Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to ppack

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 33% 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 · 4 copies · chains B
• BMA · beta-D-mannopyranose · sugar · 4 copies
• MAN · alpha-D-mannopyranose · sugar
• K · Potassium ion · metal · chains B
• NA · Sodium ion · metal · chains B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1699 Ų buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 3 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

• 5TO3 · Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a… · 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 A against A, TM-score 0.80
• P07204 · AlphaFold monomer V2.0 prediction for thrombomodulin (P07204) · a predicted model of the same protein · chain B against A, TM-score 0.28

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 P07204
• Elsewhere: RCSB PDB 5TO3 · PDBe 5TO3 · UniProt P00734 · UniProt P07204