› 5bpa

X-ray diffraction
1.79Å resolution

X-RAY Co-structure of MMP-13 with 4-[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}formamido)methyl]benzoate

Released:
DOI: 10.2210/pdb5bpa/pdb
PDB entry 5bpa coloured by chain, front view.
PDB entry 5bpa coloured by chain, side view.
PDB entry 5bpa coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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 54 8174-87 (2011)
PMID: 22017539

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155288 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Collagenase 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 171 amino acids
Theoretical weight: 19.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P45452 (Residues: 104-274; Coverage: 38%)
Gene name: MMP13
Sequence domains: Matrixin
Structure domains: Collagenase (Catalytic Domain)

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 6 x CA
Ligand 4UF 2 x 4UF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2
Unit cell:
a: 135.281Å b: 36.141Å c: 96.097Å
α: 90° β: 131.48° γ: 90°
R-values:
R R work R free
0.239 0.237 0.28
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

An overview of molecular fingerprint similarity search in virtual screening.
Muegge et al. (2016)
2 more

4 mentions without citation

Structure prediction of honey bee vitellogenin: a multi-domain protein important for insect immunity.
Leipart et al. (2022)
3 more