (protein)

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1VCZ \| pdb_00001vcz	Download File View File

Crystal structure of the RNase NT in complex with 5'-GMP

Kawano, S., Kakuta, Y., Kimura, M.

To be published

Released	2005-04-26
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nicotiana glutinosa
Macromolecule	RNase NGR3 (protein)
Unique Ligands	5GP

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1VD1 \| pdb_00001vd1	Download File View File

Crystal structure of RNase NT in complex with 5'-AMP

Kawano, S., Kakuta, Y., Kimura, M.

To be published

Released	2005-04-26
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nicotiana glutinosa
Macromolecule	RNase NGR3 (protein)
Unique Ligands	AMP

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1VD3 \| pdb_00001vd3	Download File View File

Ribonuclease NT in complex with 2'-UMP

Kawano, S., Kakuta, Y., Kimura, M.

To be published

Released	2005-04-26
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nicotiana glutinosa
Macromolecule	RNase NGR3 (protein)
Unique Ligands	U2P

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1WMI \| pdb_00001wmi	Download File View File

Crystal structure of archaeal RelE-RelB complex from Pyrococcus horikoshii OT3

Takagi, H., Kakuta, Y., Kamachi, R., Yao, M., Tanaka, I., Kimura, M.

(2005) Nat Struct Mol Biol 12: 327-331

Released	2005-03-15
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	hypothetical protein PHS013 (protein) hypothetical protein PHS014 (protein)

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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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1X0T \| pdb_00001x0t	Download File View File

Crystal structure of ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3

Kakuta, Y., Ishimatsu, I., Numata, T., Kimura, K., Yao, M., Tanaka, I., Kimura, M.

(2005) Biochemistry 44: 12086-12093

Released	2005-11-15
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Ribonuclease P protein component 4 (protein)
Unique Ligands	ZN

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2CZV \| pdb_00002czv	Download File View File

Crystal structure of archeal RNase P protein ph1481p in complex with ph1877p

Kawano, S., Kakuta, Y., Nakashima, T., Tanaka, I., Kimura, M.

(2006) J Mol Biology 357: 583-591

Released	2006-06-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Ribonuclease P protein component 2 (protein) Ribonuclease P protein component 3 (protein)
Unique Ligands	ACY, BOG