X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 31% 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
• ZN · Zinc ion · metal · 2 copies · chains L, H
• NA · Sodium ion · metal · chains H
• K · Potassium ion · metal · chains D
• CL · Chloride ion · ion · 2 copies · chains H

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

Pockets

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

Interfaces

2 interfaces between chains.

• L–H · 1140 Ų buried · 22 hydrogen bonds · protein-protein
• H–D · 558 Ų buried · 22 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

• 4DII · X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer… · 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

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 4DII · PDBe 4DII · UniProt P00734