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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kobayashi, Y."

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Search Summary

This query matches 57 Structures.

Refinements

Structure Determination Methodology

experimental (57)

Scientific Name of Source Organism

	Homo sapiens (22)
	Escherichia coli (6)
	synthetic construct (6)
	Anemonia sulcata (2)
	Aquifex aeolicus (2)
	Hydrogenobacter thermophilus (2)
	Hydrogenophilus thermoluteolus (2)
	Lophura nycthemera (2)
	Micrococcus luteus (2)
	Pseudomonas aeruginosa (2)

More...

Taxonomy

	Eukaryota (25)
	Bacteria (24)
	other sequences (6)
	Eukaryota (eukaryotes) (3)
	Duplodnaviria (2)
	Archaea (1)
	Riboviria (1)
	Riboviria (RNA viruses and viroids) (1)

Experimental Method

	X-RAY DIFFRACTION (33)
	SOLUTION NMR (18)
	ELECTRON MICROSCOPY (5)
	NEUTRON DIFFRACTION (1)

Polymer Entity Type

	Protein (57)
	DNA (4)
	RNA (1)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (5)
	1.5 - 2.0 (11)
	2.0 - 2.5 (13)
	2.5 - 3.0 (5)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (11)
	2005 - 2009 (21)
	2010 - 2014 (7)
	2015 - 2019 (8)
	2020 - 2024 (8)

Enzyme Classification Name

	Transferases (6)
	Lyases (2)
	Isomerases (1)

Membrane Protein Annotation

	OPM (1)
	PDBTM (1)

Symmetry Type

	Asymmetric (33)
	Cyclic (20)
	Helical (2)
	Dihedral (2)

SCOP Classification

	All alpha proteins (11)
	Alpha and beta proteins (a+b) (9)
	Alpha and beta proteins (a/b) (4)
	Small proteins (6)
	All beta proteins (3)
	Artifacts (2)
	Peptides (2)

AllSelected

1 to 25 of 57 Structures

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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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1DVV \| pdb_00001dvv	Download File View File

SOLUTION STRUCTURE OF THE QUINTUPLE MUTANT OF CYTOCHROME C-551 FROM PSEUDOMONAS AERUGINOSA

Hasegawa, J., Uchiyama, S., Tanimoto, Y., Mizutani, M., Kobayashi, Y., Sambongi, Y., Igarashi, Y.

(2000) J Biological Chem 275: 37824-37828

Released	2000-11-29
Method	SOLUTION NMR
Organisms	Pseudomonas aeruginosa
Macromolecule	CYTOCHROME C551 (protein)
Unique Ligands	HEM

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1GE9 \| pdb_00001ge9	Download File View File

SOLUTION STRUCTURE OF THE RIBOSOME RECYCLING FACTOR

Yoshida, T., Uchiyama, S., Nakano, H., Kashimori, H., Kijima, H., Ohshima, T., Saihara, Y., Ishino, T., Shimahara, T., Yoshida, T., Yokose, K., Ohkubo, T., Kaji, A., Kobayashi, Y.

(2001) Biochemistry 40: 2387-2396

Released	2001-05-16
Method	SOLUTION NMR
Organisms	Aquifex aeolicus
Macromolecule	RIBOSOME RECYCLING FACTOR (protein)

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1IS1 \| pdb_00001is1	Download File View File

Crystal structure of ribosome recycling factor from Vibrio parahaemolyticus

Nakano, H., Yamaichi, Y., Uchiyama, S., Yoshida, T., Nishina, K., Kato, H., Ohkubo, T., Honda, T., Yamagata, Y., Kobayashi, Y.

(2003) J Biological Chem 278: 3427-3436

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Vibrio parahaemolyticus
Macromolecule	RIBOSOME RECYCLING FACTOR (protein)

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1ISE \| pdb_00001ise	Download File View File

Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly

Nakano, H., Yoshida, T., Oka, S., Uchiyama, S., Nishina, K., Ohkubo, T., Kato, H., Yamagata, Y., Kobayashi, Y.

To be published

Released	2003-10-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	Ribosome Recycling Factor (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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1O5P \| pdb_00001o5p	Download File View File

Solution Structure of holo-Neocarzinostatin

Takashima, H., Ishino, T., Yoshida, T., Hasuda, K., Ohkubo, T., Kobayashi, Y.

(2005) J Biological Chem 280: 11340-11346

Released	2003-10-14
Method	SOLUTION NMR
Organisms	Streptomyces carzinostaticus
Macromolecule	Neocarzinostatin (protein)
Unique Ligands	CHR

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1T7H \| pdb_00001t7h	Download File View File

X-ray structure of [Lys(-2)-Arg(-1)-des(17-21)]-endothelin-1 peptide

Hoh, F., Cerdan, R., Kaas, Q., Nishi, Y., Chiche, L., Kubo, S., Chino, N., Kobayashi, Y., Dumas, C., Aumelas, A.

(2004) Biochemistry 43: 15154-15168

Released	2004-12-21
Method	X-RAY DIFFRACTION 1.13 Å
Organisms	Homo sapiens
Macromolecule	Endothelin-1 (protein)

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1V6R \| pdb_00001v6r	Download File View File

Solution Structure of Endothelin-1 with its C-terminal Folding

Takashima, H., Mimura, N., Ohkubo, T., Yoshida, T., Tamaoki, H., Kobayashi, Y.

(2004) J Am Chem Soc 126: 4504-4505

Released	2004-03-16
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Endothelin-1 (protein)

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1VA1 \| pdb_00001va1	Download File View File

Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 1)

Oka, S., Shiraishi, Y., Yoshida, T., Ohkubo, T., Sugiura, Y., Kobayashi, Y.

(2004) Biochemistry 43: 16027-16035

Released	2005-02-08
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Transcription factor Sp1 (protein)
Unique Ligands	ZN

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1VA2 \| pdb_00001va2	Download File View File

Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 2)

Oka, S., Shiraishi, Y., Yoshida, T., Ohkubo, T., Sugiura, Y., Kobayashi, Y.

(2004) Biochemistry 43: 16027-16035

Released	2005-02-08
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Transcription factor Sp1 (protein)
Unique Ligands	ZN

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1VA3 \| pdb_00001va3	Download File View File

Solution Structure of Transcription Factor Sp1 DNA Binding Domain (Zinc Finger 3)

Oka, S., Shiraishi, Y., Yoshida, T., Ohkubo, T., Sugiura, Y., Kobayashi, Y.

(2004) Biochemistry 43: 16027-16035

Released	2005-02-08
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Transcription factor Sp1 (protein)
Unique Ligands	ZN

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1WKI \| pdb_00001wki	Download File View File

solution structure of ribosomal protein L16 from thermus thermophilus HB8

Nishimura, M., Yoshida, T., Shirouzu, M., Terada, T., Kuramitsu, S., Yokoyama, S., Ohkubo, T., Kobayashi, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) J Mol Biology 344: 1369-1383

Released	2004-12-14
Method	SOLUTION NMR
Organisms	Thermus thermophilus HB8
Macromolecule	LSU ribosomal protein L16P (protein)

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1WPK \| pdb_00001wpk	Download File View File

Methylated Form of N-terminal Transcriptional Regulator Domain of Escherichia Coli Ada Protein

Takinowaki, H., Matsuda, Y., Yoshida, T., Kobayashi, Y., Ohkubo, T.

(2006) Protein Sci 15: 487-497

Released	2005-09-13
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	ADA regulatory protein (protein)
Unique Ligands	ZN

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1WZB \| pdb_00001wzb	Download File View File

Crystal structure of the collagen triple helix model [{HYP(R)-HYP(R)-GLY}10]3

Kawahara, K., Nakamura, S., Nishi, Y., Uchiyama, S., Nishiuchi, Y., Nakazawa, T., Ohkubo, T., Kobayashi, Y.

(2005) Biochemistry 44: 15812-15822

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Saimiriine herpesvirus 2
Macromolecule	Collagen triple helix (protein)

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1Y1B \| pdb_00001y1b	Download File View File

Solution structure of Anemonia elastase inhibitor

Hemmi, H., Kumazaki, T., Yoshizawa-Kumagaye, K., Nishiuchi, Y., Yoshida, T., Ohkubo, T., Kobayashi, Y.

(2005) Biochemistry 44: 9626-9636

Released	2005-07-19
Method	SOLUTION NMR
Organisms	Anemonia sulcata
Macromolecule	Elastase inhibitor (protein)

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1Y1C \| pdb_00001y1c	Download File View File

Solution structure of Anemonia elastase inhibitor analogue

Hemmi, H., Kumazaki, T., Yoshizawa-Kumagaye, K., Nishiuchi, Y., Yoshida, T., Ohkubo, T., Kobayashi, Y.

(2005) Biochemistry 44: 9626-9636

Released	2005-07-19
Method	SOLUTION NMR
Organisms	Anemonia sulcata
Macromolecule	Elastase inhibitor (protein)

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1Y69 \| pdb_00001y69	Download File View File

RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans

Wilson, D.N., Schluenzen, F., Harms, J.M., Yoshida, T., Ohkubo, T., Albrecht, R., Buerger, J., Kobayashi, Y., Fucini, P.

(2005) EMBO J 24: 251-260

Released	2005-03-01
Method	X-RAY DIFFRACTION 3.33 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 Escherichia coli K-12
Macromolecule	50S ribosomal protein L16 (protein) 50S ribosomal protein L27 (protein) Ribosome-recycling factor (protein) 23S ribosomal RNA (nucleic acid) 5S ribosomal RNA (nucleic acid)

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2AI5 \| pdb_00002ai5	Download File View File

Solution Structure of Cytochrome C552, determined by Distributed Computing Implementation for NMR data

Nakamura, S., Ichiki, S.I., Takashima, H., Uchiyama, S., Hasegawa, J., Kobayashi, Y., Sambongi, Y., Ohkubo, T.

(2006) Biochemistry 45: 6115-6123

Released	2006-05-23
Method	SOLUTION NMR
Organisms	Hydrogenobacter thermophilus
Macromolecule	Cytochrome c-552 (protein)
Unique Ligands	HEC

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2D0S \| pdb_00002d0s	Download File View File

Crystal structure of the Cytochrome C552 from moderate thermophilic bacterium, hydrogenophilus thermoluteolus

Nakamura, S., Ichiki, S.I., Takashima, H., Uchiyama, S., Hasegawa, J., Kobayashi, Y., Sambongi, Y., Ohkubo, T.

(2006) Biochemistry 45: 6115-6123

Released	2006-05-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hydrogenophilus thermoluteolus
Macromolecule	cytochrome c (protein)
Unique Ligands	HEC

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2E0I \| pdb_00002e0i	Download File View File

Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor

Fujihashi, M., Numoto, N., Kobayashi, Y., Mizushima, A., Tsujimura, M., Nakamura, A., Kawarabayashi, Y., Miki, K.

(2007) J Mol Biology 365: 903-910

Released	2006-11-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	432aa long hypothetical deoxyribodipyrimidine photolyase (protein)
Unique Ligands	FAD, MPD