Research workbench
Structure of the SNX17 atypical ferm domain bound to the npxy motif of P-selectin
Analyse Structure of the SNX17 atypical ferm domain bound to the npxy motif of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GXB
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorting nexin-17; P-selectin
- UniProt
- Q15036, Q01102
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorting nexin-17 | protein | 263 | 34% helix, 34% strand | Q15036 |
| B | P-selectin | protein | 15 | 0% helix, 27% strand | Q01102 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.41 | 0.74 | 29 | empty |
| 2 | 76 | 0.36 | 0.76 | 13 | empty |
| 3 | 105 | 0.35 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 683 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4GXB · Structure of the SNX17 atypical FERM domain bound to the NPxY motif of P-selectin · the same entry in another collection · chain A against A, 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
- Q01102 · AlphaFold monomer V2.0 prediction for P-selectin (Q01102) · a predicted model of the same protein · chain B against A, TM-score 0.29
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 Q01102
- Elsewhere: RCSB PDB 4GXB · PDBe 4GXB · UniProt Q15036 · UniProt Q01102
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