4WNI Oxidoreductase date Oct 12, 2014
title Crystal Structure Of The T229k Mutant Of Human Gapdh At 2.3 Resolution
authors E.D.Garcin, M.R.White
compound source
Molecule: Glyceraldehyde-3-Phosphate Dehydrogenase
Chain: O, A, B, C
Synonym: Gapdh,Peptidyl-Cysteine S-Nitrosylase Gapdh
Ec: 1.2.1.12,2.6.99.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Variant: T229k
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 21 21 21
R_factor 0.169 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.363 133.095 147.768 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand NAD, ZN enzyme Oxidoreductase E.C.1.2.1.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, O, C, 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] (641 Kb) [Save to disk]
  • Biological Unit Coordinates (4wni.pdb1.gz) 634 Kb
  • LPC: Ligand-Protein Contacts for 4WNI
  • CSU: Contacts of Structural Units for 4WNI
  • Structure Factors (641 Kb)
  • Retrieve 4WNI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4WNI from S2C, [Save to disk]
  • Re-refined 4wni structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4WNI 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 4WNI
  • 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 4WNI, from MSDmotif at EBI
  • Fold representative 4wni from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4wni_B] [4wni_C] [4wni] [4wni_O] [4wni_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4WNI: [Gp_dh_N ] by SMART
  • Other resources with information on 4WNI
  • Community annotation for 4WNI at PDBWiki (http://pdbwiki.org)

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