2F5Z Oxidoreductase Protein Binding date Nov 28, 2005
title Crystal Structure Of Human Dihydrolipoamide Dehydrogenase (E3) Complexed To The E3-Binding Domain Of Human E3- Binding Protein
authors C.A.Brautigam, J.L.Chuang, R.M.Wynn, D.R.Tomchick, M.Machius, D.T.Chuang
compound source
Molecule: Dihydrolipoyl Dehydrogenase
Chain: A, B, C, D, E, F, G, H, I, J
Fragment: Dihydrolipoyl Dehydrogenase, Residues 36-509
Synonym: Dihydrolipoamide Dehydrogenase, Glycine Cleavage System L Protein;
Ec: 1.8.1.4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dld, Gcsl, Lad, Phe3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl-1 Blue
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptrchisthe3

Molecule: Pyruvate Dehydrogenase Protein X Component
Chain: K, L, M, N, O
Fragment: E3-Binding Domain, Residues 173-230
Synonym: Dihydrolipoamide Dehydrogenase-Binding Protein Of Pyruvate Dehydrogenase Complex, Lipoyl-Containing Pyruvate Dehydrogenase 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: Bl-21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Lte3bd
symmetry Space Group: P 21 21 21
R_factor 0.205 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
171.153 187.728 224.392 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.18 Å
ligand FAD, SO4 enzyme Oxidoreductase E.C.1.8.1.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, E, B, H, C, D, I, G


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] (824 Kb) [Save to disk]
  • Biological Unit Coordinates (2f5z.pdb1.gz) 167 Kb
  • Biological Unit Coordinates (2f5z.pdb2.gz) 175 Kb
  • Biological Unit Coordinates (2f5z.pdb3.gz) 175 Kb
  • Biological Unit Coordinates (2f5z.pdb4.gz) 178 Kb
  • Biological Unit Coordinates (2f5z.pdb5.gz) 171 Kb
  • LPC: Ligand-Protein Contacts for 2F5Z
  • CSU: Contacts of Structural Units for 2F5Z
  • Likely Quarternary Molecular Structure file(s) for 2F5Z
  • Structure Factors (3210 Kb)
  • Retrieve 2F5Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2F5Z from S2C, [Save to disk]
  • Re-refined 2f5z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2F5Z 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 2F5Z
  • 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 2F5Z, from MSDmotif at EBI
  • Fold representative 2f5z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2f5z_D] [2f5z_E] [2f5z_F] [2f5z_B] [2f5z_K] [2f5z_H] [2f5z_L] [2f5z_A] [2f5z_C] [2f5z_J] [2f5z] [2f5z_N] [2f5z_M] [2f5z_O] [2f5z_I] [2f5z_G]
  • SWISS-PROT database: [P09622] [O00330]
  • Domain organization of [DLDH_HUMAN] [ODPX_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2F5Z with the sequences similar proteins can be viewed for 2F5Z's classification [DLDH_HUMAN] [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 [DLDH_HUMAN] [ODPX_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2F5Z
  • Community annotation for 2F5Z 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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