5L8S Hydrolase date Jun 08, 2016
title The Crystal Structure Of A Cold-Adapted Acylaminoacyl Peptid Reveals A Novel Quaternary Architecture Based On The Arm-Ex Mechanism
authors S.Brocca, C.Ferrari, A.Barbiroli, A.Pesce, M.Lotti, M.Nardini
compound source
Molecule: Amino Acyl Peptidase
Chain: A, B, C, D
Synonym: Peptidase S9
Engineered: Yes
Organism_scientific: Sporosarcina Psychrophila
Organism_taxid: 1476
Gene: Aph, Aze41_09720
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.212 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
148.080 151.100 191.230 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand SO4 enzyme
Gene AZE41
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceA bacterial acyl aminoacyl peptidase couples flexibility and stability as a result of cold adaptation., Brocca S, Ferrari C, Barbiroli A, Pesce A, Lotti M, Nardini M, FEBS J. 2016 Dec;283(23):4310-4324. doi: 10.1111/febs.13925. Epub 2016 Nov 7. PMID:27739253
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (400 Kb) [Save to disk]
  • Biological Unit Coordinates (5l8s.pdb1.gz) 201 Kb
  • Biological Unit Coordinates (5l8s.pdb2.gz) 199 Kb
  • LPC: Ligand-Protein Contacts for 5L8S
  • CSU: Contacts of Structural Units for 5L8S
  • Structure Factors (3050 Kb)
  • Retrieve 5L8S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L8S from S2C, [Save to disk]
  • Re-refined 5l8s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5L8S 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 5L8S
  • 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: [5l8s_D] [5l8s_B] [5l8s] [5l8s_C] [5l8s_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5L8S
  • Community annotation for 5L8S at PDBWiki (http://pdbwiki.org)

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