2ZDY	Transferase	date	Dec 01, 2007
title	Inhibitor-Bound Structures Of Human Pyruvate Dehydrogenase K
authors	M.Kawamoto, I.Shiromizu, M.Kukimoto-Niino, A.Tokmakov, T.Terada, M.Shirouzu, T.Matsusue, S.Yokoyama
compound		source
Molecule: Pyruvate Dehydrogenase Kinase Isozyme 4 Chain: A, B Fragment: Residues 20-411 Synonym: Pyruvate Dehydrogenase Kinase Isoform 4 Ec: 2.7.11.2 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_cell_line: Sf9 Expression_system_vector_type: Baculovirus Expression_system_vector: Pbluebac4.5
symmetry	Space Group: P 1 21 1	R_factor 0.190 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 70.713 69.090 81.492 90.00 99.66 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	ADP, EPE, MG	enzyme	Transferase E.C.2.7.11.2 BRENDA
Gene Ontology	Chain Function Process Component A, B protein kinase activity protein serine/threonine kin... pyruvate dehydrogenase (acet...
Primary reference	Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4., Kukimoto-Niino M, Tokmakov A, Terada T, Ohbayashi N, Fujimoto T, Gomi S, Shiromizu I, Kawamoto M, Matsusue T, Shirouzu M, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2011 Sep;67(Pt 9):763-73. doi:, 10.1107/S090744491102405X. Epub 2011 Aug 9. PMID:21904029

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk] Biological Unit Coordinates (2zdy.pdb1.gz) 118 Kb LPC: Ligand-Protein Contacts for 2ZDY CSU: Contacts of Structural Units for 2ZDY Likely Quarternary Molecular Structure file(s) for 2ZDY Structure Factors (441 Kb) Retrieve 2ZDY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2ZDY from S2C, [Save to disk] Re-refined 2zdy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2ZDY in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 2ZDY

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2ZDY, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2zdy] [2zdy_B] [2zdy_A] SWISS-PROT database: [Q16654] Domain organization of [PDK4_HUMAN] by SWISSPFAM Domain found in 2ZDY: [HATPase_c ] by SMART

Other resources with information on 2ZDY

Community annotation for 2ZDY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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