Crystal structure of trypsin bound O-methyl benzamidine

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 35% strand (DSSP).

Ligands and binding sites

• VN1 · 4-[(1-{(1S,2S)-1-[1-(4-aminobutyl)-1H-1,2,3-triazol-4-yl]-2-methylbutyl}-1H-1,2,3-triazol-4-yl)methoxy]-3-methoxybenzene-1-carboximidamide · ligand · 4 copies · chains A, C, B, D
• CA · Calcium ion · metal · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 4 copies · chains A, C, D
• CL · Chloride ion · ion · 2 copies · chains B, D
• GOL · Glycerol · additive · chains D

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

Pockets

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

Interfaces

5 interfaces between chains.

• B–D · 858 Ų buried · 11 hydrogen bonds · protein-protein
• A–C · 853 Ų buried · 13 hydrogen bonds · protein-protein
• A–B · 412 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 321 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 301 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

• 7JWX · Crystal Structure of Trypsin Bound O-methyl Benzamidine · the same entry in another collection · chain C against C, TM-score 1.00
• 1TNH · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D against A, TM-score 1.00
• 1TNI · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D against A, TM-score 1.00
• 1TNL · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D against A, TM-score 1.00
• 1TNG · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D against A, TM-score 1.00
• 1TNJ · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D against A, TM-score 1.00
• 1TNK · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain D against A, 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 P00760
• Elsewhere: RCSB PDB 7JWX · PDBe 7JWX · UniProt P00760