MolNFT v1 · #106630 · protein
Structure of the SNX17 ferm domain bound to the second npxf motif of KRIT1
4TKN · Sorting nexin-17: “Structure of the SNX17 ferm domain bound to the second npxf motif of KRIT1”. X-ray diffraction, 16 pockets (best druggability 0.70). MolNFT v1 #106630 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TKN
- Type
- protein
- Length
- 788 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorting nexin-17; Krev interaction trapped protein 1
- UniProt
- Q15036, O00522
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorting nexin-17 | protein | 256 | 35% helix, 34% strand | Q15036 |
| B | Sorting nexin-17 | protein | 247 | 36% helix, 33% strand | Q15036 |
| C | Sorting nexin-17 | protein | 257 | 35% helix, 34% strand | Q15036 |
| D | Krev interaction trapped protein 1 | protein | 10 | 0% helix, 20% strand | O00522 |
| E, F | Krev interaction trapped protein 1 | protein | 9 | 0% helix, 22% strand | O00522 |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.70 | 0.97 | 20 | empty |
| 2 | 50 | 0.65 | 0.95 | 17 | empty |
| 3 | 465 | 0.64 | 0.77 | 46 | empty |
| 4 | 107 | 0.55 | 0.84 | 20 | empty |
| 5 | 185 | 0.53 | 0.79 | 38 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1152 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 557 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 556 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 521 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 174 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4TKN · Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 · the same entry in another collection · chain F against F, TM-score 1.00
- Q15036 · AlphaFold monomer V2.0 prediction for sorting nexin-17 (Q15036) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O00522 · AlphaFold monomer V2.0 prediction for krev interaction trapped protein 1 (O00522) · a predicted model of the same protein · chain E against A, TM-score 0.43
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 Q15036
- Every structure of UniProt O00522
- Elsewhere: RCSB PDB 4TKN · PDBe 4TKN · UniProt Q15036 · UniProt O00522
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.