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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Kyogoku, Y."

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Search Summary

This query matches 23 Structures.

Refinements

Structure Determination Methodology

experimental (23)

Scientific Name of Source Organism

	Mus musculus (6)
	Homo sapiens (2)
	Hydrogenobacter thermophilus (2)
	Lophura nycthemera (2)
	Escherichia coli K-12 (1)
	Halocynthia roretzi (1)
	Lambdavirus lambda (1)
	Saccharomyces cerevisiae (1)
	Schizosaccharomyces pombe (1)
	Thermus thermophilus (1)

Taxonomy

	Eukaryota (13)
	Bacteria (4)
	Duplodnaviria (1)

Experimental Method

	SOLUTION NMR (18)
	X-RAY DIFFRACTION (5)

Polymer Entity Type

	Protein (18)
	DNA (6)
	NA-hybrid (2)
	RNA (2)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (3)
	2.5 - 3.0 (1)

Release Date

	1995 - 1999 (14)
	2000 - 2004 (8)
	2005 - 2009 (1)

Enzyme Classification Name

	Transferases (2)
	Hydrolases (2)

Symmetry Type

	Asymmetric (15)
	Cyclic (4)

SCOP Classification

	All alpha proteins (11)
	Coiled coil proteins (1)
	Small proteins (5)
	Alpha and beta proteins (a+b) (2)

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1 to 23 of 23 Structures

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1A0A \| pdb_00001a0a	Download File View File

PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX

Shimizu, T., Toumoto, A., Ihara, K., Shimizu, M., Kyogoku, Y., Ogawa, N., Oshima, Y., Hakoshima, T.

(1997) EMBO J 16: 4689-4697

Released	1998-03-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4) (protein) DNA (5'-D(CPTPAPGPTPCPCPCPAPCPGPTPGPTPGPAPG )-3') (nucleic acid) DNA (5'-D(CPTPCPAPCPAPCPGPTPGPGPGPAPCPTPAPG )-3') (nucleic acid)

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1AYG \| pdb_00001ayg	Download File View File

SOLUTION STRUCTURE OF CYTOCHROME C-552, NMR, 20 STRUCTURES

Hasegawa, J., Yoshida, T., Yamazaki, T., Sambongi, Y., Yu, Y., Igarashi, Y., Kodama, T., Yamazaki, K., Hakusui, H., Kyogoku, Y., Kobayashi, Y.

(1998) Biochemistry 37: 9641-9649

Released	1998-11-25
Method	SOLUTION NMR
Organisms	Hydrogenobacter thermophilus
Macromolecule	CYTOCHROME C-552 (protein)
Unique Ligands	HEC

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1BQT \| pdb_00001bqt	Download File View File

THREE-DIMENSIONAL STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR-I (IGF-I) DETERMINED BY 1H-NMR AND DISTANCE GEOMETRY, 6 STRUCTURES

Sato, A., Nishimura, S., Ohkubo, T., Kyogoku, Y., Koyama, S., Kobayashi, M., Yasuda, T., Kobayashi, Y.

(1993) Int J Pept Protein Res 41: 433-440

Released	1999-05-18
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	INSULIN-LIKE GROWTH FACTOR-I (protein)

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1C4L \| pdb_00001c4l	Download File View File

SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR

Tanaka, Y., Kojima, C., Yamazaki, T., Kodama, T.S., Yasuno, K., Miyashita, S., Ono, A.M., Ono, A.S., Kainosho, M., Kyogoku, Y.

(2000) Biochemistry 39: 7074-7080

Released	2000-08-09
Method	SOLUTION NMR
Macromolecule	RNA (5'-R(CPCPUPGPCPGPUPCPG)-3') (nucleic acid) RNA (5'-R(CPGPAPCPUPCPAPGPG)-3') (nucleic acid)

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1C9F \| pdb_00001c9f	Download File View File

NMR STRUCTURE OF THE CAD DOMAIN OF CASPASE-ACTIVATED DNASE

Yamazaki, T., Uegaki, K.

(2000) J Mol Biology 297: 1121-1128

Released	2000-02-16
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	CASPASE-ACTIVATED DNASE (protein)

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1COO \| pdb_00001coo	Download File View File

THE COOH-TERMINAL DOMAIN OF RNA POLYMERASE ALPHA SUBUNIT

Jeon, Y.H., Negishi, T., Shirakawa, M., Yamazaki, T., Fujita, N., Ishihama, A., Kyogoku, Y.

(1995) Science 270: 1495-1497

Released	1996-03-08
Method	SOLUTION NMR
Organisms	Escherichia coli K-12
Macromolecule	RNA POLYMERASE ALPHA SUBUNIT (protein)

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1COP \| pdb_00001cop	Download File View File

THREE-DIMENSIONAL DIMER STRUCTURE OF THE LAMBDA-CRO REPRESSOR IN SOLUTION AS DETERMINED BY HETERONUCLEAR MULTIDIMENSIONAL NMR

Matsuo, H., Shirakawa, M., Kyogoku, Y.

(1995) J Mol Biology 254: 668-680

Released	1995-10-15
Method	SOLUTION NMR
Organisms	Lambdavirus lambda
Macromolecule	CRO REPRESSOR (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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1DHH \| pdb_00001dhh	Download File View File

NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC)

Nishizaki, T., Iwai, S., Ohkubo, T., Kojima, C., Nakamura, H., Kyogoku, Y., Ohtsuka, E.

(1996) Biochemistry 35: 4016-4025

Released	1996-04-03
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(GPTPCPAPTPCPTPCPC)-3') (nucleic acid) DNA/RNA (5'-D(GPG)-R(PAPGPAPU)-D(PGPAPC)-3') (hybrid)

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1DOQ \| pdb_00001doq	Download File View File

THE C-TERMINAL DOMAIN OF THE RNA POLYMERASE ALPHA SUBUNIT FROM THERMUS THERMOPHILUS

Wada, T., Yamazaki, T., Kyogoku, Y.

(2000) J Biological Chem 275: 16057-16063

Released	2000-01-05
Method	SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	RNA POLYMERASE ALPHA SUBUNIT (protein)

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1DRN \| pdb_00001drn	Download File View File

NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC)

Nishizaki, T., Iwai, S., Ohkubo, T., Kojima, C., Nakamura, H., Kyogoku, Y., Ohtsuka, E.

(1996) Biochemistry 35: 4016-4025

Released	1996-04-03
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(GPTPCPAPTPCPTPCPC)-3') (nucleic acid) DNA/RNA (5'-D(GPGPAPGPA)-R(PUPGPAPC)-3') (hybrid)

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1F2R \| pdb_00001f2r	Download File View File

NMR STRUCTURE OF THE HETERODIMERIC COMPLEX BETWEEN CAD DOMAINS OF CAD AND ICAD

Otomo, T., Sakahira, H., Uegaki, K., Nagata, S., Yamazaki, T.

(2000) Nat Struct Biol 7: 658-662

Released	2000-06-08
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	CASPASE-ACTIVATED DNASE (protein) INHIBITOR OF CASPASE-ACTIVATED DNASE (protein)

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1GD2 \| pdb_00001gd2	Download File View File

CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA

Fujii, Y., Shimizu, T., Toda, T., Yanagida, M., Hakoshima, T.

(2000) Nat Struct Biol 7: 889-893

Released	2000-10-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	TRANSCRIPTION FACTOR PAP1 (protein) DNA (5'-D(APGPGPTPTPAPCPGPTPAPAPCP*C)-3') (nucleic acid)

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1IRF \| pdb_00001irf	Download File View File

INTERFERON REGULATORY FACTOR-2 DNA BINDING DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE

Furui, J., Uegaki, K., Yamazaki, T., Shirakawa, M., Swindells, M.B., Harada, H., Taniguchi, T., Kyogoku, Y.

(1998) Structure 6: 491-500

Released	1998-01-28
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	INTERFERON REGULATORY FACTOR-2 (protein)

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1IRG \| pdb_00001irg	Download File View File

INTERFERON REGULATORY FACTOR-2 DNA BINDING DOMAIN, NMR, 20 STRUCTURES

Furui, J., Uegaki, K., Yamazaki, T., Shirakawa, M., Swindells, M.B., Harada, H., Taniguchi, T., Kyogoku, Y.

(1998) Structure 6: 491-500

Released	1998-03-18
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	INTERFERON REGULATORY FACTOR-2 (protein)

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1IW4 \| pdb_00001iw4	Download File View File

Solution structure of ascidian trypsin inhibitor

Hemmi, H., Yoshida, T., Kumazaki, T., Nemoto, N., Hasegawa, J., Nishioka, F., Kyogoku, Y., Yokosawa, H., Kobayashi, Y.

(2002) Biochemistry 41: 10657-10664

Released	2002-08-28
Method	SOLUTION NMR
Organisms	Halocynthia roretzi
Macromolecule	trypsin inhibitor (protein)

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1IY5 \| pdb_00001iy5	Download File View File

Solution structure of wild type OMSVP3

Hemmi, H., Kumazaki, T., Yamazaki, T., Kojima, S., Yoshida, T., Kyogoku, Y., Katsu, M., Yokosawa, H., Miura, K., Kobayashi, Y.

(2003) Biochemistry 42: 2524-2534

Released	2003-03-11
Method	SOLUTION NMR
Organisms	Lophura nycthemera
Macromolecule	OMSVP3 (protein)

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1IY6 \| pdb_00001iy6	Download File View File

Solution structure of OMSVP3 variant, P14C/N39C

Hemmi, H., Kumazaki, T., Yamazaki, T., Kojima, S., Yoshida, T., Kyogoku, Y., Katsu, M., Yokosawa, H., Miura, K., Kobayashi, Y.

(2003) Biochemistry 42: 2524-2534

Released	2003-03-11
Method	SOLUTION NMR
Organisms	Lophura nycthemera
Macromolecule	OMSVP3 (protein)

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1OCP \| pdb_00001ocp	Download File View File

SOLUTION STRUCTURE OF OCT3 POU-HOMEODOMAIN

Morita, E.H., Hayashi, F., Shirakawa, M., Kyogoku, Y.

(1995) Protein Sci 4: 729-739

Released	1995-09-15
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	OCT-3 (protein)

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1XPA \| pdb_00001xpa	Download File View File

SOLUTION STRUCTURE OF THE DNA-AND RPA-BINDING DOMAIN OF THE HUMAN REPAIR FACTOR XPA, NMR, 1 STRUCTURE

Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K., Shirakawa, M.

(1998) Nat Struct Biol 5: 701-706

Released	1999-07-22
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	XPA (protein)
Unique Ligands	ZN

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1YNR \| pdb_00001ynr	Download File View File

Crystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0 resolution

Travaglini-Allocatelli, C., Gianni, S., Dubey, V.K., Borgia, A., Di Matteo, A., Bonivento, D., Cutruzzola, F., Bren, K.L., Brunori, M.

(2005) J Biological Chem 280: 25729-25734

Released	2005-05-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Hydrogenobacter thermophilus
Macromolecule	Cytochrome c-552 (protein)
Unique Ligands	HEC, MPD, SO4

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2IRF \| pdb_00002irf	Download File View File

CRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX.

Fujii, Y., Shimizu, T., Kusumoto, M., Kyogoku, Y., Taniguchi, T., Hakoshima, T.

(1999) EMBO J 18: 5028-5041

Released	1999-10-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Mus musculus
Macromolecule	INTERFERON REGULATORY FACTOR 2 (protein) DNA (5'-D(TPTPCPAPCPTPTPTPCPAPCP(5IU)PT)-3') (nucleic acid) DNA (5'-D(PAPAPGPTPGPAPAPAPGP(5IU)PGP*A)-3') (nucleic acid)
Unique Ligands	K