X-ray structure of the complex between human alpha thrombin and NU172, a DUPLEX/QUADRUPLEX 26-mer DNA aptamer, in the presence of potassium ions.

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 30% 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 · 3 copies · chains H
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• GAL · beta-D-galactopyranose · sugar
• SIA · N-acetyl-alpha-neuraminic acid · sugar
• NA · Sodium ion · metal · chains H
• K · Potassium ion · metal · chains E
• GOL · Glycerol · additive · chains H, E

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

Pockets

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

Interfaces

2 interfaces between chains.

• L–H · 1408 Ų buried · 36 hydrogen bonds · protein-protein
• H–E · 607 Ų buried · 15 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

• 6EVV · X-ray structure of the complex between human alpha thrombin and NU172, a… · the same entry in another collection · chain E against E, 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

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 6EVV · PDBe 6EVV · UniProt P00734