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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Tomabechi, Y."

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Search Summary

This query matches 70 Structures.

Refinements

Structure Determination Methodology

experimental (70)

Scientific Name of Source Organism

	Homo sapiens (52)
	Severe acute respiratory syndrome coronavirus 2 (12)
	Aequorea victoria (3)
	Mus musculus (3)
	Bifidobacterium bifidum JCM 1254 (2)
	Gallus gallus (2)
	Oplophorus gracilirostris (2)
	Schistosoma japonicum (2)
	Hepatitis B virus subtype adyw (1)
	Influenza A virus (A/Okuda/1957(H2N2)) (1)

More...

Taxonomy

	Eukaryota (64)
	Riboviria (14)
	Bacteria (2)
	Archaea (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (55)
	ELECTRON MICROSCOPY (13)
	SOLUTION NMR (2)

Polymer Entity Type

Protein (70)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (15)
	2.0 - 2.5 (24)
	2.5 - 3.0 (12)
	3.0 - 3.5 (5)
	3.5 - 4.0 (3)
	4.0 - 4.5 (7)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (29)
	2015 - 2019 (15)
	2020 - 2024 (23)

Enzyme Classification Name

	Transferases (36)
	Hydrolases (4)
	Oxidoreductases (2)
	Ligases (1)

Symmetry Type

	Asymmetric (62)
	Cyclic (8)
	Dihedral (3)

SCOP Classification

	Artifacts (24)
	Alpha and beta proteins (a+b) (32)
	All alpha proteins (5)
	All beta proteins (20)
	Alpha and beta proteins (a/b) (2)

AllSelected

1 to 25 of 70 Structures

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2E5S \| pdb_00002e5s	Download File View File

Solution structure of the zf-CCCHx2 domain of muscleblind-like 2, isoform 1 [Homo sapiens]

Dang, W., Muto, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Protein Sci 18: 80-91

Released	2007-06-26
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	OTTHUMP00000018578 (protein)
Unique Ligands	ZN

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2RPP \| pdb_00002rpp	Download File View File

Solution structure of Tandem zinc finger domain 12 in Muscleblind-like protein 2

Abe, C., Dang, W., Tsuda, K., Muto, Y., Inoue, M., Kigawa, T., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Protein Sci 18: 80-91

Released	2009-05-12
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Muscleblind-like protein 2 (protein)
Unique Ligands	ZN

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2ZV2 \| pdb_00002zv2	Download File View File

Crystal structure of human calcium/calmodulin-dependent protein kinase kinase 2, beta, CaMKK2 kinase domain in complex with STO-609

Yoshikawa, S., Kukimoto-niino, M., Shirouzu, M., Suzuki, A., Lee, S., Minokoshi, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2011) J Biological Chem 286: 22570-22579

Released	2009-11-03
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Calcium/calmodulin-dependent protein kinase kinase 2 (protein)
Unique Ligands	609

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3AU3 \| pdb_00003au3	Download File View File

Crystal structure of armadillo repeat domain of APC

Murayama, K., Kato-Murayama, M., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2011) Structure 19: 1496-1508

Released	2011-11-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Adenomatous polyposis coli protein (protein)

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3QHE \| pdb_00003qhe	Download File View File

Crystal structure of the complex between the armadillo repeat domain of adenomatous polyposis coli and the tyrosine-rich domain of Sam68

Morishita, E.C.J., Murayama, K., Kato-Murayama, M., Ishizuku-Katsura, Y., Tomabechi, Y., Terada, T., Handa, N., Shirouzu, M., Akiyama, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2011) Structure 19: 1496-1508

Released	2011-11-02
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Adenomatous polyposis coli protein (protein) KH domain-containing, RNA-binding, signal transduction-associated protein 1 (protein)

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3UIX \| pdb_00003uix	Download File View File

Crystal structure of Pim1 kinase in complex with small molecule inhibitor

Parker, L.J.

(2012) J Mol Biology 417: 240-252

Released	2012-04-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Proto-oncogene serine/threonine-protein kinase pim-1 (protein)
Unique Ligands	CA, CL, GOL, Q17, SO4

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3UMX \| pdb_00003umx	Download File View File

Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indol-3-yl)methylene]-7-(azepan-1-ylmethyl)-6-hydroxybenzofuran-3(2H)-one

Parker, L.J., Handa, N., Yokoyama, S.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 860-866

Released	2012-08-08
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	Proto-oncogene serine/threonine-protein kinase pim-1 (protein)
Unique Ligands	Q18, SO4

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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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3VUZ \| pdb_00003vuz	Download File View File

Crystal structure of histone methyltransferase SET7/9 in complex with AAM-1

Niwa, H., Handa, N., Tomabechi, Y., Honda, K., Toyama, M., Ohsawa, N., Shirouzu, M., Kagechika, H., Hirano, T., Umehara, T., Yokoyama, S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 595-602

Released	2013-03-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Histone-lysine N-methyltransferase SETD7 (protein)
Unique Ligands	K15

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3VV0 \| pdb_00003vv0	Download File View File

Crystal structure of histone methyltransferase SET7/9 in complex with DAAM-3

Niwa, H., Handa, N., Tomabechi, Y., Honda, K., Toyama, M., Ohsawa, N., Shirouzu, M., Kagechika, H., Hirano, T., Umehara, T., Yokoyama, S.

(2013) Acta Crystallogr D Biol Crystallogr 69: 595-602

Released	2013-03-27
Method	X-RAY DIFFRACTION 2.001 Å
Organisms	Homo sapiens
Macromolecule	Histone-lysine N-methyltransferase SETD7 (protein)
Unique Ligands	KH3

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3WE4 \| pdb_00003we4	Download File View File

Crystal structure of S6K1 kinase domain in complex with a pyrimidine derivative PF-4708671 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole

Niwa, H., Shirouzu, M., Yokoyama, S.

(2014) J Struct Funct Genomics 15: 153-164

Released	2014-08-06
Method	X-RAY DIFFRACTION 1.995 Å
Organisms	Homo sapiens
Macromolecule	Ribosomal protein S6 kinase beta-1 (protein)
Unique Ligands	5FI, ZN

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3WF5 \| pdb_00003wf5	Download File View File

Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine

Niwa, H., Shirouzu, M., Yokoyama, S.

(2014) J Struct Funct Genomics 15: 153-164

Released	2014-08-06
Method	X-RAY DIFFRACTION 2.099 Å
Organisms	Homo sapiens
Macromolecule	Ribosomal protein S6 kinase beta-1 (protein)
Unique Ligands	FZ8, ZN

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3WF6 \| pdb_00003wf6	Download File View File

Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-indol-3-yl)-3,6-dihydropyridin-1(2H)-yl]-1H-pyrazolo[3,4-d]pyrimidine

Niwa, H., Shirouzu, M., Yokoyama, S.

(2014) J Struct Funct Genomics 15: 153-164

Released	2014-08-06
Method	X-RAY DIFFRACTION 2.031 Å
Organisms	Homo sapiens
Macromolecule	Ribosomal protein S6 kinase beta-1 (protein)
Unique Ligands	FZ9, ZN

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3WF7 \| pdb_00003wf7	Download File View File

Crystal structure of S6K1 kinase domain in complex with a purine derivative 1-(9H-purin-6-yl)-N-[3-(trifluoromethyl)phenyl]piperidine-4-carboxamide

Niwa, H., Shirouzu, M., Yokoyama, S.

(2014) J Struct Funct Genomics 15: 153-164

Released	2014-08-06
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	Ribosomal protein S6 kinase beta-1 (protein)
Unique Ligands	FS9, GOL, ZN

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3WF8 \| pdb_00003wf8	Download File View File

Crystal structure of S6K1 kinase domain in complex with a quinoline derivative 2-oxo-2-[(4-sulfamoylphenyl)amino]ethyl 7,8,9,10-tetrahydro-6H-cyclohepta[b]quinoline-11-carboxylate

Niwa, H., Shirouzu, M., Yokoyama, S.

(2014) J Struct Funct Genomics 15: 153-164

Released	2014-08-06
Method	X-RAY DIFFRACTION 1.975 Å
Organisms	Homo sapiens
Macromolecule	Ribosomal protein S6 kinase beta-1 (protein)
Unique Ligands	F76, GOL, ZN

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3WF9 \| pdb_00003wf9	Download File View File

Crystal structure of S6K1 kinase domain in complex with a quinoline derivative 1-oxo-1-[(4-sulfamoylphenyl)amino]propan-2-yl-2-methyl-1,2,3,4-tetrahydroacridine-9-carboxylate

Niwa, H., Shirouzu, M., Yokoyama, S.

(2014) J Struct Funct Genomics 15: 153-164

Released	2014-08-06
Method	X-RAY DIFFRACTION 2.035 Å
Organisms	Homo sapiens
Macromolecule	Ribosomal protein S6 kinase beta-1 (protein)
Unique Ligands	FS7, GOL, ZN

1 to 25 of 70 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

Symmetry Type

SCOP Classification

2E5S | pdb_00002e5s

2RPP | pdb_00002rpp

2ZV2 | pdb_00002zv2

3AU3 | pdb_00003au3

3QHE | pdb_00003qhe

3UIX | pdb_00003uix

3UMX | pdb_00003umx

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

3VUZ | pdb_00003vuz

3VV0 | pdb_00003vv0

3WE4 | pdb_00003we4

3WF5 | pdb_00003wf5

3WF6 | pdb_00003wf6

3WF7 | pdb_00003wf7

3WF8 | pdb_00003wf8

3WF9 | pdb_00003wf9