RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Citation Author = "Kobayashi, K."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 145 Structures.

Refinements

Structure Determination Methodology

experimental (145)

Scientific Name of Source Organism

	Homo sapiens (60)
	Bos taurus (20)
	Rattus norvegicus (14)
	Ignavibacterium album JCM 16511 (12)
	unidentified (12)
	Saccharolobus solfataricus (8)
	synthetic construct (7)
	Canis lupus familiaris (6)
	Severe acute respiratory syndrome-related coronavirus (5)
	Tetrahymena pyriformis (5)

More...

Taxonomy

	Eukaryota (80)
	Bacteria (37)
	Archaea (14)
	unclassified sequences (12)
	Riboviria (7)
	other sequences (7)
	Eukaryota (eukaryotes) (4)

Experimental Method

	X-RAY DIFFRACTION (91)
	ELECTRON MICROSCOPY (45)
	SOLUTION NMR (9)
	NEUTRON DIFFRACTION (1)

Polymer Entity Type

	Protein (145)
	RNA (7)
	DNA (3)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (14)
	1.5 - 2.0 (35)
	2.0 - 2.5 (22)
	2.5 - 3.0 (26)
	3.0 - 3.5 (23)
	3.5 - 4.0 (10)
	4.0 - 4.5 (3)
	> 4.5 (3)

Release Date

	1980 - 1984 (1)
	1995 - 1999 (7)
	2000 - 2004 (4)
	2005 - 2009 (7)
	2010 - 2014 (15)
	2015 - 2019 (25)
	2020 - 2024 (80)
	2025 - 2029 (6)

Enzyme Classification Name

	Hydrolases (40)
	Transferases (19)
	Oxidoreductases (4)

Membrane Protein Annotation

	PDBTM (36)
	MemProtMD (24)
	OPM (29)
	mpstruc (21)

Symmetry Type

	Asymmetric (87)
	Cyclic (67)

SCOP Classification

	All beta proteins (20)
	All alpha proteins (13)
	Alpha and beta proteins (a/b) (11)
	Membrane and cell surface proteins and peptides (1)
	Small proteins (7)
	Peptides (1)

AllSelected

1 to 25 of 145 Structures

Page 1 of 6

Sort by

Explore in 3D

1AO6 \| pdb_00001ao6	Download File View File

CRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN

Sugio, S., Mochizuki, S., Noda, M., Kashima, A.

(1999) Protein Eng 12: 439-446

Released	1998-05-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	SERUM ALBUMIN (protein)

Explore in 3D

1BM0 \| pdb_00001bm0	Download File View File

CRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN

Sugio, S., Kashima, A., Mochizuki, S., Noda, M., Kobayashi, K.

(1999) Protein Eng 12: 439-446

Released	1999-07-28
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	SERUM ALBUMIN (protein)

Explore in 3D

1EH9 \| pdb_00001eh9	Download File View File

CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS GLYCOSYLTREHALOSE TREHALOHYDROLASE

Feese, M.D., Kato, Y., Tamada, T., Kato, M., Komeda, T., Kobayashi, K., Kuroki, R.

(2000) J Mol Biology 301: 451-464

Released	2001-02-19
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharolobus solfataricus
Macromolecule	GLYCOSYLTREHALOSE TREHALOHYDROLASE (protein)

Explore in 3D

1EHA \| pdb_00001eha	Download File View File

CRYSTAL STRUCTURE OF GLYCOSYLTREHALOSE TREHALOHYDROLASE FROM SULFOLOBUS SOLFATARICUS

Feese, M.D., Kato, Y., Tamada, T., Kato, M., Komeda, T., Kobayashi, K., Kuroki, R.

(2000) J Mol Biology 301: 451-464

Released	2001-02-19
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharolobus solfataricus
Macromolecule	GLYCOSYLTREHALOSE TREHALOHYDROLASE (protein)

Explore in 3D

1F3K \| pdb_00001f3k	Download File View File

THREE-DIMENSIONAL SOLUTION STRUCTURE OF OMEGA-CONOTOXIN TXVII, AN L-TYPE CALCIUM CHANNEL BLOCKER

Kobayashi, K., Sasaki, T., Sato, K., Kohno, T.

(2000) Biochemistry 39: 14761-14767

Released	2000-12-13
Method	SOLUTION NMR
Organisms	Conus textile
Macromolecule	OMEGA-CONOTOXIN TXVII (protein)

Explore in 3D

1FU3 \| pdb_00001fu3	Download File View File

THREE-DIMENSIONAL STRUCTURE IN SOLUTION OF THE SODIUM CHANNEL AGONIST/ANTAGONIST DELTA-CONOTOXIN TXVIA

Kohno, T., Sasaki, T., Fainzilber, M., Sato, K.

(2002) J Biological Chem 277: 36387-36391

Released	2002-09-20
Method	SOLUTION NMR
Organisms	Conus textile
Macromolecule	DELTA-CONOTOXIN TXVIA (protein)

Explore in 3D

1NDH \| pdb_00001ndh	Download File View File

CRYSTAL STRUCTURE OF NADH-CYTOCHROME B5 REDUCTASE FROM PIG LIVER AT 2.4 ANGSTROMS RESOLUTION

Nishida, H., Miki, K.

(1995) Biochemistry 34: 2763-2767

Released	1995-02-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Sus scrofa
Macromolecule	CYTOCHROME B5 REDUCTASE (protein)
Unique Ligands	FAD

Explore in 3D

1OMG \| pdb_00001omg	Download File View File

NMR STUDY OF OMEGA-CONOTOXIN MVIIA

Kohno, T., Kim, J.-I., Kobayashi, K., Kodera, Y., Maeda, T., Sato, K.

(1995) Biochemistry 34: 10256-10265

Released	1996-04-03
Method	SOLUTION NMR
Organisms	Conus magus
Macromolecule	OMEGA-CONOTOXIN MVIIA (protein)

Explore in 3D

1PRU \| pdb_00001pru	Download File View File

PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING

Nagadoi, A., Morikawa, S., Nakamura, H., Enari, M., Kobayashi, K., Yamamoto, H., Sampei, G., Mizobuchi, K., Schumacher, M.A., Brennan, R.G., Nishimura, Y.

(1995) Structure 3: 1217-1224

Released	1996-03-08
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PURINE REPRESSOR (protein)

Explore in 3D

1PRV \| pdb_00001prv	Download File View File

PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING

Nagadoi, A., Morikawa, S., Nakamura, H., Enari, M., Kobayashi, K., Yamamoto, H., Sampei, G., Mizobuchi, K., Schumacher, M.A., Brennan, R.G., Nishimura, Y.

(1995) Structure 3: 1217-1224

Released	1996-03-08
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PURINE REPRESSOR (protein)

Explore in 3D

1QCM \| pdb_00001qcm	Download File View File

AMYLOID BETA PEPTIDE (25-35), NMR, 20 STRUCTURES

Kohno, T., Kobayashi, K., Maeda, T., Sato, K., Takashima, A.

(1996) Biochemistry 35: 16094-16104

Released	1997-07-07
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	AMYLOID BETA PEPTIDE (protein)

Explore in 3D

1V4Q \| pdb_00001v4q	Download File View File

Three-dimensional solution structure of the analogue peptide of omega-conotoxin MVIIC

Kobayashi, K., Sasaki, T., Sato, K., Kohno, T.

To be published

Released	2005-03-01
Method	SOLUTION NMR
Organisms	Conus magus
Macromolecule	omega-conotoxin MVIIC (protein)

Explore in 3D

1V4R \| pdb_00001v4r	Download File View File

Solution structure of Streptmycal repressor TraR

Tanaka, T., Komatsu, C., Kobayashi, K., Sugai, M., Kataoka, M., Kohno, T.

To be published

Released	2005-03-01
Method	SOLUTION NMR
Organisms	Streptomyces
Macromolecule	Transcriptional Repressor (protein)

Explore in 3D

1WQB \| pdb_00001wqb	Download File View File

Three-dimensional Solution Strucutre of Aptotoxin VII, from the venom of a Trap-door Spider

Kobayashi, K., Kim, J.-I., Sato, K., Kohno, T.

To be published

Released	2005-12-13
Method	SOLUTION NMR
Organisms	Apomastus schlingeri
Macromolecule	Aptotoxin VII (protein)

Explore in 3D

2ZHG \| pdb_00002zhg	Download File View File

Crystal structure of SoxR in complex with DNA

Watanabe, S., Kita, A., Kobayashi, K., Miki, K.

(2008) Proc Natl Acad Sci U S A 105: 4121-4126

Released	2008-03-25
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli K-12
Macromolecule	Redox-sensitive transcriptional activator soxR (protein) DNA (5'-D(DGPDCPDCPDTPDCPDAPDAPDGPDTPDTPDAPDAPDCPDTPDTPDGPDAPDGPDGPDC)-3') (nucleic acid)
Unique Ligands	DTT, FES, GOL

Explore in 3D

2ZHH \| pdb_00002zhh	Download File View File

Crystal structure of SoxR

Watanabe, S., Kita, A., Kobayashi, K., Miki, K.

(2008) Proc Natl Acad Sci U S A 105: 4121-4126

Released	2008-03-25
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Escherichia coli K-12
Macromolecule	Redox-sensitive transcriptional activator soxR (protein)
Unique Ligands	DTT, FES

Explore in 3D

2ZON \| pdb_00002zon	Download File View File

Crystal structure of electron transfer complex of nitrite reductase with cytochrome c

Nojiri, M., Koteishi, H., Yamaguchi, K., Suzuki, S.

(2009) Nature 462: 117-120

Released	2009-06-09
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Achromobacter xylosoxidans
Macromolecule	Dissimilatory copper-containing nitrite reductase (protein) cytochrome c551 (protein)
Unique Ligands	CU, HEM

Explore in 3D

2ZOO \| pdb_00002zoo	Download File View File

Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125

Nojiri, M., Tsuda, A., Yamaguchi, K., Suzuki, S.

To be published

Released	2009-06-09
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Pseudoalteromonas translucida TAC125
Macromolecule	Probable nitrite reductase (protein)
Unique Ligands	CU, HEM, SO4
Unique branched monosaccharides	FRU, GLC

Explore in 3D

3AGK \| pdb_00003agk	Download File View File

Crystal structure of archaeal translation termination factor, aRF1

Kobayashi, K., Kikuno, I., Ishitani, R., Ito, K., Nureki, O.

(2010) Proc Natl Acad Sci U S A 107: 19242-19247

Released	2010-11-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Aeropyrum pernix
Macromolecule	Peptide chain release factor subunit 1 (protein)

Explore in 3D

3AQ5 \| pdb_00003aq5	Download File View File

Crystal structure of truncated hemoglobin from Tetrahymena pyriformis, Fe(II)-O2 form

Igarashi, J., Kobayashi, K., Matsuoka, A.

(2011) J Biol Inorg Chem 16: 599-609

Released	2011-04-20
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Tetrahymena pyriformis
Macromolecule	Group 1 truncated hemoglobin (protein)
Unique Ligands	HEM, OXY