Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 29% strand (DSSP).

Ligands and binding sites

• 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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 · 1176 Ų buried · 21 hydrogen bonds · protein-protein
• H–J · 709 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 1TMU · Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due… · 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 0.91
• P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain J against A, TM-score 0.58

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 1TMU · PDBe 1TMU · UniProt P00734 · UniProt P09945