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_factor R_Free 0.229
crystal cell	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 Diffraction	resolution	1.85 Å
ligand	4UM, CA, ZN	enzyme	Hydrolase E.C.3.4.24 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Fragment-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] (70 Kb) [Save to disk] Biological Unit Coordinates (5bot.pdb1.gz) 64 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

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 5BOT, from MSDmotif at EBI

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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