› 3d6m

X-ray diffraction
1.8Å resolution

Crystal structure of human caspase-1 with a naturally-occurring Lys319->Arg substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)

Released:
DOI: 10.2210/pdb3d6m/pdb
PDB entry 3d6m coloured by chain, front view.
PDB entry 3d6m coloured by chain, side view.
PDB entry 3d6m coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Rosen-Wolff A, Roesler J, Romanowski MJ

Function and Biology Details

Reaction catalysed: 
Strict requirement for an Asp residue at position P1 and has a preferred cleavage sequence of Tyr-Val-Ala-Asp-|-.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151503 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Caspase-1 subunit p20 Chain: A
Molecule details ›
Chain: A
Length: 179 amino acids
Theoretical weight: 20 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P29466 (Residues: 120-297; Coverage: 44%)
Gene names: CASP1, IL1BC, IL1BCE
Sequence domains: Caspase domain
Structure domains: Rossmann fold
Caspase-1 subunit p10 Chain: B
Molecule details ›
Chain: B
Length: 89 amino acids
Theoretical weight: 10.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P29466 (Residues: 317-404; Coverage: 22%)
  • Best match: P29466-4 (Residues: 195-263)
Gene names: CASP1, IL1BC, IL1BCE
Sequence domains: Caspase domain
Structure domains: Caspase-like
N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide Chain: C
Molecule details ›
Chain: C
Length: 5 amino acids
Theoretical weight: 472 Da

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P43212
Unit cell:
a: 62.968Å b: 62.968Å c: 161.783Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.195 0.247
Expression system: Escherichia coli

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