5YZM Hydrolase date Dec 15, 2017
title Crystal Structure Of S9 Peptidase (Inactive Form) From Deino Radiodurans R1
authors P.Yadav, S.N.Jamdar, A.Kumar, B.Ghosh, R.D.Makde
compound source
Molecule: Acyl-Peptide Hydrolase, Putative
Chain: A, B, C, D
Synonym: S9 Prolyl Oligopeptidase
Engineered: Yes
 Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;
Gene: Dr_0165
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst50tr
symmetry Space Group: P 1 21 1
R_factor 0.189 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.702 195.092 107.715 90.00 99.97 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand ACT enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (770 Kb) [Save to disk]
  • Biological Unit Coordinates (5yzm.pdb1.gz) 763 Kb
  • LPC: Ligand-Protein Contacts for 5YZM
  • CSU: Contacts of Structural Units for 5YZM
  • Structure Factors (6015 Kb)
  • Retrieve 5YZM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YZM from S2C, [Save to disk]
    • View 5YZM 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 5YZM
  • 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: [5yzm_C] [5yzm_A] [5yzm_D] [5yzm_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5YZM
  • Community annotation for 5YZM at PDBWiki (http://pdbwiki.org)

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