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 = "Kimura, A."

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 46 Structures.

Refinements

Structure Determination Methodology

experimental (46)

Scientific Name of Source Organism

	Kribbella flavida DSM 17836 (13)
	Beta vulgaris (6)
	Niallia circulans (6)
	Paenibacillus sp. 598K (5)
	Streptococcus mutans (5)
	Oryza sativa Indica Group (2)
	Streptomyces thermolilacinus (2)
	Thermoanaerobacter pseudethanolicus ATCC 33223 (2)
	Bacteroides thetaiotaomicron (1)
	Bacteroides thetaiotaomicron VPI-5482 (1)

More...

Taxonomy

	Bacteria (36)
	Eukaryota (9)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (46)

Polymer Entity Type

Protein (46)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (17)
	2.0 - 2.5 (16)
	2.5 - 3.0 (7)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (20)
	2015 - 2019 (19)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (38)
	Transferases (11)

Symmetry Type

	Asymmetric (35)
	Cyclic (10)
	Dihedral (1)

SCOP Classification

	All beta proteins (9)
	Alpha and beta proteins (a/b) (13)
	Artifacts (4)

AllSelected

1 to 25 of 46 Structures

Page 1 of 2

Sort by

Explore in 3D

1WE5 \| pdb_00001we5	Download File View File

Crystal Structure of Alpha-Xylosidase from Escherichia coli

Ose, T., Kitamura, M., Okuyama, M., Mori, H., Kimura, A., Watanabe, N., Yao, M., Tanaka, I.

To be published

Released	2005-02-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli
Macromolecule	Putative family 31 glucosidase yicI (protein)
Unique Ligands	MES

Explore in 3D

2ZIC \| pdb_00002zic	Download File View File

Crystal structure of Streptococcus mutans dextran glucosidase

Hondoh, H., Saburi, W., Mori, H., Okuyama, M., Nakada, T., Matsuura, Y., Kimura, A.

(2008) J Mol Biology 378: 911-920

Released	2008-06-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Streptococcus mutans
Macromolecule	Dextran glucosidase (protein)
Unique Ligands	CA, GOL, TRS

Explore in 3D

2ZID \| pdb_00002zid	Download File View File

Crystal structure of dextran glucosidase E236Q complex with isomaltotriose

Hondoh, H., Saburi, W., Mori, H., Okuyama, M., Nakada, T., Matsuura, Y., Kimura, A.

(2008) J Mol Biology 378: 911-920

Released	2008-06-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Streptococcus mutans
Macromolecule	Dextran glucosidase (protein)
Unique Ligands	CA
Unique branched monosaccharides	GLC

Explore in 3D

3KSC \| pdb_00003ksc	Download File View File

Crystal structure of pea prolegumin, an 11S seed globulin from Pisum sativum L.

Tandang-Silvas, M.R.G., Fukuda, T., Fukuda, C., Prak, K., Cabanos, C., Kimura, A., Itoh, T., Mikami, B., Maruyama, N., Utsumi, S.

(2010) Biochim Biophys Acta 1804: 1432-1442

Released	2010-04-21
Method	X-RAY DIFFRACTION 2.606 Å
Organisms	Pisum sativum
Macromolecule	LegA class (protein)
Unique Ligands	GOL, SO4

Explore in 3D

3VJF \| pdb_00003vjf	Download File View File

Crystal structure of de novo 4-helix bundle protein WA20

Arai, R., Kimura, A., Kobayashi, N., Matsuo, K., Sato, T., Wang, A.F., Platt, J.M., Bradley, L.H., Hecht, M.H.

(2012) J Phys Chem B 116: 6789-6797

Released	2012-03-28
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	synthetic construct
Macromolecule	WA20 (protein)
Unique Ligands	K

Explore in 3D

3VMN \| pdb_00003vmn	Download File View File

Crystal structure of dextranase from Streptococcus mutans

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Okuyama, M., Mori, H., Funane, K., Kimura, A.

(2012) J Biological Chem 287: 19916-19926

Released	2012-02-15
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptococcus mutans
Macromolecule	Dextranase (protein)
Unique Ligands	PO4

Explore in 3D

3VMO \| pdb_00003vmo	Download File View File

Crystal structure of dextranase from Streptococcus mutans in complex with isomaltotriose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Okuyama, M., Mori, H., Funane, K., Kimura, A.

(2012) J Biological Chem 287: 19916-19926

Released	2012-02-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Streptococcus mutans
Macromolecule	Dextranase (protein)
Unique Ligands	PO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3VMP \| pdb_00003vmp	Download File View File

Crystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Okuyama, M., Mori, H., Funane, K., Kimura, A.

(2012) J Biological Chem 287: 19916-19926

Released	2012-02-15
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Streptococcus mutans
Macromolecule	Dextranase (protein)
Unique Ligands	E5G, PO4

Explore in 3D

3W37 \| pdb_00003w37	Download File View File

Sugar beet alpha-glucosidase with acarbose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2013) J Biological Chem 288: 19296-19303

Released	2013-05-29
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	ACY, GOL, NAG, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

Explore in 3D

3W38 \| pdb_00003w38	Download File View File

Sugar beet alpha-glucosidase

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2013) J Biological Chem 288: 19296-19303

Released	2013-05-29
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	NAG, SO4
Unique branched monosaccharides	FUC, NAG

Explore in 3D

3WEL \| pdb_00003wel	Download File View File

Sugar beet alpha-glucosidase with acarviosyl-maltotriose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2014) J Biological Chem 290: 1796-1803

Released	2014-07-16
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

Explore in 3D

3WEM \| pdb_00003wem	Download File View File

Sugar beet alpha-glucosidase with acarviosyl-maltotetraose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2014) J Biological Chem 290: 1796-1803

Released	2014-07-16
Method	X-RAY DIFFRACTION 2.591 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	NAG, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

Explore in 3D

3WEN \| pdb_00003wen	Download File View File

Sugar beet alpha-glucosidase with acarviosyl-maltopentaose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2014) J Biological Chem 290: 1796-1803

Released	2014-07-16
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	NAG, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

Explore in 3D

3WEO \| pdb_00003weo	Download File View File

Sugar beet alpha-glucosidase with acarviosyl-maltohexaose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2014) J Biological Chem 290: 1796-1803

Released	2014-07-16
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	GOL, NAG, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

Explore in 3D

3WFA \| pdb_00003wfa	Download File View File

Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase

Okuyama, M., Yoshida, T., Hondoh, H., Mori, H., Yao, M., Kimura, A.

To be published

Released	2014-07-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bacteroides thetaiotaomicron
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	EDT, NA

Explore in 3D

3WNK \| pdb_00003wnk	Download File View File

Crystal Structure of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	ACT, CA, CD, GOL, NA

Explore in 3D

3WNL \| pdb_00003wnl	Download File View File

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltohexaose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Suzuki, S., Kitamura, S., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, MES, NA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3WNM \| pdb_00003wnm	Download File View File

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoheptaose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Suzuki, S., Kitamura, S., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, MES, NA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3WNN \| pdb_00003wnn	Download File View File

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltooctaose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Suzuki, S., Kitamura, S., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, MES, NA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3WNO \| pdb_00003wno	Download File View File

D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with cycloisomaltooctaose

Suzuki, N., Fujimoto, Z., Kim, Y.M., Momma, M., Kishine, N., Suzuki, R., Kobayashi, M., Kimura, A., Funane, K.

(2014) J Biological Chem 289: 12040-12051

Released	2014-02-05
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, EDO, MES, NA, SO4
Unique branched monosaccharides	GLC

Explore in 3D

3WNP \| pdb_00003wnp	Download File View File

D308A, F268V, D469Y, A513V, and Y515S quintuple mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoundecaose

Suzuki, R., Suzuki, N., Fujimoto, Z., Momma, M., Kimura, K., Kitamura, S., Kimura, A., Funane, K.

(2015) Biochem J 467: 259-270

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Niallia circulans
Macromolecule	Cycloisomaltooligosaccharide glucanotransferase (protein)
Unique Ligands	CA, MES, NA, SO4
Unique branched monosaccharides	BGC, GLC

Explore in 3D

3WSU \| pdb_00003wsu	Download File View File

Crystal structure of beta-mannanase from Streptomyces thermolilacinus

Kumagai, Y., Yamashita, K., Okuyama, M., Hatanaka, T., Yao, M., Kimura, A.

(2015) FEBS J 282: 4001-4014

Released	2015-05-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces thermolilacinus
Macromolecule	Beta-mannanase (protein)
Unique Ligands	GOL, NA

Explore in 3D

4JHO \| pdb_00004jho	Download File View File

Structural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase

Tankrathok, A., Luang, S., Robinson, R.C., Kimura, A., Hrmova, M., Ketudat Cairns, J.R.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2124-2135

Released	2013-10-09
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Oryza sativa Indica Group
Macromolecule	Beta-mannosidase/beta-glucosidase (protein)
Unique Ligands	EPE, GOL

Explore in 3D

4JIE \| pdb_00004jie	Download File View File

Structural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase

Tankrathok, A., Luang, S., Robinson, R.C., Kimura, A., Hrmova, M., Ketudat Cairns, J.R.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2124-2135

Released	2013-10-09
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Oryza sativa Indica Group
Macromolecule	Beta-mannosidase/beta-glucosidase (protein)
Unique Ligands	BMA, EPE, GOL

Explore in 3D

4Y7E \| pdb_00004y7e	Download File View File

Crystal structure of beta-mannanase from Streptomyces thermolilacinus with mannohexaose

Kumagai, Y., Yamashita, K., Okuyama, M., Hatanaka, T., Yao, M., Kimura, A.

(2015) FEBS J 282: 4001-4014

Released	2015-09-23
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Streptomyces thermolilacinus
Macromolecule	Endoglucanase (protein)
Unique Ligands	BMA, CA, GOL
Unique branched monosaccharides	BMA

1 to 25 of 46 Structures

Page 1 of 2

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1WE5 | pdb_00001we5

2ZIC | pdb_00002zic

2ZID | pdb_00002zid

3KSC | pdb_00003ksc

3VJF | pdb_00003vjf

3VMN | pdb_00003vmn

3VMO | pdb_00003vmo

3VMP | pdb_00003vmp

3W37 | pdb_00003w37

3W38 | pdb_00003w38

3WEL | pdb_00003wel

3WEM | pdb_00003wem

3WEN | pdb_00003wen

3WEO | pdb_00003weo

3WFA | pdb_00003wfa

3WNK | pdb_00003wnk

3WNL | pdb_00003wnl

3WNM | pdb_00003wnm

3WNN | pdb_00003wnn

3WNO | pdb_00003wno

3WNP | pdb_00003wnp

3WSU | pdb_00003wsu

4JHO | pdb_00004jho

4JIE | pdb_00004jie

4Y7E | pdb_00004y7e