› 3u8o

X-ray diffraction
1.28Å resolution

Human thrombin complexed with D-Phe-Pro-D-Arg-D-Thr

Released:
DOI: 10.2210/pdb3u8o/pdb
PDB entry 3u8o coloured by chain, front view.
PDB entry 3u8o coloured by chain, side view.
PDB entry 3u8o coloured by chain, top view.
Source organisms:
Primary publication:
Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors.
Figueiredo AC, Clement CC, Zakia S, Gingold J, Philipp M, Pereira PJ
PLoS One 7 e34354 (2012)
PMID: 22457833

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-133120 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 30 amino acids
Theoretical weight: 3.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 334-363; Coverage: 5%)
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
D-PHE-PRO-D-ARG-D-THR DERIVED DIRECT THROMBIN INHIBITOR Chain: I
Molecule details ›
Chain: I
Length: 5 amino acids
Theoretical weight: 519 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand NAG 1 x NAG
Ligand NA 1 x NA
Ligand IOD 1 x IOD
Ligand CL 1 x CL
Ligand MRD 2 x MRD
3 modified residues:
Ligand DPN 1 x DPN
Ligand DAR 1 x DAR
Ligand DTH 1 x DTH

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 57.446Å b: 72.68Å c: 83.09Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.129 0.128 0.149
Expression system: Not provided

Quick links

Citations

1 review citation

Non-Canonical Amino Acids in Analyses of Protease Structure and Function.
Goettig et al. (2023)
15 other articles

3 mentions without citation

Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors.
Figueiredo et al. (2012)
2 more