› 4e05

X-ray diffraction
2.3Å resolution

Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding mechanism

Released:
DOI: 10.2210/pdb4e05/pdb
PDB entry 4e05 coloured by chain, front view.
PDB entry 4e05 coloured by chain, side view.
PDB entry 4e05 coloured by chain, top view.
Source organisms:
Primary publication:
Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector.
Figueiredo AC, de Sanctis D, Gutiérrez-Gallego R, Cereija TB, Macedo-Ribeiro S, Fuentes-Prior P, Pereira PJ
Proc Natl Acad Sci U S A 109 E3649-58 (2012)
PMID: 23223529

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133134 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Salivary anti-thrombin peptide anophelin Chain: I
Molecule details ›
Chain: I
Length: 61 amino acids
Theoretical weight: 6.54 KDa
Source organism: Anopheles albimanus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NJS1 (Residues: 23-83; Coverage: 100%)
Gene name: AT
Sequence domains: Thrombin inhibitor from mosquito

Ligands and Environments

2 bound ligands:
Ligand NAG 1 x NAG
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P3112
Unit cell:
a: 120.18Å b: 120.18Å c: 77.81Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.171 0.169 0.201
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions.
Meng et al. (2017)
4 more

3 mentions without citation

Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands.
Troisi et al. (2021)
2 more