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 Diffractionresolution 2.50 Å
ligand RED enzyme Transferase E.C.2.7.11.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B


Primary referenceCrystal 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 (679 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.
  • 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_E] [2pnr_A] [2pnr_B] [2pnr_G] [2pnr] [2pnr_C] [2pnr_F]
  • SWISS-PROT database: [P10515] [Q15120]
  • Domain organization of [ODP2_HUMAN] [PDK3_HUMAN] by SWISSPFAM
  • Domain found in 2PNR: [HATPase_c ] by SMART
  • Other resources with information on 2PNR
  • Community annotation for 2PNR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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