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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "DiDonato, M."

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Search Summary

This query matches 60 Structures.

Refinements

Structure Determination Methodology

experimental (60)

Scientific Name of Source Organism

	Homo sapiens (41)
	Sphingobium sp. SYK-6 (6)
	Gallus gallus (5)
	Mumps orthorubulavirus (2)
	Severe acute respiratory syndrome coronavirus 2 (2)
	Grammostola rosea (1)
	Pandinus imperator (1)
	Pseudomonas sp. Os17 (1)
	Thermococcus litoralis (1)

Taxonomy

	Eukaryota (46)
	Bacteria (7)
	Riboviria (4)
	Eukaryota (eukaryotes) (2)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (53)
	SOLUTION NMR (7)

Polymer Entity Type

Protein (60)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (7)
	2.0 - 2.5 (15)
	2.5 - 3.0 (24)
	3.0 - 3.5 (4)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (6)
	2010 - 2014 (10)
	2015 - 2019 (25)
	2020 - 2024 (17)

Enzyme Classification Name

	Transferases (33)
	Hydrolases (13)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Cyclic (41)
	Asymmetric (24)
	Dihedral (1)

SCOP Classification

	All beta proteins (14)
	Alpha and beta proteins (a/b) (7)
	Alpha and beta proteins (a+b) (16)
	Artifacts (6)
	Small proteins (4)

AllSelected

1 to 25 of 60 Structures

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1IE6 \| pdb_00001ie6	Download File View File

SOLUTION STRUCTURE OF IMPERATOXIN A

Lee, C.W., Takeuchi, K., Takahashi, H., Sato, K., Shimada, I., Kim, D.H., Kim, J.I.

(2004) Biochem J 377: 385-394

Released	2003-06-10
Method	SOLUTION NMR
Organisms	Pandinus imperator
Macromolecule	IMPERATOXIN A (protein)

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1KOZ \| pdb_00001koz	Download File View File

SOLUTION STRUCTURE OF OMEGA-GRAMMOTOXIN SIA

Takeuchi, K., Park, E.J., Lee, C.W., Kim, J.I., Takahashi, H., Swartz, K.J., Shimada, I.

(2002) J Mol Biology 321: 517-526

Released	2002-08-28
Method	SOLUTION NMR
Organisms	Grammostola rosea
Macromolecule	Voltage-dependent Channel Inhibitor (protein)

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2B86 \| pdb_00002b86	Download File View File

Solution structure of the first Src homology 3 domain of Nck2

Park, S., Takeuchi, K., Wagner, G.

(2006) J Biomol NMR 34: 203-208

Released	2006-05-09
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Cytoplasmic protein NCK2 (protein)

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2D5R \| pdb_00002d5r	Download File View File

Crystal Structure of a Tob-hCaf1 Complex

Horiuchi, M., Suzuki, N.N., Muroya, N., Takahasi, K., Nishida, M., Yoshida, Y., Ikematsu, N., Nakamura, T., Kawamura-Tsuzuku, J., Yamamoto, T., Inagaki, F.

(2009) J Biological Chem 284: 13244-13255

Released	2006-12-12
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	CCR4-NOT transcription complex subunit 7 (protein) Tob1 protein (protein)

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2JOG \| pdb_00002jog	Download File View File

Structure of the calcineurin-NFAT complex

Takeuchi, K., Roehrl, M.H., Sun, Z.Y., Wagner, G.

(2007) Structure 15: 587-597

Released	2007-05-22
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Calmodulin-dependent calcineurin A subunit alpha isoform (protein) NFAT (protein)

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2JXB \| pdb_00002jxb	Download File View File

Structure of CD3epsilon-Nck2 first SH3 domain complex

Takeuchi, K., Yang, H., Ng, E., Park, S., Sun, Z.J., Reinherz, E.L., Wagner, G.

(2008) J Mol Biology 380: 704-716

Released	2008-09-23
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	T-cell surface glycoprotein CD3 epsilon chain, Cytoplasmic protein NCK2 (protein)

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2KY6 \| pdb_00002ky6	Download File View File

Structure of ARC92VBD/MED25ACID

Milbradt, A.G., Sun, Z.J., Selenko, P., Takeuchi, K., Naar, A.M., Wagner, G.

(2011) Nat Struct Mol Biol 18: 410-415

Released	2011-03-09
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Mediator of RNA polymerase II transcription subunit 25 (protein)

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2ONC \| pdb_00002onc	Download File View File

Crystal structure of human DPP-4

Feng, J., Zhang, Z., Wallace, M.B., Stafford, J.A., Kaldor, S.W., Kassel, D.B., Navre, M., Shi, L., Skene, R.J., Asakawa, T., Takeuchi, K., Xu, R., Webb, D.R., Gwaltney, S.L.

(2007) J Med Chem 50: 2297-2300

Released	2008-03-04
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	Dipeptidyl peptidase 4 (protein)
Unique Ligands	NAG, SY1
Unique branched monosaccharides	NAG

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2RSG \| pdb_00002rsg	Download File View File

Solution structure of the CERT PH domain

Sugiki, T., Takeuchi, K., Tokunaga, Y., Kumagai, K., Kawano, M., Nishijima, M., Hanada, K., Takahashi, H., Shimada, I.

(2012) J Biological Chem 287: 33706-33718

Released	2012-08-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Collagen type IV alpha-3-binding protein (protein)

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2ZC0 \| pdb_00002zc0	Download File View File

Crystal structure of an archaeal alanine:glyoxylate aminotransferase

Sakuraba, H., Yoneda, K., Tsuge, H., Ohshima, T.

(2008) Acta Crystallogr D Biol Crystallogr 64: 696-699

Released	2008-06-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermococcus litoralis
Macromolecule	Alanine glyoxylate transaminase (protein)
Unique Ligands	IMD, PMP, ZN

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3B0B \| pdb_00003b0b	Download File View File

Crystal structure of the chicken CENP-S/CENP-X complex

Nishino, T., Takeuchi, K., Gascoigne, K.E., Suzuki, A., Hori, T., Oyama, T., Morikawa, K., Cheeseman, I.M., Fukagawa, T.

(2012) Cell 148: 487-501

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Gallus gallus
Macromolecule	Centromere protein S (protein) Centromere protein X (protein)

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3B0C \| pdb_00003b0c	Download File View File

Crystal structure of the chicken CENP-T histone fold/CENP-W complex, crystal form I

Nishino, T., Takeuchi, K., Gascoigne, K.E., Suzuki, A., Hori, T., Oyama, T., Morikawa, K., Cheeseman, I.M., Fukagawa, T.

(2012) Cell 148: 487-501

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.201 Å
Organisms	Gallus gallus
Macromolecule	Centromere protein T (protein) Centromere protein W (protein)
Unique Ligands	CIT

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3B0D \| pdb_00003b0d	Download File View File

Crystal structure of the chicken CENP-T histone fold/CENP-W complex, crystal form II

Nishino, T., Takeuchi, K., Gascoigne, K.E., Suzuki, A., Hori, T., Oyama, T., Morikawa, K., Cheeseman, I.M., Fukagawa, T.

(2012) Cell 148: 487-501

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.197 Å
Organisms	Gallus gallus
Macromolecule	Centromere protein T (protein) Centromere protein W (protein)
Unique Ligands	CIT

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3O95 \| pdb_00003o95	Download File View File

Crystal Structure of Human DPP4 Bound to TAK-100

Yano, J.K., Aertgeerts, K.

(2011) J Med Chem 53: 3517-3531

Released	2011-01-26
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	Dipeptidyl peptidase 4 (protein)
Unique Ligands	01T, NAG
Unique branched monosaccharides	NAG

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3O9V \| pdb_00003o9v	Download File View File

Crystal Structure of Human DPP4 Bound to TAK-986

Yano, J.K., Aertgeerts, K.

(2011) J Med Chem 53: 3517-3531

Released	2011-02-09
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Homo sapiens
Macromolecule	Dipeptidyl peptidase 4 (protein)
Unique Ligands	10T, NAG
Unique branched monosaccharides	NAG

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3OPM \| pdb_00003opm	Download File View File

Crystal Structure of Human DPP4 Bound to TAK-294

Yano, J.K., Aertgeerts, K.

(2011) Bioorg Med Chem 19: 4953-4970

Released	2011-10-19
Method	X-RAY DIFFRACTION 2.72 Å
Organisms	Homo sapiens
Macromolecule	Dipeptidyl peptidase 4 (protein)
Unique Ligands	LUI, NAG
Unique branched monosaccharides	NAG

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3VH5 \| pdb_00003vh5	Download File View File

Crystal structure of the chicken CENP-T histone fold/CENP-W/CENP-S/CENP-X heterotetrameric complex, crystal form I

Nishino, T., Takeuchi, K., Gascoigne, K.E., Suzuki, A., Hori, T., Oyama, T., Morikawa, K., Cheeseman, I.M., Fukagawa, T.

(2012) Cell 148: 487-501

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.402 Å
Organisms	Gallus gallus
Macromolecule	CENP-S (protein) CENP-T (protein) CENP-W (protein) CENP-X (protein)

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3VH6 \| pdb_00003vh6	Download File View File

Crystal structure of the chicken CENP-T histone fold/CENP-W/CENP-S/CENP-X heterotetrameric complex, crystal form II

Nishino, T., Takeuchi, K., Gascoigne, K.E., Suzuki, A., Hori, T., Oyama, T., Morikawa, K., Cheeseman, I.M., Fukagawa, T.

(2012) Cell 148: 487-501

Released	2012-03-07
Method	X-RAY DIFFRACTION 3.351 Å
Organisms	Gallus gallus
Macromolecule	CENP-S (protein) CENP-T (protein) CENP-W (protein) CENP-X (protein)

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3WZZ \| pdb_00003wzz	Download File View File

Crystal structure of PIP4KIIBETA

Takeuchi, K., Lo, Y.H., Sumita, K., Senda, M., Terakawa, J., Dimitoris, A., Locasale, J.W., Sasaki, M., Yoshino, H., Zhang, Y., Kahoud, E.R., Takano, T., Yokota, T., Emerling, B., Asara, J.A., Ishida, T., Shimada, I., Daikoku, T., Cantley, L.C., Senda, T., Sasaki, A.T.

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)

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3X01 \| pdb_00003x01	Download File View File

Crystal structure of PIP4KIIBETA complex with AMP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	AMP

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3X02 \| pdb_00003x02	Download File View File

Crystal structure of PIP4KIIBETA complex with GMP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	5GP

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3X03 \| pdb_00003x03	Download File View File

Crystal structure of PIP4KIIBETA complex with AMPPNP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	ANP

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3X04 \| pdb_00003x04	Download File View File

Crystal structure of PIP4KIIBETA complex with GMPPNP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	GNP

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3X05 \| pdb_00003x05	Download File View File

Crystal structure of PIP4KIIBETA T201M complex with AMP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	AMP

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3X06 \| pdb_00003x06	Download File View File

Crystal structure of PIP4KIIBETA T201M complex with GMP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	5GP

1 to 25 of 60 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

1IE6 | pdb_00001ie6

1KOZ | pdb_00001koz

2B86 | pdb_00002b86

2D5R | pdb_00002d5r

2JOG | pdb_00002jog

2JXB | pdb_00002jxb

2KY6 | pdb_00002ky6

2ONC | pdb_00002onc

2RSG | pdb_00002rsg

2ZC0 | pdb_00002zc0

3B0B | pdb_00003b0b

3B0C | pdb_00003b0c

3B0D | pdb_00003b0d

3O95 | pdb_00003o95

3O9V | pdb_00003o9v

3OPM | pdb_00003opm

3VH5 | pdb_00003vh5

3VH6 | pdb_00003vh6

3WZZ | pdb_00003wzz

3X01 | pdb_00003x01

3X02 | pdb_00003x02

3X03 | pdb_00003x03

3X04 | pdb_00003x04

3X05 | pdb_00003x05

3X06 | pdb_00003x06