5BOT Hydrolase Hydrolase Inhibitor date May 27, 2015
title X-Ray Co-Structure Of Mmp-13 With Ethyl 5-Carbamoyl-1h-Indol Carboxylate
authors N.A.Farrow, A.K.Padyana
compound source
Molecule: Collagenase 3
Chain: A, B
Fragment: Unp Residues 104-274
Synonym: Matrix Metalloproteinase-13,Mmp-13
Ec: 3.4.24.-
Engineered: Yes
Fragment: 104-274
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mmp13
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: C 1 2 1
R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
134.641 35.953 95.824 90.00 130.78 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand 4UM, CA, ZN enzyme Hydrolase E.C.3.4.24 BRENDA
Primary referenceFragment-based discovery of indole inhibitors of matrix metalloproteinase-13., Taylor SJ, Abeywardane A, Liang S, Muegge I, Padyana AK, Xiong Z, Hill-Drzewi M, Farmer B, Li X, Collins B, Li JX, Heim-Riether A, Proudfoot J, Zhang Q, Goldberg D, Zuvela-Jelaska L, Zaher H, Li J, Farrow NA, J Med Chem. 2011 Dec 8;54(23):8174-87. doi: 10.1021/jm201129m. Epub 2011 Nov 9. PMID:22017539
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (5bot.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 5BOT
  • CSU: Contacts of Structural Units for 5BOT
  • Structure Factors (354 Kb)
  • Retrieve 5BOT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BOT from S2C, [Save to disk]
  • Re-refined 5bot structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5BOT 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 5BOT
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 5BOT, from MSDmotif at EBI
  • Fold representative 5bot from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5bot_A] [5bot_B] [5bot]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5BOT: [ZnMc ] by SMART
  • Other resources with information on 5BOT
  • Community annotation for 5BOT at PDBWiki (http://pdbwiki.org)

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