MolNFT v1 · #81662 · protein
Bovine trypsin variant X(TRIPLEGLU217PHE227) in complex with small molecule inhibitor
3UY9 · Cationic trypsin: “Bovine trypsin variant X(TRIPLEGLU217PHE227) in complex with small molecule inhibitor”. X-ray diffraction, 3 ligands (BEN, CA, CL), 20 pockets (best druggability 0.85). MolNFT v1 #81662 on GenesisL1: 3D structure…
- PDB
- 3UY9
- Type
- protein
- Length
- 3,568 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cationic trypsin
- EC
- 3.4.21.4
- UniProt
- P00760
- Ligands
- BEN, CA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Cationic trypsin (EC 3.4.21.4) | protein | 223 | 9% helix, 39% strand | P00760 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 16 copies · chains A, D, B, F, C, E, G, H, I, N, J, P, K, O, L, M
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- CL · Chloride ion · ion · 3 copies · chains E, P, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.85 | 0.97 | 44 | BEN |
| 2 | 249 | 0.85 | 0.97 | 43 | BEN |
| 3 | 232 | 0.85 | 0.97 | 45 | BEN |
| 4 | 244 | 0.84 | 0.96 | 42 | BEN |
| 5 | 235 | 0.84 | 0.97 | 44 | BEN |
Interfaces
34 interfaces between chains.
- L–M · 1240 Ų buried · 28 hydrogen bonds · protein-protein
- K–O · 1231 Ų buried · 23 hydrogen bonds · protein-protein
- I–N · 1229 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1165 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 1160 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 disulfide (disulfide).
Compared structures
- 3UY9 · Bovine trypsin variant X(tripleGlu217Phe227) in complex with small molecule inhibitor · the same entry in another collection · chain I against I, 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 3UY9 · PDBe 3UY9 · UniProt P00760
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