Thrombin in complex with D-phe-pro-3-chloro-1,3-dihydroxybenzylamide derivative (13C)

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).

Ligands and binding sites

• DPN · D-phenylalanine · ligand · chains H
• PRO · Proline · ligand · chains H
• OJK · 2-(aminomethyl)-5-chloranyl-benzene-1,4-diol · 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
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains H

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

Pockets

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

Interfaces

2 interfaces between chains.

• L–H · 1120 Ų buried · 27 hydrogen bonds · protein-protein
• H–I · 606 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).

Compared structures

• 6YB6 · Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c) · the same entry in another collection · chain L against L, 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 0.50

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 6YB6 · PDBe 6YB6 · UniProt P00734 · UniProt P09945