5GKQ Lyase date Jul 05, 2016
title Structure Of Pl6 Family Alginate Lyase Alygc Mutant-R241a
authors Y.Z.Zhang, P.Wang, F.Xu
compound source
Molecule: Alygc Mutant - R241a
Chain: A, B
Engineered: Yes
 Organism_scientific: Glaciecola Chathamensis S18k6
Organism_taxid: 1127672
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.658 122.830 195.332 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.57 Å
ligand BEM, CA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceNovel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6., Xu F, Dong F, Wang P, Cao HY, Li CY, Li PY, Pang XH, Zhang YZ, Chen XL, J Biol Chem. 2017 Mar 17;292(11):4457-4468. doi: 10.1074/jbc.M116.766030. Epub, 2017 Feb 1. PMID:28154171
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (237 Kb) [Save to disk]
  • Biological Unit Coordinates (5gkq.pdb1.gz) 231 Kb
  • Biological Unit Coordinates (5gkq.pdb2.gz) 118 Kb
  • Biological Unit Coordinates (5gkq.pdb3.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 5GKQ
  • CSU: Contacts of Structural Units for 5GKQ
  • Structure Factors (1728 Kb)
  • Retrieve 5GKQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GKQ from S2C, [Save to disk]
  • Re-refined 5gkq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5GKQ 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 5GKQ
  • 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: [5gkq] [5gkq_B] [5gkq_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5GKQ
  • Community annotation for 5GKQ at PDBWiki (http://pdbwiki.org)

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