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: Structure Author = "Nakamura, S."

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 75 Structures.

Refinements

Structure Determination Methodology

experimental (75)

Scientific Name of Source Organism

	Flavobacterium johnsoniae UW101 (12)
	Homo sapiens (11)
	Severe acute respiratory syndrome coronavirus 2 (11)
	synthetic construct (11)
	Clostridium perfringens (5)
	Mus musculus (5)
	Bacillus sp. TAR1 (4)
	Escherichia coli (4)
	Bacillus sp. 41M-1 (3)
	Vibrio cholerae (3)

More...

Taxonomy

	Bacteria (43)
	Eukaryota (18)
	Riboviria (12)
	other sequences (11)
	Duplodnaviria (3)
	Archaea (1)
	Eukaryota (eukaryotes) (1)
	Riboviria (RNA viruses and viroids) (1)

Experimental Method

	X-RAY DIFFRACTION (69)
	ELECTRON MICROSCOPY (4)
	SOLUTION NMR (2)

Polymer Entity Type

Protein (75)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (8)
	1.5 - 2.0 (29)
	2.0 - 2.5 (21)
	2.5 - 3.0 (6)
	3.5 - 4.0 (3)
	4.0 - 4.5 (2)
	> 4.5 (3)

Release Date

	1990 - 1994 (1)
	2000 - 2004 (2)
	2005 - 2009 (19)
	2010 - 2014 (8)
	2015 - 2019 (12)
	2020 - 2024 (20)
	2025 - 2029 (13)

Enzyme Classification Name

	Hydrolases (21)
	Oxidoreductases (5)
	Transferases (5)

Membrane Protein Annotation

	MemProtMD (3)
	OPM (3)
	PDBTM (3)

Symmetry Type

	Asymmetric (45)
	Cyclic (23)
	Dihedral (6)
	Helical (2)

SCOP Classification

	Alpha and beta proteins (a/b) (9)
	Alpha and beta proteins (a+b) (9)
	All alpha proteins (8)
	All beta proteins (4)
	Artifacts (4)
	Small proteins (1)

AllSelected

1 to 25 of 75 Structures

Page 1 of 3

Sort by

Explore in 3D

1TAB \| pdb_00001tab	Download File View File

STRUCTURE OF THE TRYPSIN-BINDING DOMAIN OF BOWMAN-BIRK TYPE PROTEASE INHIBITOR AND ITS INTERACTION WITH TRYPSIN

Tsunogae, Y., Tanaka, I., Yamane, T., Kikkawa, J.-I., Ashida, T., Ishikawa, C., Watanabe, K., Nakamura, S., Takahashi, K.

(1986) J Biochem 100: 1637-1646

Released	1992-01-15
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bos taurus Phaseolus angularis
Macromolecule	BOWMAN-BIRK TYPE PROTEINASE INHIBITOR (protein) TRYPSIN (protein)

Explore in 3D

1V53 \| pdb_00001v53	Download File View File

The crystal structure of 3-isopropylmalate dehydrogenase from Bacillus coagulans

Fujita, K., Minami, H., Suzuki, K., Tsunoda, M., Sekiguchi, T., Mizui, R., Tsuzaki, S., Nakamura, S., Takenaka, A.

To be published

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Heyndrickxia coagulans
Macromolecule	3-isopropylmalate dehydrogenase (protein)

Explore in 3D

1V5B \| pdb_00001v5b	Download File View File

The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans

Fujita, K., Minami, H., Suzuki, K., Tsunoda, M., Sekiguchi, T., Mizui, R., Tsuzaki, S., Nakamura, S., Takenaka, A.

To be published

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Heyndrickxia coagulans
Macromolecule	3-isopropylmalate dehydrogenase (protein)
Unique Ligands	SO4

Explore in 3D

1V5C \| pdb_00001v5c	Download File View File

The crystal structure of the inactive form chitosanase from Bacillus sp. K17 at pH3.7

Adachi, W., Shimizu, S., Sunami, T., Fukazawa, T., Suzuki, M., Yatsunami, R., Nakamura, S., Takenaka, A.

(2004) J Mol Biology 343: 785-795

Released	2004-12-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bacillus sp. (in: firmicutes)
Macromolecule	chitosanase (protein)
Unique Ligands	SO4

Explore in 3D

1V5D \| pdb_00001v5d	Download File View File

The crystal structure of the active form chitosanase from Bacillus sp. K17 at pH6.4

Adachi, W., Shimizu, S., Sunami, T., Fukazawa, T., Suzuki, M., Yatsunami, R., Nakamura, S., Takenaka, A.

(2004) J Mol Biology 343: 785-795

Released	2004-12-07
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Bacillus sp. (in: firmicutes)
Macromolecule	chitosanase (protein)
Unique Ligands	PIN

Explore in 3D

1VBR \| pdb_00001vbr	Download File View File

Crystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose

Ihsanawati, Kumasaka, T., Kaneko, T., Nakamura, S., Tanaka, N.

(2005) Proteins 61: 999-1009

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermotoga maritima
Macromolecule	endo-1,4-beta-xylanase B (protein)
Unique Ligands	ACY
Unique branched monosaccharides	XYP, XYS

Explore in 3D

1VBU \| pdb_00001vbu	Download File View File

Crystal structure of native xylanase 10B from Thermotoga maritima

Ihsanawati, Kumasaka, T., Kaneko, T., Nakamura, S., Tanaka, N.

(2005) Proteins 61: 999-1009

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermotoga maritima
Macromolecule	endo-1,4-beta-xylanase B (protein)
Unique Ligands	ACY, GOL, SO4

Explore in 3D

1WQL \| pdb_00001wql	Download File View File

Cumene dioxygenase (cumA1A2) from Pseudomonas fluorescens IP01

Dong, X., Fushinobu, S., Fukuda, E., Terada, T., Nakamura, S., Shimizu, K., Nojiri, H., Omori, T., Shoun, H., Wakagi, T.

(2005) J Bacteriol 187: 2483-2490

Released	2005-03-29
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudomonas fluorescens
Macromolecule	ethylbenzene dioxygenase small subunit (protein) iron-sulfur protein large subunit of cumene dioxygenase (protein)
Unique Ligands	FE2, FES, OXY

Explore in 3D

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)

Explore in 3D

1YT6 \| pdb_00001yt6	Download File View File

NMR structure of peptide SD

Murata, T., Hemmi, H., Nakamura, S., Shimizu, K., Suzuki, Y., Yamaguchi, I.

(2005) FEBS J 272: 4938-4948

Released	2005-09-27
Method	SOLUTION NMR
Macromolecule	peptide SD (protein)

Explore in 3D

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

Explore in 3D

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

Explore in 3D

2DCJ \| pdb_00002dcj	Download File View File

A two-domain structure of alkaliphilic XynJ from Bacillus sp. 41M-1

Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.

To be published

Released	2007-03-20
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Bacillus sp. 41M-1
Macromolecule	xylanase J (protein)
Unique Ligands	CA, GOL, MPD

Explore in 3D

2DCK \| pdb_00002dck	Download File View File

A tetragonal-lattice structure of alkaliphilic XynJ from Bacillus sp. 41M-1

Fibriansah, G., Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.

To be published

Released	2007-03-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bacillus sp. 41M-1
Macromolecule	xylanase J (protein)
Unique Ligands	CA, GOL

Explore in 3D

2DKN \| pdb_00002dkn	Download File View File

Crystal structure of the 3-alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831 complexed with NADH

Nakamura, S.

(2006) J Biological Chem 281: 31876-31884

Released	2006-08-15
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas sp. B-0831
Macromolecule	3-alpha-hydroxysteroid dehydrogenase (protein)
Unique Ligands	NAI

Explore in 3D

2DT4 \| pdb_00002dt4	Download File View File

Crystal structure of Pyrococcus horikoshii a plant- and prokaryote-conserved (PPC) protein at 1.60 resolution

Lin, L., Nakano, H., Uchiyama, S., Fujimoto, S., Matsunaga, S., Nakamura, S.

(2007) Proteins 67: 505-507

Released	2007-05-22
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Hypothetical protein PH0802 (protein)
Unique Ligands	GOL

Explore in 3D

2E5B \| pdb_00002e5b	Download File View File

Crystal structure of Human NMPRTase as free-form

Takahashi, R., Nakamura, S., Kobayashi, Y., Ohkubo, T.

(2010) J Biochem 147: 95-107

Released	2007-12-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Nicotinamide phosphoribosyltransferase (protein)

Explore in 3D

2E5C \| pdb_00002e5c	Download File View File

Crystal structure of Human NMPRTase complexed with 5'-phosphoribosyl-1'-pyrophosphate

Takahashi, R., Nakamura, S., Kobayashi, Y., Ohkubo, T.

(2010) J Biochem 147: 95-107

Released	2007-12-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Nicotinamide phosphoribosyltransferase (protein)
Unique Ligands	PRP

Explore in 3D

2E5D \| pdb_00002e5d	Download File View File

Crystal structure of Human NMPRTase complexed with nicotinamide

Takahashi, R., Nakamura, S., Kobayashi, Y., Ohkubo, T.

(2010) J Biochem 147: 95-107

Released	2007-12-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Nicotinamide phosphoribosyltransferase (protein)
Unique Ligands	NCA

Explore in 3D

2HYK \| pdb_00002hyk	Download File View File

The crystal structure of an endo-beta-1,3-glucanase from alkaliphilic Nocardiopsis sp.strain F96

Fibriansah, G., Nakamura, S., Kumasaka, T.

(2007) Proteins 69: 683-690

Released	2007-10-02
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Nocardiopsis sp. F96
Macromolecule	Beta-1,3-glucanase (protein)
Unique Ligands	CA, EOH, GOL, SO4

Explore in 3D

2Z2T \| pdb_00002z2t	Download File View File

Crystal structure of the complex between gp41 fragment N36 and fusion inhibitor SC34EK

Nakamura, S., Ohkubo, T., Kobayashi, Y.

To be published

Released	2008-06-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Human immunodeficiency virus type 1 group M subtype B (isolate LW123)
Macromolecule	Fusion inhibitor peptide SC34EK (protein) gp41 fragment N36 (protein)
Unique Ligands	ACY, SO4

Explore in 3D

2ZXY \| pdb_00002zxy	Download File View File

Crystal Structure of Cytochrome c555 from Aquifex aeolicus

Obuchi, M., Kawahara, K., Motooka, D., Nakamura, S., Yamanaka, M., Takeda, T., Uchiyama, S., Kobayashi, Y., Ohkubo, T., Sambongi, Y.

(2009) Acta Crystallogr D Biol Crystallogr 65: 804-813

Released	2009-08-04
Method	X-RAY DIFFRACTION 1.15 Å
Organisms	Aquifex aeolicus
Macromolecule	Cytochrome c552 (protein)
Unique Ligands	HEC

Explore in 3D

3AHA \| pdb_00003aha	Download File View File

Crystal structure of the complex between gp41 fragments N36 and C34 mutant N126K/E137Q

Izumi, K., Nakamura, S., Nakano, H., Shimura, K., Sakagami, Y., Oishi, S., Uchiyama, S., Ohkubo, T., Kobayashi, Y., Fujii, N., Matsuoka, M., Kodama, E.N.

(2010) Antiviral Res

Released	2010-05-19
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Transmembrane protein gp41 (protein)
Unique Ligands	CL, MPD