5BOY	Hydrolase Hydrolase Inhibitor	date	May 27, 2015
title	X-Ray Co-Structure Of Mmp-13 With Ethyl 5-(1-Methyl-1h-Imida 1h-Indole-2-Carboxylate
authors	N.A.Farrow
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 0.160 R_Free 0.190
crystal cell	length a length b length c angle alpha angle beta angle gamma 135.079 36.051 95.908 90.00 131.26 90.00
method	X-Ray Diffraction	resolution	2.03 Å
ligand	4UE, 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] (69 Kb) [Save to disk] Biological Unit Coordinates (5boy.pdb1.gz) 62 Kb LPC: Ligand-Protein Contacts for 5BOY CSU: Contacts of Structural Units for 5BOY Structure Factors (195 Kb) Retrieve 5BOY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5BOY from S2C, [Save to disk] Re-refined 5boy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5BOY 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 5BOY

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 5BOY, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5boy_A] [5boy_B] [5boy] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5BOY: [ZnMc ] by SMART

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