2PNR	Transferase	date	Apr 25, 2007
title	Crystal Structure Of The Asymmetric Pdk3-L2 Complex
authors	D.G.Vassylyev, C.N.Steussy, Y.Devedjiev
compound		source
Molecule: [Pyruvate Dehydrogenase [Lipoamide]] Kinase Isozyme 3; Chain: A, B, E, F Synonym: Pyruvate Dehydrogenase Kinase Isoform 3 Ec: 2.7.11.2 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pdk3 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptrchisb
Molecule: Dihydrolipoyllysine-Residue Acetyltransferase Component Of Pyruvate Dehydrogenase Complex; Chain: C, G Synonym: Pyruvate Dehydrogenase Complex E2 Subunit, Pdce2, E2, Dihydrolipoamide S-Acetyltransferase Component Of Pyruvate Dehydrogenase Complex, Pdc-E2, 70 Kda Mitochondrial Autoantigen Of Primary Biliary Cirrhosis, Pbc, M2 Antigen Complex 70 Kda Subunit; Ec: 2.3.1.12 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Dlat, Dlta Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptrchisb
symmetry	Space Group: P 41	R_factor 0.176 R_Free 0.229
crystal cell	length a length b length c angle alpha angle beta angle gamma 96.155 96.155 222.984 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	RED	enzyme	Transferase E.C.2.7.11.2 BRENDA
Gene Ontology	Chain Function Process Component F, A, E, B nucleotide binding protein kinase activity protein serine/threonine kin... pyruvate dehydrogenase (acet... protein binding ATP binding kinase activity transferase activity carbohydrate metabolic proce... glucose metabolic process pyruvate metabolic process regulation of acetyl-CoA bio... regulation of glucose metabo... phosphorylation peptidyl-serine phosphorylat... peroxisome proliferator acti... small molecule metabolic pro... cellular response to glucose... cellular response to fatty a... hypoxia-inducible factor-1al... regulation of reactive oxyge... mitochondrion mitochondrial matrix
Primary reference	Crystal structure of an asymmetric complex of pyruvate dehydrogenase kinase 3 with lipoyl domain 2 and its biological implications., Devedjiev Y, Steussy CN, Vassylyev DG, J Mol Biol. 2007 Jul 13;370(3):407-16. Epub 2007 May 10. PMID:17532006

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (281 Kb) [Save to disk] Biological Unit Coordinates (2pnr.pdb1.gz) 138 Kb Biological Unit Coordinates (2pnr.pdb2.gz) 139 Kb LPC: Ligand-Protein Contacts for 2PNR CSU: Contacts of Structural Units for 2PNR Likely Quarternary Molecular Structure file(s) for 2PNR Structure Factors (674 Kb) Retrieve 2PNR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2PNR from S2C, [Save to disk] Re-refined 2pnr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2PNR 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2PNR

Cartoon representation from PDB Cartoon 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 Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2PNR, from MSDmotif at EBI Fold representative 2pnr from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2pnr_A] [2pnr_B] [2pnr_C] [2pnr_E] [2pnr_F] [2pnr_G] SWISS-PROT database: [P10515] [Q15120] Domain organization of [ODP2_HUMAN] [PDK3_HUMAN] by SWISSPFAM Domain found in 2PNR: [HATPase_c ] by SMART Alignments of the sequence of 2PNR with the sequences similar proteins can be viewed for 2PNR's classification [ODP2_HUMAN] [PDK3_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [ODP2_HUMAN] [PDK3_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2PNR

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

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