MolNFT v1 · #118402 · protein
Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (semet labeled)
5F0P · Vacuolar protein sorting-associated protein 35: “Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (semet labeled)”. X-ray diffraction, 2 ligands (ZN, SO4), 9 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 5F0P
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- 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, P49281
- Ligands
- ZN, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 45% 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 | 293 | 3% helix, 61% strand | O75436 |
| C | Sorting nexin-3 | protein | 147 | 40% helix, 19% strand | O60493 |
| D | Natural resistance-associated macrophage protein 2 | protein | 15 | 0% helix, 33% strand | P49281 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C
- GOL · Glycerol · additive · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.69 | 0.79 | 55 | empty |
| 2 | 220 | 0.53 | 0.77 | 28 | empty |
| 3 | 193 | 0.51 | 0.77 | 24 | empty |
| 4 | 128 | 0.48 | 0.79 | 25 | SO4 |
| 5 | 122 | 0.41 | 0.75 | 25 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1067 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 908 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 863 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 708 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 131 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 5F0P · Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.97
- 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
- O60493 · AlphaFold monomer V2.0 prediction for sorting nexin-3 (O60493) · a predicted model of the same protein · chain C against A, TM-score 0.88
- P49281 · AlphaFold monomer V2.0 prediction for natural resistance-associated macrophage protein 2… · a predicted model of the same protein · chain D against A, TM-score 0.28
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
- Every structure of UniProt P49281
- Elsewhere: RCSB PDB 5F0P · PDBe 5F0P · UniProt Q96QK1 · UniProt O75436 · UniProt O60493 · UniProt P49281
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