MolNFT v1 · #15492 · protein
Tricorn protease in complex with tetrapeptide chloromethyl ketone derivative
1N6D: “Tricorn protease in complex with tetrapeptide chloromethyl ketone derivative”. X-ray diffraction, 2 ligands (D10, CHM), 20 pockets (best druggability 0.87). MolNFT v1 #15492 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1N6D
- Type
- protein
- Length
- 6,162 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tricorn protease; Rvrk
- EC
- 3.4.21.-
- UniProt
- P96086
- Ligands
- D10, CHM
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 40% 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, 40% strand | P96086 |
| G, H, I, J, K, L | Rvrk | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · 6 copies · chains A, G, B, H, C, I, D, J, E, K, F, L
- CHM · 1,3-dichloro-propan-2-one · ion · 6 copies · chains A, G, B, H, C, I, D, J, E, K, F, 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 | 1060 | 0.87 | 0.88 | 100 | empty |
| 2 | 571 | 0.86 | 0.91 | 77 | empty |
| 3 | 610 | 0.85 | 0.90 | 79 | empty |
| 4 | 608 | 0.85 | 0.90 | 80 | empty |
| 5 | 611 | 0.85 | 0.90 | 76 | empty |
Interfaces
24 interfaces between chains.
- A–B · 6467 Ų buried · 129 hydrogen bonds · protein-protein
- C–D · 6435 Ų buried · 134 hydrogen bonds · protein-protein
- E–F · 6409 Ų buried · 126 hydrogen bonds · protein-protein
- C–F · 1831 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1803 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 1N6D · Tricorn protease in complex with tetrapeptide chloromethyl ketone derivative · 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 P96086
- Elsewhere: RCSB PDB 1N6D · PDBe 1N6D · UniProt P96086
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