Research workbench
Structure of the SNX17 ferm domain bound to the second npxf motif of KRIT1
Analyse Structure of the SNX17 ferm domain bound to the second npxf motif of KRIT1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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