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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Saito, Y."

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Search Summary

This query matches 69 Structures.

Refinements

Structure Determination Methodology

experimental (69)

Scientific Name of Source Organism

	Homo sapiens (38)
	Serratia marcescens (6)
	Mus musculus (4)
	Saccharophagus degradans 2-40 (4)
	synthetic construct (4)
	Bacillus subtilis (3)
	Photorhabdus laumondii subsp. laumondii TTO1 (3)
	Staphylococcus aureus subsp. aureus MRSA252 (3)
	Enterococcus hirae ATCC 9790 (2)
	Achromobacter cycloclastes (1)

More...

Taxonomy

	Eukaryota (42)
	Bacteria (24)
	other sequences (4)
	Riboviria (2)

Experimental Method

	X-RAY DIFFRACTION (49)
	ELECTRON MICROSCOPY (20)

Polymer Entity Type

Protein (69)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (4)
	1.5 - 2.0 (7)
	2.0 - 2.5 (27)
	2.5 - 3.0 (19)
	3.0 - 3.5 (10)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (3)
	2005 - 2009 (4)
	2010 - 2014 (10)
	2015 - 2019 (22)
	2020 - 2024 (30)

Enzyme Classification Name

	Oxidoreductases (4)
	Transferases (16)
	Hydrolases (8)
	Isomerases (3)
	Translocases (2)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (51)
	Cyclic (23)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (18)
	All beta proteins (15)
	Artifacts (15)
	Alpha and beta proteins (a/b) (7)
	All alpha proteins (4)

AllSelected

1 to 25 of 69 Structures

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1VAC \| pdb_00001vac	Download File View File

MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND CHICKEN OVALBUMIN

Fremont, D.H., Wilson, I.A.

(1995) Proc Natl Acad Sci U S A 92: 2479-2483

Released	1996-06-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Gallus gallus Mus musculus
Macromolecule	BETA-2 MICROGLOBULIN (protein) CHICKEN OVALBUMIN (protein) MHC CLASS I H-2KB HEAVY CHAIN (protein)

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2VAA \| pdb_00002vaa	Download File View File

MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN

Fremont, D.H., Wilson, I.A.

(1992) Science 257: 919-927

Released	1996-06-20
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Mus musculus Vesicular stomatitis virus
Macromolecule	BETA-2 MICROGLOBULIN (protein) MHC CLASS I H-2KB HEAVY CHAIN (protein) VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN (protein)

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2VAB \| pdb_00002vab	Download File View File

MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND SENDAI VIRUS NUCLEOPROTEIN

Fremont, D.H., Wilson, I.A.

(1992) Science 257: 919-927

Released	1996-06-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mus musculus Respirovirus muris
Macromolecule	BETA-2 MICROGLOBULIN (protein) MHC CLASS I H-2KB HEAVY CHAIN (protein) SENDAI VIRUS NUCLEOPROTEIN (protein)

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2YRF \| pdb_00002yrf	Download File View File

Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion

Tamura, H., Inoue, T., Kai, Y., Matsumura, H.

(2008) Protein Sci 17: 126-135

Released	2008-01-22
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Bacillus subtilis
Macromolecule	Methylthioribose-1-phosphate isomerase (protein)
Unique Ligands	SO4

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2YVK \| pdb_00002yvk	Download File View File

Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis

Tamura, H., Inoue, T., Kai, Y., Matsumura, H.

(2008) Protein Sci 17: 126-135

Released	2008-01-22
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bacillus subtilis
Macromolecule	Methylthioribose-1-phosphate isomerase (protein)
Unique Ligands	MRU

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2YWQ \| pdb_00002ywq	Download File View File

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-15
Method	X-RAY DIFFRACTION 2.64 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribosomal subunit interface protein (protein)

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2ZVI \| pdb_00002zvi	Download File View File

Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis

Tamura, H., Yadani, T., Kai, Y., Inoue, T., Matsumura, H.

(2009) Acta Crystallogr D Biol Crystallogr 65: 942-951

Released	2009-09-01
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus subtilis
Macromolecule	2,3-diketo-5-methylthiopentyl-1-phosphate enolase (protein)

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3VRY \| pdb_00003vry	Download File View File

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 4-Amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl-cyclopentane

Kuratani, M., Tomabechi, Y., Niwa, H., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.481 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	B43, CA, CL

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3VRZ \| pdb_00003vrz	Download File View File

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 1-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]-3-benzylurea

Kuratani, M., Tomabechi, Y., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.218 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, CL, VRZ

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3VS0 \| pdb_00003vs0	Download File View File

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor N-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]benzamide

Kuratani, M., Honda, K., Tomabechi, Y., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.934 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, CL, VS0

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3VS1 \| pdb_00003vs1	Download File View File

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 1-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]-3-phenylurea

Kuratani, M., Tomabechi, Y., Toyama, M., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.464 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, CL, VSA

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3VS2 \| pdb_00003vs2	Download File View File

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 7-[cis-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine

Kuratani, M., Tomabechi, Y., Niwa, H., Parker, J.L., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.609 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, CL, VSB

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3VS3 \| pdb_00003vs3	Download File View File

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine

Kuratani, M., Tomaebchi, Y., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, CL, VSE

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3VS4 \| pdb_00003vs4	Download File View File

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 5-(4-phenoxyphenyl)-7-(tetrahydro-2H-pyran-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine

Kuratani, M., Tomabechi, Y., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.747 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, CL, VSF

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3VS5 \| pdb_00003vs5	Download File View File

Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 7-(1-methylpiperidin-4-yl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine

Kuratani, M., Tomabechi, Y., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.851 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, VSG

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3VS6 \| pdb_00003vs6	Download File View File

Crystal structure of HCK complexed with a pyrazolo-pyrimidine inhibitor tert-butyl {4-[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]-2-methoxyphenyl}carbamate

Kuratani, M., Honda, K., Tomabechi, Y., Toyama, M., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.373 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, CL, VSH

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3VS7 \| pdb_00003vs7	Download File View File

Crystal structure of HCK complexed with a pyrazolo-pyrimidine inhibitor 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine

Kuratani, M., Honda, K., Niwa, H., Toyama, M., Handa, N., Yokoyama, S.

(2013) Sci Transl Med 5: 181ra52-181ra52

Released	2013-05-01
Method	X-RAY DIFFRACTION 3.001 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	CA, CL, KS1

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4Z2G \| pdb_00004z2g	Download File View File

Serratia marcescens Chitinase B complexed with macrolide inhibitor 26

Maita, N., Sugawara, A., Sunazuka, T.

(2015) J Med Chem 58: 4984-4997

Released	2015-07-01
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Serratia marcescens
Macromolecule	Chitinase B (protein)
Unique Ligands	M6V

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4Z2H \| pdb_00004z2h	Download File View File

Serratia marcescens Chitinase B complexed with macrolide inhibitor 29

Maita, N., Sugawara, A., Sunazuka, T.

(2015) J Med Chem 58: 4984-4997

Released	2015-07-01
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Serratia marcescens
Macromolecule	Chitinase B (protein)
Unique Ligands	CL, GOL, M6A

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4Z2I \| pdb_00004z2i	Download File View File

Serratia marcescens Chitinase B complexed with macrolide inhibitor 30

Maita, N., Sugawara, A., Sunazuka, T.

(2015) J Med Chem 58: 4984-4997

Released	2015-07-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Serratia marcescens
Macromolecule	Chitinase B (protein)
Unique Ligands	GOL, M6B, MOH, NA, PO3

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4Z2J \| pdb_00004z2j	Download File View File

Serratia marcescens Chitinase B complexed with macrolide inhibitor 31

Maita, N., Sugawara, A., Sunazuka, T.

(2015) J Med Chem 58: 4984-4997

Released	2015-07-01
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Serratia marcescens
Macromolecule	Chitinase B (protein)
Unique Ligands	GOL, M6G, PO4

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4Z2K \| pdb_00004z2k	Download File View File

Serratia marcescens Chitinase B complexed with macrolide inhibitor 32

Maita, N., Sugawara, A., Sunazuka, T.

(2015) J Med Chem 58: 4984-4997

Released	2015-07-01
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Serratia marcescens
Macromolecule	Chitinase B (protein)
Unique Ligands	GOL, M6E

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4Z2L \| pdb_00004z2l	Download File View File

Serratia marcescens Chitinase B complexed with macrolide inhibitor 33

Maita, N., Sugawara, A., Sunazuka, T.

(2015) J Med Chem 58: 4984-4997

Released	2015-07-01
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Serratia marcescens
Macromolecule	Chitinase B (protein)
Unique Ligands	CL, GOL, M6F

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4ZLE \| pdb_00004zle	Download File View File

Cellobionic acid phosphorylase - ligand free structure

Nam, Y.W., Arakawa, T., Fushinobu, S.

(2015) J Biological Chem 290: 18281-18292

Released	2015-06-10
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharophagus degradans 2-40
Macromolecule	Putative b-glycan phosphorylase (protein)
Unique Ligands	CL, GOL, SO4

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4ZLF \| pdb_00004zlf	Download File View File

Cellobionic acid phosphorylase - cellobionic acid complex

Nam, Y.W., Arakawa, T., Fushinobu, S.

(2015) J Biological Chem 290: 18281-18292

Released	2015-06-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Saccharophagus degradans 2-40
Macromolecule	Putative b-glycan phosphorylase (protein)
Unique Ligands	CEZ, CL, GOL, SO4

1 to 25 of 69 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1VAC | pdb_00001vac

2VAA | pdb_00002vaa

2VAB | pdb_00002vab

2YRF | pdb_00002yrf

2YVK | pdb_00002yvk

2YWQ | pdb_00002ywq

2ZVI | pdb_00002zvi

3VRY | pdb_00003vry

3VRZ | pdb_00003vrz

3VS0 | pdb_00003vs0

3VS1 | pdb_00003vs1

3VS2 | pdb_00003vs2

3VS3 | pdb_00003vs3

3VS4 | pdb_00003vs4

3VS5 | pdb_00003vs5

3VS6 | pdb_00003vs6

3VS7 | pdb_00003vs7

4Z2G | pdb_00004z2g

4Z2H | pdb_00004z2h

4Z2I | pdb_00004z2i

4Z2J | pdb_00004z2j

4Z2K | pdb_00004z2k

4Z2L | pdb_00004z2l

4ZLE | pdb_00004zle

4ZLF | pdb_00004zlf