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 = "Ito, 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 64 Structures.

Refinements

Structure Determination Methodology

experimental (64)

Scientific Name of Source Organism

	Homo sapiens (34)
	Severe acute respiratory syndrome coronavirus 2 (12)
	Paenibacillus sp. TS12 (6)
	Pseudomonas putida (6)
	Influenza A virus (A/Viet Nam/1203/2004(H5N1)) (3)
	Paenibacillus sp. (3)
	Meleagris gallopavo (2)
	Pseudomonas aeruginosa (2)
	Escherichia coli (1)
	Influenza A virus (1)

More...

Taxonomy

	Eukaryota (37)
	Bacteria (22)
	Riboviria (17)

Experimental Method

	X-RAY DIFFRACTION (52)
	ELECTRON MICROSCOPY (12)

Polymer Entity Type

Protein (64)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (3)
	1.5 - 2.0 (22)
	2.0 - 2.5 (14)
	2.5 - 3.0 (12)
	3.0 - 3.5 (3)
	3.5 - 4.0 (2)
	4.0 - 4.5 (7)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (1)
	2000 - 2004 (1)
	2005 - 2009 (13)
	2010 - 2014 (11)
	2015 - 2019 (16)
	2020 - 2024 (21)

Enzyme Classification Name

	Hydrolases (23)
	Transferases (10)
	Oxidoreductases (8)
	Isomerases (1)

Membrane Protein Annotation

OPM (2)

Symmetry Type

	Asymmetric (60)
	Cyclic (4)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (7)
	All alpha proteins (7)
	All beta proteins (6)
	Artifacts (3)
	Coiled coil proteins (2)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 64 Structures

Page 1 of 3

Sort by

Explore in 3D

1FHG \| pdb_00001fhg	Download File View File

HIGH RESOLUTION REFINEMENT OF TELOKIN

Tomchick, D.R., Minor, W., Kiyatkin, A., Lewinski, K., Somlyo, A.V., Somlyo, A.P.

(1992) J Mol Biology 227: 840-851

Released	2000-08-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Meleagris gallopavo
Macromolecule	TELOKIN (protein)

Explore in 3D

1LOP \| pdb_00001lop	Download File View File

CYCLOPHILIN A COMPLEXED WITH SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE

Konno, M.

(1996) J Mol Biology 256: 897-908

Released	1996-12-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	CYCLOPHILIN A (protein) SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE (protein)

Explore in 3D

1TLK \| pdb_00001tlk	Download File View File

X-RAY STRUCTURE DETERMINATION OF TELOKIN, THE C-TERMINAL DOMAIN OF MYOSIN LIGHT CHAIN KINASE, AT 2.8 ANGSTROMS RESOLUTION

Holden, H.M., Rayment, I.

(1992) J Mol Biology 227: 840-851

Released	1993-10-31
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Meleagris gallopavo
Macromolecule	TELOKIN (protein)

Explore in 3D

2DDX \| pdb_00002ddx	Download File View File

Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4

Sakaguchi, K.

To be published

Released	2007-02-13
Method	X-RAY DIFFRACTION 0.86 Å
Organisms	Vibrio sp. AX-4
Macromolecule	beta-1,3-xylanase (protein)
Unique Ligands	GOL, MG

Explore in 3D

2E9L \| pdb_00002e9l	Download File View File

Crystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related Prote:KLrP) complex with Glucose and fatty acids

Kakuta, Y., Hayashi, Y., Okino, N., Ito, M.

(2007) J Biological Chem 282: 30889-30900

Released	2007-09-11
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Cytosolic beta-glucosidase (protein)
Unique Ligands	BGC, GOL, OLA, PLM

Explore in 3D

2E9M \| pdb_00002e9m	Download File View File

Crystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related Prote:KLrP) complex with Galactose and fatty acids

Kakuta, Y., Hayashi, Y., Okino, N., Ito, M.

(2007) J Biological Chem 282: 30889-30900

Released	2007-09-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Cytosolic beta-glucosidase (protein)
Unique Ligands	GAL, OLA, PLM

Explore in 3D

2IBX \| pdb_00002ibx	Download File View File

Influenza virus (VN1194) H5 HA

Yamada, S., Russell, R.J., Gamblin, S.J., Skehel, J.J., Kawaoka, Y.

(2006) Nature 444: 378-382

Released	2006-11-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Influenza A virus
Macromolecule	Hemagglutinin (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

Explore in 3D

2Z4T \| pdb_00002z4t	Download File View File

Crystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2,6-sialyltransferase in a Ternary Complex with Donor Product CMP and Accepter Substrate Lactose

Kakuta, Y., Okino, N., Kajiwara, H., Ichikawa, M., Takakura, Y., Ito, M., Yamamoto, T.

(2008) Glycobiology 18: 66-73

Released	2008-04-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Photobacterium sp. JT-ISH-224
Macromolecule	Beta-galactoside alpha-2,6-sialyltransferase (protein)
Unique Ligands	C5P, GOL, MG, PO4
Unique branched monosaccharides	GAL, GLC

Explore in 3D

2ZOX \| pdb_00002zox	Download File View File

Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase

Noguchi, J., Hayashi, Y., Baba, Y., Okino, N., Kimura, M., Ito, M., Kakuta, Y.

(2008) Biochem Biophys Res Commun 374: 549-552

Released	2008-09-30
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Cytosolic beta-glucosidase (protein)
Unique Ligands	GLC, GOL, MG, OLA, PLM, PNG, PO4

Explore in 3D

2ZSC \| pdb_00002zsc	Download File View File

Tamavidin2, Novel Avidin-like Biotin-Binding Proteins from an Edible Mushroom

Kakuta, Y., Okino, N., Ito, M., Yamamoto, T., Takakura, Y.

(2009) FEBS J 276: 1383-1397

Released	2009-02-17
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Pleurotus cornucopiae
Macromolecule	Tamavidin2 (protein)
Unique Ligands	BTN, GOL, MG

Explore in 3D

2ZWI \| pdb_00002zwi	Download File View File

Crystal structure of alpha/beta-Galactoside alpha-2,3-Sialyltransferase from a Luminous Marine Bacterium, <I>Photobacterium phosphoreum</I>

Iwatani, T., Okino, N., Sakakura, M., Kajiwara, H., Ichikawa, M., Takakura, Y., Kimura, M., Ito, M., Yamamoto, T., Kakuta, Y.

(2009) FEBS Lett 583: 2083-2087

Released	2009-06-09
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Photobacterium phosphoreum
Macromolecule	Alpha-/beta-galactoside alpha-2,3-sialyltransferase (protein)
Unique Ligands	C5P, CL, GOL, ZN

Explore in 3D

2ZWS \| pdb_00002zws	Download File View File

Crystal Structure Analysis of neutral ceramidase from Pseudomonas aeruginosa

Kakuta, Y., Okino, N., Inoue, T., Okano, H., Ito, M.

(2009) J Biological Chem 284: 9566-9577

Released	2009-03-03
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Neutral ceramidase (protein)
Unique Ligands	FMT, GOL, MG, PLM, ZN

Explore in 3D

2ZXC \| pdb_00002zxc	Download File View File

Ceramidase complexed with C2

Okano, H., Inoue, T., Okino, N., Kakuta, Y., Matsumura, H., Ito, M.

(2009) J Biological Chem 284: 9566-9577

Released	2009-02-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Neutral ceramidase (protein)
Unique Ligands	2ED, DMS, FMT, MG, ZN

Explore in 3D

3GH4 \| pdb_00003gh4	Download File View File

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12

Sumida, T., Ishii, R., Yanagisawa, T., Yokoyama, S., Ito, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) J Mol Biology 392: 87-99

Released	2009-07-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Paenibacillus sp.
Macromolecule	beta-hexosaminidase (protein)
Unique Ligands	ACY, SO4

Explore in 3D

3GH5 \| pdb_00003gh5	Download File View File

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with GlcNAc

Sumida, T., Ishii, R., Yanagisawa, T., Yokoyama, S., Ito, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) J Mol Biology 392: 87-99

Released	2009-07-07
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Paenibacillus sp.
Macromolecule	beta-hexosaminidase (protein)
Unique Ligands	NAG, SO4

Explore in 3D

3GH7 \| pdb_00003gh7	Download File View File

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with GalNAc

Sumida, T., Ishii, R., Yanagisawa, T., Yokoyama, S., Ito, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) J Mol Biology 392: 87-99

Released	2009-07-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Paenibacillus sp.
Macromolecule	beta-hexosaminidase (protein)
Unique Ligands	NGA, SO4

Explore in 3D

3KC6 \| pdb_00003kc6	Download File View File

Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1)

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

(2010) PLoS Pathog 6: e1001034-e1001034

Released	2010-03-09
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Macromolecule	Polymerase PB2 (protein)
Unique Ligands	EDO

Explore in 3D

3KHW \| pdb_00003khw	Download File View File

Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/mexico/indre4487/2009(h1n1)

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

(2010) PLoS Pathog 6: e1001034-e1001034

Released	2010-03-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Influenza A virus (A/Mexico/InDRE4487/2009(H1N1))
Macromolecule	Polymerase PB2 (protein)
Unique Ligands	GOL