6ESM Hydrolase date Oct 23, 2017
title Crystal Structure Of Mmp9 In Complex With Inhibitor Be4.
authors L.Ciccone, L.Tepshi, E.Nuti, A.Rossello, E.A.Stura
compound source
Molecule: Matrix Metalloproteinase-9,Matrix Metalloproteina
Chain: A
Synonym: Mmp-9,92 Kda Gelatinase,92 Kda Type Iv Collagenase Gelatinase B,Gelb,Mmp-9,92 Kda Gelatinase,92 Kda Type Iv Co Gelatinase B,Gelb;
Ec: 3.4.24.35,3.4.24.35
Engineered: Yes
Mutation: Yes
Other_details: Catalytic Domain Of Mmp-9 Without The Fibron Domains.
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mmp9, Clg4b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 32 2 1
R_factor 0.156 R_Free 0.172
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.690 39.690 163.660 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.10 Å
ligand B9Z, CA, PZE, ZN enzyme Hydrolase E.C.3.4.24.35 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDevelopment of Thioaryl-based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR and Crystallographic Studies., Nuti E, Cuffaro D, Bernardini E, Camodeca C, Panelli L, Chaves S, Ciccone L, Tepshi L, Vera L, Orlandini E, Nencetti S, Stura EA, Santos MA, Dive V, Rossello A, J Med Chem. 2018 May 4. doi: 10.1021/acs.jmedchem.8b00096. PMID:29727184
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (6esm.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 6ESM
  • CSU: Contacts of Structural Units for 6ESM
  • Structure Factors (879 Kb)
  • Retrieve 6ESM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6ESM from S2C, [Save to disk]
  • View 6ESM 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 6ESM
  • 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: [6esm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6ESM
  • Community annotation for 6ESM at PDBWiki (http://pdbwiki.org)

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