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

233,249 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 = "Morishita, M."

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 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Streptobacillus moniliformis DSM 12112 (6)
	Streptococcus agalactiae NEM316 (5)
	Lacticaseibacillus rhamnosus (4)
	Bacillus subtilis subsp. subtilis str. 168 (2)
	Pectobacterium carotovorum subsp. carotovorum (2)
	Streptococcus pyogenes serotype M1 (1)

Taxonomy

Bacteria (20)

Experimental Method

X-RAY DIFFRACTION (20)

Polymer Entity Type

Protein (20)

Refinement Resolution (Å)

	1.5 - 2.0 (13)
	2.0 - 2.5 (2)
	2.5 - 3.0 (4)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (4)
	2015 - 2019 (12)
	2020 - 2024 (4)

Enzyme Classification Name

	Isomerases (4)
	Oxidoreductases (3)
	Hydrolases (1)
	Transferases (1)

Symmetry Type

	Asymmetric (10)
	Cyclic (4)
	Dihedral (8)

SCOP Classification

	Alpha and beta proteins (a/b) (7)
	All alpha proteins (1)

AllSelected

1 to 20 of 20 Structures

Page 1 of 1

Sort by

Explore in 3D

3WUX \| pdb_00003wux	Download File View File

Crystal structure of unsaturated glucuronyl hydrolase mutant D115N/K370S from Streptococcus agalactiae

Nakamichi, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

To be published

Released	2014-05-28
Method	X-RAY DIFFRACTION 1.792 Å
Organisms	Streptococcus agalactiae NEM316
Macromolecule	Unsaturated chondroitin disaccharide hydrolase (protein)
Unique Ligands	EDO

Explore in 3D

4TKZ \| pdb_00004tkz	Download File View File

Crystal structure of phosphotransferase system component EIIA from Streptococcus agalactiae

Nakamichi, Y., Maruyama, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

To be published

Released	2014-08-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptococcus agalactiae NEM316
Macromolecule	Putative uncharacterized protein gbs1890 (protein)
Unique Ligands	GOL

Explore in 3D

4U8E \| pdb_00004u8e	Download File View File

Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase from Streptococcus agalactiae

Maruyama, y., Oiki, S., Takase, R., Mikami, B., Murata, K., Hashimoto, W.

(2015) J Biological Chem 290: 6281-6292

Released	2015-01-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptococcus agalactiae NEM316
Macromolecule	Putative uncharacterized protein gbs1892 (protein)

Explore in 3D

4U8F \| pdb_00004u8f	Download File View File

Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase complexed with a tartrate

Maruyama, Y., Oiki, S., Takase, R., Mikami, B., Murata, K., Hashimoto, W.

(2015) J Biological Chem 290: 6281-6292

Released	2014-12-24
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Streptococcus agalactiae NEM316
Macromolecule	Putative uncharacterized protein gbs1892 (protein)
Unique Ligands	TLA

Explore in 3D

4U8G \| pdb_00004u8g	Download File View File

Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus agalactiae

Maruyama, Y., Oiki, S., Takase, R., Mikami, B., Murata, K., Hashimoto, W.

(2015) J Biological Chem 290: 6281-6292

Released	2014-12-24
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Streptococcus agalactiae NEM316
Macromolecule	Putative uncharacterized protein gbs1891 (protein)

Explore in 3D

4Z9X \| pdb_00004z9x	Download File View File

Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus pyogenes

Maruyama, Y., Takase, R., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

(2016) Proteins 84: 934-947

Released	2015-04-29
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Streptococcus pyogenes serotype M1
Macromolecule	Gluconate 5-dehydrogenase (protein)

Explore in 3D

4Z9Y \| pdb_00004z9y	Download File View File

Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Pectobacterium carotovorum

Takase, R., Maruyama, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

(2016) Proteins 84: 934-947

Released	2015-04-29
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Pectobacterium carotovorum subsp. carotovorum
Macromolecule	2-deoxy-D-gluconate 3-dehydrogenase (protein)
Unique Ligands	SO4

Explore in 3D

4ZA2 \| pdb_00004za2	Download File View File

Crystal structure of Pectobacterium carotovorum 2-keto-3-deoxy-D-gluconate dehydrogenase complexed with NAD+

Takase, R., Maruyama, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

(2016) Proteins 84: 934-947

Released	2015-04-29
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Pectobacterium carotovorum subsp. carotovorum
Macromolecule	2-deoxy-D-gluconate 3-dehydrogenase (protein)
Unique Ligands	NAD

Explore in 3D

5GUB \| pdb_00005gub	Download File View File

Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide

Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

(2017) Sci Rep 7: 1069-1069

Released	2017-07-19
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Streptobacillus moniliformis DSM 12112
Macromolecule	Extracellular solute-binding protein family 1 (protein)
Unique Ligands	CA, EDO, MES
Unique branched monosaccharides	GCD, NGA

Explore in 3D

5GX6 \| pdb_00005gx6	Download File View File

Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-4 position of GalNAc

Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

(2017) Sci Rep 7: 1069-1069

Released	2017-07-26
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Streptobacillus moniliformis DSM 12112
Macromolecule	Extracellular solute-binding protein family 1 (protein)
Unique Ligands	CA, EDO
Unique branched monosaccharides	ASG, GCD

Explore in 3D

5GX7 \| pdb_00005gx7	Download File View File

Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-6 position of GalNAc

Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

(2017) Sci Rep 7: 1069-1069

Released	2017-07-19
Method	X-RAY DIFFRACTION 1.991 Å
Organisms	Streptobacillus moniliformis DSM 12112
Macromolecule	Extracellular solute-binding protein family 1 (protein)
Unique Ligands	CA
Unique branched monosaccharides	GCD, NG6

Explore in 3D

5GX8 \| pdb_00005gx8	Download File View File

Crystal structure of solute-binding protein related to glycosaminoglycans

Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

(2017) Sci Rep 7: 1069-1069

Released	2017-07-19
Method	X-RAY DIFFRACTION 1.778 Å
Organisms	Streptobacillus moniliformis DSM 12112
Macromolecule	Extracellular solute-binding protein family 1 (protein)
Unique Ligands	CA, EDO, SO4, TAR

Explore in 3D

5XS8 \| pdb_00005xs8	Download File View File

Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with two sulfate groups at C-4 and C-6 positions of GalNAc

Oiki, S., Kamochi, R., Mikami, B., Murata, K., Hashimoto, W.

(2017) Sci Rep 7: 17005-17005

Released	2018-01-17
Method	X-RAY DIFFRACTION 1.952 Å
Organisms	Streptobacillus moniliformis DSM 12112
Macromolecule	Extracellular solute-binding protein family 1 (protein)
Unique Ligands	CA
Unique branched monosaccharides	8EX, GCD

Explore in 3D

5Z6B \| pdb_00005z6b	Download File View File

Crystal structure of sugar-binding protein YesO in complex with rhamnogalacturonan trisaccharide

Sugiura, H., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

To be published

Released	2019-01-23
Method	X-RAY DIFFRACTION 1.582 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	Putative ABC transporter substrate-binding protein YesO (protein)
Unique branched monosaccharides	GAD, GAL, RAM

Explore in 3D

5Z6C \| pdb_00005z6c	Download File View File

Crystal structure of Bacillus subtilis sugar-binding protein YesO involved in import of rhamnogalacturonan

Sugiura, H., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

To be published

Released	2019-01-23
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	Putative ABC transporter substrate-binding protein YesO (protein)

Explore in 3D

6INZ \| pdb_00006inz	Download File View File

Crystal structure of solute-binding protein complexed with unsaturated hyaluronan disaccharide

Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

(2019) Biosci Biotechnol Biochem 83: 1946-1954

Released	2019-09-11
Method	X-RAY DIFFRACTION 2.289 Å
Organisms	Streptobacillus moniliformis DSM 12112
Macromolecule	Extracellular solute-binding protein family 1 (protein)
Unique Ligands	CA, SO4
Unique branched monosaccharides	GCD, NAG

Explore in 3D

7E4S \| pdb_00007e4s	Download File View File

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with HEPES

Yamamoto, Y., Takase, R., Mikami, B., Hashimoto, W.

(2023) J Appl Glycosci (1999)

Released	2022-02-23
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Lacticaseibacillus rhamnosus
Macromolecule	5-dehydro-4-deoxy-D-glucuronate isomerase (protein)
Unique Ligands	EPE, ZN

Explore in 3D

7VGK \| pdb_00007vgk	Download File View File

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI

Iwase, H., Oiki, S., Mikami, B., Takase, R., Hashimoto, W.

(2023) J Appl Glycosci (1999)

Released	2022-10-19
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Lacticaseibacillus rhamnosus
Macromolecule	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (protein)

Explore in 3D

7YE3 \| pdb_00007ye3	Download File View File

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with MES

Yamamoto, Y., Oiki, S., Takase, R., Mikami, B., Hashimoto, W.

(2023) J Appl Glycosci (1999) 70: 99-107

Released	2023-07-05
Method	X-RAY DIFFRACTION 2.553 Å
Organisms	Lacticaseibacillus rhamnosus
Macromolecule	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (protein)
Unique Ligands	MES, ZN

Explore in 3D

7YRS \| pdb_00007yrs	Download File View File

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with MOPS

Yamamoto, Y., Oiki, S., Takase, R., Mikami, B., Hashimoto, W.

(2023) J Appl Glycosci (1999) 70: 99-107

Released	2023-08-16
Method	X-RAY DIFFRACTION 2.802 Å
Organisms	Lacticaseibacillus rhamnosus
Macromolecule	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (protein)
Unique Ligands	MPO, ZN

1 to 20 of 20 Structures

Page 1 of 1

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.

3WUX | pdb_00003wux

Crystal structure of unsaturated glucuronyl hydrolase mutant D115N/K370S from Streptococcus agalactiae

4TKZ | pdb_00004tkz

Crystal structure of phosphotransferase system component EIIA from Streptococcus agalactiae

4U8E | pdb_00004u8e

Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase from Streptococcus agalactiae

4U8F | pdb_00004u8f

Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase complexed with a tartrate

4U8G | pdb_00004u8g

Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus agalactiae

4Z9X | pdb_00004z9x

Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus pyogenes

4Z9Y | pdb_00004z9y

Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Pectobacterium carotovorum

4ZA2 | pdb_00004za2

Crystal structure of Pectobacterium carotovorum 2-keto-3-deoxy-D-gluconate dehydrogenase complexed with NAD+

5GUB | pdb_00005gub

Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide

5GX6 | pdb_00005gx6

Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-4 position of GalNAc

5GX7 | pdb_00005gx7

Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-6 position of GalNAc

5GX8 | pdb_00005gx8

Crystal structure of solute-binding protein related to glycosaminoglycans

5XS8 | pdb_00005xs8

Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with two sulfate groups at C-4 and C-6 positions of GalNAc

5Z6B | pdb_00005z6b

Crystal structure of sugar-binding protein YesO in complex with rhamnogalacturonan trisaccharide

5Z6C | pdb_00005z6c

Crystal structure of Bacillus subtilis sugar-binding protein YesO involved in import of rhamnogalacturonan

6INZ | pdb_00006inz

Crystal structure of solute-binding protein complexed with unsaturated hyaluronan disaccharide

7E4S | pdb_00007e4s

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with HEPES

7VGK | pdb_00007vgk

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI

7YE3 | pdb_00007ye3

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with MES

7YRS | pdb_00007yrs

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with MOPS

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

3WUX | pdb_00003wux

4TKZ | pdb_00004tkz

4U8E | pdb_00004u8e

4U8F | pdb_00004u8f

4U8G | pdb_00004u8g

4Z9X | pdb_00004z9x

4Z9Y | pdb_00004z9y

4ZA2 | pdb_00004za2

5GUB | pdb_00005gub

5GX6 | pdb_00005gx6

5GX7 | pdb_00005gx7

5GX8 | pdb_00005gx8

5XS8 | pdb_00005xs8

5Z6B | pdb_00005z6b

5Z6C | pdb_00005z6c

6INZ | pdb_00006inz

7E4S | pdb_00007e4s

7VGK | pdb_00007vgk

7YE3 | pdb_00007ye3

7YRS | pdb_00007yrs