Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N- (5-chloro-2-(HYDROXYMETHYL)BENZY L)PYRROLIDINE-2-carboxamide

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).

Ligands and binding sites

• 6TH · (2~{S})-1-[(2~{R})-2-azanyl-3-cyclohexyl-propanoyl]-~{N}-[[5-chloranyl-2-(hydroxymethyl) phenyl]methyl]pyrrolidine-2-carboxamide · ligand · chains H
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
• NA · Sodium ion · metal · 2 copies · chains H
• PO4 · Phosphate ion · ion · chains H
• GOL · Glycerol · additive · 3 copies · chains H
• DMS · Dimethyl sulfoxide · additive · chains H
• EDO · 1,2-ethanediol · additive · chains H

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

2 interfaces between chains.

• L–H · 1129 Ų buried · 26 hydrogen bonds · protein-protein
• H–I · 626 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 5LCE · Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(5-chloro-2-(hydroxym… · the same entry in another collection · chain L against L, TM-score 1.00

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 5LCE · PDBe 5LCE · UniProt P00734 · UniProt P09945