5KYM Transferase date Jul 21, 2016
title Crystal Structure Of The 1-Acyl-Sn-Glycerophosphate (Lpa) Acyltransferase, Plsc, From Thermotoga Maritima
authors R.M.Robertson, J.Yao, S.Gajewski, G.Kumar, E.W.Martin, C.O.Rock, S
compound source
Molecule: 1-Acyl-Sn-Glycerol-3-Phosphate Acyltransferase
Chain: A, B
Ec: 2.3.1.51
Engineered: Yes
Organism_scientific: Thermotoga Maritima (Strain Atcc 43589 Dsm 3109 Jcm 10099);
Organism_taxid: 243274
Strain: Atcc 43589 Msb8 Dsm 3109 Jcm 10099
Gene: Tmari_1701
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: I 2 3
R_factor 0.219 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
173.836 173.836 173.836 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand DD9, HGX, LMT enzyme Transferase E.C.2.3.1.51 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceA two-helix motif positions the lysophosphatidic acid acyltransferase active site for catalysis within the membrane bilayer., Robertson RM, Yao J, Gajewski S, Kumar G, Martin EW, Rock CO, White SW, Nat Struct Mol Biol. 2017 Jul 17. doi: 10.1038/nsmb.3436. PMID:28714993
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (5kym.pdb1.gz) 84 Kb
  • Biological Unit Coordinates (5kym.pdb2.gz) 84 Kb
  • LPC: Ligand-Protein Contacts for 5KYM
  • CSU: Contacts of Structural Units for 5KYM
  • Structure Factors (1459 Kb)
  • Retrieve 5KYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KYM from S2C, [Save to disk]
  • Re-refined 5kym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KYM 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 5KYM
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kym_A] [5kym_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5KYM
  • Community annotation for 5KYM at PDBWiki (http://pdbwiki.org)

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