5L79 Hydrolase date Jun 02, 2016
title Crystal Structure Of Mmp12 In Complex With Rxp470.1 Conjugat Fluorophore Cy5,5 In Space Group P21212.
authors L.Tepshi, T.Bordenave, L.Devel, V.Dive, E.A.Stura
compound source
Molecule: Macrophage Metalloelastase
Chain: A
Synonym: Mme,Macrophage Elastase,Hme,Matrix Metalloproteina 12;
Ec: 3.4.24.65
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mmp12, Hme
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.206 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.900 62.790 37.740 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.07 Å
ligand 6PJ, CA, EDO, GOL, R47, ZN enzyme Hydrolase E.C.3.4.24.65 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSynthesis, in vitro and in vivo evaluation of MMP-12 selective optical probes., Bordenave T, Helle M, Beau F, Georgiadis D, Tepshi L, Bernes M, Yunpeng Y, Levenez L, Poquet E, Nozach H, Razavian M, Toczek J, Stura EA, Dive V, Sadeghi MM, Devel L, Bioconjug Chem. 2016 Aug 26. PMID:27564088
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk]
  • Biological Unit Coordinates (5l79.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 5L79
  • CSU: Contacts of Structural Units for 5L79
  • Structure Factors (232 Kb)
  • Retrieve 5L79 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L79 from S2C, [Save to disk]
  • Re-refined 5l79 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5L79 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 5L79
  • 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: [5l79] [5l79_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5L79: [ZnMc ] by SMART
  • Other resources with information on 5L79
  • Community annotation for 5L79 at PDBWiki (http://pdbwiki.org)

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