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3.4.24.B4: matrix metalloproteinase-13

This is an abbreviated version!
For detailed information about matrix metalloproteinase-13, go to the full flat file.

Word Map on EC 3.4.24.B4

Reaction

proteolytic degradation of proteins =

Synonyms

collagenase, collagenase 3, collagenase-3, M10.013, matrix metalloproteinase 13, matrix metalloproteinase-13, MMP-13, MMP13, MMP13a, More, UMRCASE

ECTree

     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.24 Metalloendopeptidases
                3.4.24.B4 matrix metalloproteinase-13

Crystallization

Crystallization on EC 3.4.24.B4 - matrix metalloproteinase-13

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
a complex of human MMP-13 with bovine TIMP-2 is crystallized using the sitting-drop vapour diffusion method in 100 mM MES (pH 6.5), 200 mM magnesium acetate, 20% (w/v) PEG 8000
comparison of more than 40 X-ray co-crystal structures of the human MMP-13 with bound inhibitors to gain the structural insights such as conserved direct interactions with binding site residues, namely Ala-238, Thr-245 and Thr-247. Docking-based screening of existing drugs and binding free-energy calculation suggests eltrombopag, cilostazol and domperidone as potential MMP-13 inhibitors
crystal structures of catalytically inactive full-length MMP-13 mutant E223A in complex with peptides of 14-26 amino acids derived from the cleaved prodomain during activation. Peptides are bound to the active site of the enzyme by forming an extended beta-strand with Glu40 or Tyr46 inserted into the S1' specificity pocket
enzyme catalytic domain in complex with inhibitor N,N'-bis(pyridin-3-ylmethyl)pyrimidine-4,6-dicarboxamide, N,N'-bis(3-methylbenzyl)pyrimidine-4,6-dicarboxamide or N,N'-bis(4-fluoro-3-methylbenzyl)pyrimidine-4,6-dicarboxamide
hanging drop vapor diffusion method, using 10% (w/v) PEG4000, 1 M ammonium formate, and 100 mM Tris, pH 8.0
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in complex with inhibitor SM-25453, comparison with structure of EC 3.4.24.17 with inhibitor
molecular dynamics simulations and multiway explorative data analysis on MMP13 complexed with Marimastat and two cis-1(S)2(R)-amino-2-indanol ligands, and comparison with proteases ADAMTS4, ADAMTS5. Determinant characteristics for ligand binding and selectivity among the three enzymes are to be found in the different protein conformation flexibility
molecular modeling of binding of homochiral (3S,3’S)-astaxanthin to enzyme
recombinant enzyme, hanging-drop vapour diffusion method, 20 mM Tris-HCl, pH 7.3, 5 mM CaCl2, 300 mM NaCl, addition of 1 M ammonium sulfate solution, pH 9.0, equilibrated against ammonium sulfate at 1.2 M, 20°C, 1 week, X-ray structure determination at 2.7 A resolution and analyis of the C-terminal haemopexin-like domain
X-ray crystal structure of MMP-13 complexed with inhibitor
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enzyme complexed with a hydroxamate inhibitor, hanging-drop vapour diffusion method, 17 mg/ml protein in 10 mM HEPES, pH 7.5, with ammonium sufate to saturation, 18°C, 60 days, X-ray diffraction structure determination at 2.0 A resolution, and analysis
X-ray crystal structure of MMP-13 complexed with inhibitor
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