MolNFT v1 · #118396 · protein
Structure of retromer VPS26-VPS35 subunits bound to SNX3
5F0J · Vacuolar protein sorting-associated protein 35: “Structure of retromer VPS26-VPS35 subunits bound to SNX3”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.69). MolNFT v1 #118396 on GenesisL1: 3D structure, binding…
- PDB
- 5F0J
- Type
- protein
- Length
- 919 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 35; Vacuolar protein sorting-associated…
- UniProt
- Q96QK1, O75436, O60493
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 35 | protein | 458 | 74% helix, 0% strand | Q96QK1 |
| B | Vacuolar protein sorting-associated protein 26A | protein | 306 | 3% helix, 60% strand | O75436 |
| C | Sorting nexin-3 | protein | 155 | 37% helix, 17% strand | O60493 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.69 | 0.79 | 57 | empty |
| 2 | 238 | 0.55 | 0.77 | 30 | empty |
| 3 | 200 | 0.53 | 0.78 | 29 | empty |
| 4 | 134 | 0.51 | 0.80 | 26 | SO4 |
| 5 | 118 | 0.40 | 0.75 | 20 | EDO |
Interfaces
3 interfaces between chains.
- B–C · 1206 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 889 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 863 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5F0J · Structure of retromer VPS26-VPS35 subunits bound to SNX3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q96QK1 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 35… · a predicted model of the same protein · chain A against A, TM-score 0.96
- O75436 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 26A… · a predicted model of the same protein · chain B against A, TM-score 0.93
- O60493 · AlphaFold monomer V2.0 prediction for sorting nexin-3 (O60493) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 Q96QK1
- Every structure of UniProt O75436
- Every structure of UniProt O60493
- Elsewhere: RCSB PDB 5F0J · PDBe 5F0J · UniProt Q96QK1 · UniProt O75436 · UniProt O60493
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