3WV3	Hydrolase Hydrolase Inhibitor	date	May 12, 2014
title	Crystal Structure Of The Catalytic Domain Of Mmp-13 Complexe (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine- Carboxamide
authors	H.Oki, Y.Tanaka
compound		source
Molecule: Collagenase 3 Chain: A, B Fragment: Catalytic Domain, Residues 104-274 Synonym: Matrix Metalloproteinase-13, Mmp-13 Ec: 3.4.24.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Mmp13 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
symmetry	Space Group: C 1 2 1	R_factor 0.163 R_Free 0.212
crystal cell	length a length b length c angle alpha angle beta angle gamma 135.558 36.352 95.853 90.00 130.64 90.00
method	X-Ray Diffraction	resolution	1.60 Å
ligand	CA, EDO, FMT, NA, WLL, ZN	enzyme	Hydrolase E.C.3.4.24 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Thieno[2,3-d]pyrimidine-2-carboxamides bearing a carboxybenzene group at 5-position: Highly potent, selective, and orally available MMP-13 inhibitors interacting with the S1'' binding site., Nara H, Sato K, Naito T, Mototani H, Oki H, Yamamoto Y, Kuno H, Santou T, Kanzaki N, Terauchi J, Uchikawa O, Kori M, Bioorg Med Chem. 2014 Oct 1;22(19):5487-505. doi: 10.1016/j.bmc.2014.07.025. Epub, 2014 Aug 7. PMID:25192810

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk] Biological Unit Coordinates (3wv3.pdb1.gz) 60 Kb Biological Unit Coordinates (3wv3.pdb2.gz) 58 Kb Biological Unit Coordinates (3wv3.pdb3.gz) 116 Kb LPC: Ligand-Protein Contacts for 3WV3 CSU: Contacts of Structural Units for 3WV3 Structure Factors (696 Kb) Retrieve 3WV3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3WV3 from S2C, [Save to disk] Re-refined 3wv3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3WV3 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 3WV3

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 3WV3, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3wv3] [3wv3_B] [3wv3_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3WV3: [ZnMc ] by SMART

Other resources with information on 3WV3

Community annotation for 3WV3 at PDBWiki (http://pdbwiki.org)

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