› 5mjt

X-ray diffraction
1.4Å resolution

Thrombin Mutant A190S in complex with (S) -1 - ((R) -2-amino-3,3-diphenylpropanoyl) -N- (3-chlorobenzyl) pyrrolidine-2-carboxamide

Released:
DOI: 10.2210/pdb5mjt/pdb
Model geometry
Fit model/data
PDB entry 5mjt coloured by chain, front view.
PDB entry 5mjt coloured by chain, side view.
PDB entry 5mjt coloured by chain, top view.
Source organisms:
Entry authors: Marca A, Sandner A, Heine A, Klebe G

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
Expression system: Escherichia coli BL21(DE3)
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: 29.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-2 Chain: D

Ligands and Environments

5 bound ligands:
Ligand 23U 1 x 23U
Ligand DMS 1 x DMS
Ligand PO4 1 x PO4
Ligand GOL 5 x GOL
Ligand NA 2 x NA
1 modified residue:
Ligand TYS 1 x TYS

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 69.492Å b: 71.613Å c: 72.129Å
α: 90° β: 99.73° γ: 90°
R-values:
R R work R free
0.149 0.148 0.172
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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