2XS3 Hydrolase date Sep 24, 2010
title Structure Of Karilysin Catalytic Mmp Domain
authors N.Cerda-Costa, T.Guevara, A.Y.Karim, M.Ksiazek, K.A.Nguyen, J.L. J.Potempa, F.X.Gomis-Ruth
compound source
Molecule: Karilysin Protease
Chain: A, B
Fragment: Residues 35-200
Synonym: Karilysin Catalytic Domain Kly18
Engineered: Yes
Organism_scientific: Tannerella Forsythia
Organism_taxid: 28112
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21

Molecule: Peptide Ala-Phe-Thr-Ser
Chain: C, D

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.189 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.370 53.110 86.300 90.00 134.55 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand TRS, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenologue of animal matrix metalloproteinases., Cerda-Costa N, Guevara T, Karim AY, Ksiazek M, Nguyen KA, Arolas JL, Potempa J, Gomis-Ruth FX, Mol Microbiol. 2011 Jan;79(1):119-132. doi:, 10.1111/j.1365-2958.2010.07434.x. Epub 2010 Nov 2. PMID:21166898
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (2xs3.pdb1.gz) 59 Kb
  • Biological Unit Coordinates (2xs3.pdb2.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 2XS3
  • CSU: Contacts of Structural Units for 2XS3
  • Structure Factors (267 Kb)
  • Retrieve 2XS3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XS3 from S2C, [Save to disk]
  • Re-refined 2xs3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XS3 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 2XS3
  • 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
  • 3D motif for 2XS3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xs3_C] [2xs3] [2xs3_D] [2xs3_B] [2xs3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2XS3: [ZnMc ] by SMART
  • Other resources with information on 2XS3
  • Community annotation for 2XS3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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