Thrombin in complex with 5-chlorothiophene-2-carboxamide

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).

Ligands and binding sites

• FQI · 5-chloro-2-thiophenecarboxamide · ligand · chains H
• TYS · O-sulfo-L-tyrosine · ligand · chains H, I
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
• NA · Sodium ion · metal · 2 copies · chains H
• PO4 · Phosphate ion · ion · chains H
• GOL · Glycerol · additive · 3 copies · chains H
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains H
• EDO · 1,2-ethanediol · additive · 2 copies · chains H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• H–L · 1116 Ų buried · 27 hydrogen bonds · protein-protein
• H–I · 499 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

• 4UD9 · Thrombin in complex with 5-chlorothiophene-2-carboxamide · the same entry in another collection · chain H against H, TM-score 1.00
• P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.92
• P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.49

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P00734
• Every structure of UniProt P09945
• Elsewhere: RCSB PDB 4UD9 · PDBe 4UD9 · UniProt P00734 · UniProt P09945