2F60 Protein Binding date Nov 28, 2005
title Crystal Structure Of The Dihydrolipoamide Dehydrogenase (E3) Domain Of Human E3-Binding Protein
authors C.A.Brautigam, J.L.Chuang, R.M.Wynn, D.R.Tomchick, M.Machius, D.T
compound source
Molecule: Pyruvate Dehydrogenase Protein X Component
Chain: K
Fragment: E3-Binding Domain, Residues 173-230
Synonym: Dihydrolipoamide Dehydrogenase-Binding Protein Of Dehydrogenase Complex, Lipoyl-Containing Pyruvate Dehydroge Complex Component X, E3-Binding Protein, E3bp, Prox;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdhx, Pdx1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Lte3bd
symmetry Space Group: P 65 2 2
R_factor 0.206 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.845 36.845 191.542 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.55 Å
ligand GOL enzyme
Primary referenceStructural Insight into Interactions between Dihydrolipoamide Dehydrogenase (E3) and E3 Binding Protein of Human Pyruvate Dehydrogenase Complex., Brautigam CA, Wynn RM, Chuang JL, Machius M, Tomchick DR, Chuang DT, Structure. 2006 Mar;14(3):611-21. Epub 2006 Jan 26. PMID:16442803
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (2f60.pdb1.gz) 12 Kb
  • LPC: Ligand-Protein Contacts for 2F60
  • CSU: Contacts of Structural Units for 2F60
  • Likely Quarternary Molecular Structure file(s) for 2F60
  • Structure Factors (85 Kb)
  • Retrieve 2F60 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2F60 from S2C, [Save to disk]
  • Re-refined 2f60 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2F60 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 2F60
  • 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 2F60, from MSDmotif at EBI
  • Fold representative 2f60 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2f60] [2f60_K]
  • SWISS-PROT database: [O00330]
  • Domain organization of [ODPX_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2F60 with the sequences similar proteins can be viewed for 2F60's classification [ODPX_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 [ODPX_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2F60
  • Community annotation for 2F60 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science