Thrombin in complex with D-phe-pro-M-trifluoromethylbenzylamide derivative (PHE2)

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 31% strand (DSSP).

Ligands and binding sites

• OGZ · [3-(trifluoromethyl)phenyl]methanamine · ligand · chains H, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
• NA · Sodium ion · metal · 2 copies · chains H
• PO4 · Phosphate ion · ion · 2 copies · chains H
• DMS · Dimethyl sulfoxide · additive · chains H

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• L–H · 1116 Ų buried · 26 hydrogen bonds · protein-protein
• H–I · 640 Ų buried · 6 hydrogen bonds · protein-protein
• H–C · 292 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 covalent, 1 d-amino, 1 glycan, 1 modified (disulfide, covalent ligand, D-amino acid, N-glycosylation, sulfation).

Compared structures

• 6Y9H · Thrombin in complex with D-Phe-Pro-m-Trifluoromethylbenzylamide derivative (phe2) · the same entry in another collection · chain L against L, TM-score 1.00
• P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.50

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 6Y9H · PDBe 6Y9H · UniProt P00734 · UniProt P09945