› 5d63

X-ray diffraction
1.65Å resolution

MOA-Z-VAD-fmk inhibitor complex, direct/inverted dual orientation

Released:
DOI: 10.2210/pdb5d63/pdb
PDB entry 5d63 coloured by chain, front view.
PDB entry 5d63 coloured by chain, side view.
PDB entry 5d63 coloured by chain, top view.
Source organisms:
Primary publication:
An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor.
Cordara G, van Eerde A, Grahn EM, Winter HC, Goldstein IJ, Krengel U
OpenAccess logo PLoS One 11 e0149407 (2016)
PMID: 26901797

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165549 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Agglutinin Chain: A
Molecule details ›
Chain: A
Length: 293 amino acids
Theoretical weight: 32.33 KDa
Source organism: Marasmius oreades
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8X123 (Residues: 1-293; Coverage: 100%)
Sequence domains:
Structure domains:
Z-VAD-fmk Chain: L
Molecule details ›
Chain: L
Length: 5 amino acids
Theoretical weight: 472 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GAL, FUC, GLA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: FUC, GLA
Carbohydrate polymer
5 bound ligands:
Ligand EDO 3 x EDO
Ligand DMS 2 x DMS
Ligand CL 3 x CL
Ligand CA 2 x CA
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P6322
Unit cell:
a: 121.066Å b: 121.066Å c: 99.95Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.163 0.162 0.187
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 citation in other articles

Structural characterization of the hypothetical protein Lpg2622, a new member of the C1 family peptidases from Legionella pneumophila.
Gong et al. (2018)
2 more

3 mentions without citation

An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor.
Cordara et al. (2016)
2 more