4WNC Oxidoreductase date Oct 11, 2014
title Crystal Structure Of Human Wild-Type Gapdh At 1.99 Angstroms Resolution
authors E.D.Garcin
compound source
Molecule: Glyceraldehyde-3-Phosphate Dehydrogenase
Chain: O, A, B, C, D, E, F, G
Synonym: Gapdh,Peptidyl-Cysteine S-Nitrosylase Gapdh
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gapdh, Gapd, Cdabp0047, Oksw-Cl.12
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Pripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a
symmetry Space Group: P 1 21 1
R_factor 0.139 R_Free 0.179
length a length b length c angle alpha angle beta angle gamma
132.537 81.423 147.802 90.00 90.06 90.00
method X-Ray Diffractionresolution 1.99 Å
ligand ACT, NAD, ZN enzyme Oxidoreductase E.C. BRENDA
F, A, O, D, C, G, E, B

Primary referenceA Dimer Interface Mutation in Glyceraldehyde 3-Phosphate Dehydrogenase Regulates its Binding to AU-rich RNA., White MR, Khan MM, Deredge D, Ross CR, Quintyn R, Zucconi BE, Wysocki VH, Wintrode PL, Wilson GM, Garcin ED, J Biol Chem. 2014 Dec 1. pii: jbc.M114.618165. PMID:25451934
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1297 Kb) [Save to disk]
  • Biological Unit Coordinates (4wnc.pdb1.gz) 644 Kb
  • Biological Unit Coordinates (4wnc.pdb2.gz) 645 Kb
  • LPC: Ligand-Protein Contacts for 4WNC
  • CSU: Contacts of Structural Units for 4WNC
  • Structure Factors (1622 Kb)
  • Retrieve 4WNC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4WNC from S2C, [Save to disk]
  • Re-refined 4wnc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4WNC 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 4WNC
  • 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 4WNC, from MSDmotif at EBI
  • Fold representative 4wnc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4wnc_B] [4wnc_O] [4wnc_C] [4wnc_D] [4wnc_E] [4wnc] [4wnc_F] [4wnc_G] [4wnc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4WNC: [Gp_dh_N ] by SMART
  • Other resources with information on 4WNC
  • Community annotation for 4WNC at PDBWiki (http://pdbwiki.org)

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