MolNFT v1 · #15494 · protein
Tricorn protease in complex with Z-phe-diketo-arg-glu-phe
1N6F: “Tricorn protease in complex with Z-phe-diketo-arg-glu-phe”. X-ray diffraction, 1 ligand (DKT), 20 pockets (best druggability 0.86). MolNFT v1 #15494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1N6F
- Type
- protein
- Length
- 6,138 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tricorn protease
- EC
- 3.4.21.-
- UniProt
- P96086
- Ligands
- DKT
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Tricorn protease (EC 3.4.21.-) | protein | 1023 | 15% helix, 39% strand | P96086 |
Ligands and binding sites
- DKT · 4-[2-(3-benzyloxycarbonylamino-4-cyclohexyl-1-hydroxy-2-oxo-butylamino)-5-guanidino-pentanoylamino]-4-(1-carboxy-2-cyclohexyl-ethylcarbamoyl)-butyric acid · ligand · 6 copies · chains A, B, C, D, E, F
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 | 770 | 0.86 | 0.89 | 89 | empty |
| 2 | 582 | 0.86 | 0.91 | 77 | empty |
| 3 | 608 | 0.85 | 0.90 | 78 | empty |
| 4 | 616 | 0.85 | 0.90 | 78 | empty |
| 5 | 1007 | 0.85 | 0.86 | 91 | DKT |
Interfaces
12 interfaces between chains.
- A–B · 6414 Ų buried · 133 hydrogen bonds · protein-protein
- C–D · 6414 Ų buried · 141 hydrogen bonds · protein-protein
- E–F · 6407 Ų buried · 142 hydrogen bonds · protein-protein
- C–F · 1900 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1891 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
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 1N6F · PDBe 1N6F · UniProt P96086
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