MolNFT v1 · #15493 · protein
Tricorn protease in complex with a tridecapeptide chloromethyl ketone derivative
1N6E: “Tricorn protease in complex with a tridecapeptide chloromethyl ketone derivative”. X-ray diffraction, 1 ligand (CHM), 20 pockets (best druggability 0.86). MolNFT v1 #15493 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1N6E
- Type
- protein
- Length
- 6,204 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tricorn protease; Dqtqkaaaeltff
- EC
- 3.4.21.-
- UniProt
- P96086
- Ligands
- CHM
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Tricorn protease (EC 3.4.21.-) | protein | 1023 | 15% helix, 40% strand | P96086 |
| B, D, F, H, J, L | Dqtqkaaaeltff | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- CHM · 1,3-dichloro-propan-2-one · ion · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.86 | 0.94 | 59 | empty |
| 2 | 457 | 0.86 | 0.93 | 60 | empty |
| 3 | 1005 | 0.85 | 0.86 | 76 | empty |
| 4 | 1048 | 0.85 | 0.86 | 89 | empty |
| 5 | 959 | 0.85 | 0.86 | 73 | empty |
Interfaces
24 interfaces between chains.
- E–G · 6469 Ų buried · 134 hydrogen bonds · protein-protein
- A–C · 6449 Ų buried · 129 hydrogen bonds · protein-protein
- I–K · 6446 Ų buried · 137 hydrogen bonds · protein-protein
- E–K · 1953 Ų buried · 27 hydrogen bonds · protein-protein
- C–I · 1938 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- P96086 · AlphaFold monomer V2.0 prediction for tricorn protease (P96086) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P96086
- Elsewhere: RCSB PDB 1N6E · PDBe 1N6E · UniProt P96086
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