Crystal structure of human alpha-THROMBIN*RWJ-51438 complex at 1.7 a

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 29% strand (DSSP).

Ligands and binding sites

• 1Z0 · N-methyl-D-phenylalanyl-N-{(1S)-4-carbamimidamido-1-[(6-carboxy-1,3-benzothiazol-2-yl)carbonyl]butyl}-L-prolinamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
• NA · Sodium ion · metal · 2 copies · chains A

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

1 interface between chains.

• A–B · 677 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 1DOJ · Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 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 0.91
• P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain B against A, TM-score 0.48

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 1DOJ · PDBe 1DOJ · UniProt P00734 · UniProt P09945