› 6y02

X-ray diffraction
1.48Å resolution

Thrombin in complex with 13k

Released:
DOI: 10.2210/pdb6y02/pdb
Model geometry
Fit model/data
PDB entry 6y02 coloured by chain, front view.
PDB entry 6y02 coloured by chain, side view.
PDB entry 6y02 coloured by chain, top view.
Source organisms:
Entry authors: Sandner A, Heine A, Klebe G, Abazi N

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-133076 (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
Hirudin variant-2 Chain: C

Ligands and Environments

6 bound ligands:
Ligand NA 2 x NA
Ligand PO4 1 x PO4
Ligand DMS 2 x DMS
Ligand GOL 2 x GOL
Ligand O5Z 1 x O5Z
Ligand NAG 1 x NAG
1 modified residue:
Ligand TYS 1 x TYS

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2
Unit cell:
a: 70.131Å b: 71.404Å c: 72.892Å
α: 90° β: 100.51° γ: 90°
R-values:
R R work R free
0.14 0.139 0.164
Expression system: Not provided

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