5K4G Hydrolase date May 20, 2016
title Wolinella Succinogenes L-Asparaginase S121 + L-Aspartic Acid Conformation
authors H.A.Nguyen, A.Lave
compound source
Molecule: L-Asparaginase
Chain: A, B, C, D
Synonym: L-Asnase,L-Asparagine Amidohydrolase
Ec: 3.5.1.1
Engineered: Yes
 Organism_scientific: Wolinella Succinogenes (Strain Atcc 29 1740 Lmg 7466 Nctc 11488 Fdc 602w);
Organism_taxid: 273121
Strain: Atcc 29543 Dsm 1740 Lmg 7466 Nctc 11488 Fdc
Gene: Ansa, Ansb, Ws0660
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.166 R_Free 0.201
crystal
cell
length a length b length c angle alpha angle beta angle gamma
146.097 71.202 142.600 90.00 118.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand ASP enzyme Hydrolase E.C.3.5.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural Insight into Substrate Selectivity of Erwinia chrysanthemi l-Asparaginase., Nguyen HA, Su Y, Lavie A, Biochemistry. 2016 Mar 1;55(8):1246-53. doi: 10.1021/acs.biochem.5b01351. Epub, 2016 Feb 17. PMID:26855287
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (229 Kb) [Save to disk]
  • Biological Unit Coordinates (5k4g.pdb1.gz) 222 Kb
  • Biological Unit Coordinates (5k4g.pdb2.gz) 226 Kb
  • LPC: Ligand-Protein Contacts for 5K4G
  • CSU: Contacts of Structural Units for 5K4G
  • Structure Factors (3655 Kb)
  • Retrieve 5K4G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K4G from S2C, [Save to disk]
  • Re-refined 5k4g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5K4G 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 5K4G
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k4g_A] [5k4g_D] [5k4g] [5k4g_B] [5k4g_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5K4G
  • Community annotation for 5K4G at PDBWiki (http://pdbwiki.org)

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