Thrombin in complex with D-phe-pro-M-methoxybenzylamide derivative (16A)

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).

Ligands and binding sites

• SZ4 · 1-(3-methoxyphenyl)methanamine · ligand · chains H
• 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 · 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, 1 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• L–H · 1153 Ų buried · 28 hydrogen bonds · protein-protein
• H–I · 611 Ų buried · 4 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

• 6YHG · Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a) · 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 0.52

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 6YHG · PDBe 6YHG · UniProt P00734 · UniProt P09945