Crystal structure of the anticoagulant thrombin mutant W215A/E217A bound to ppack

Structure

x-ray diffraction · 2 distinct chains · 18% 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 B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
• ZN · Zinc ion · metal · 3 copies · chains A, B

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

1 interface between chains.

• A–B · 1703 Ų buried · 33 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 1TQ7 · Crystal structure of the anticoagulant thrombin mutant W215A/E217A bound to PPACK · the same entry in another collection · chain A against A, TM-score 1.00
• P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.92

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
• Elsewhere: RCSB PDB 1TQ7 · PDBe 1TQ7 · UniProt P00734