Research workbench
Mouse retromer (VPS26/VPS35/VPS29) heterotrimer
Analyse Mouse retromer (VPS26/VPS35/VPS29) heterotrimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VAC
- Type
- protein
- Length
- 1,202 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 35; Vacuolar protein sorting-associated…
- UniProt
- Q9EQH3, P40336, Q9QZ88
- Pockets
- 12 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 35 | protein | 730 | 72% helix, 0% strand | Q9EQH3 |
| B | Vacuolar protein sorting-associated protein 26A | protein | 293 | 1% helix, 46% strand | P40336 |
| C | Vacuolar protein sorting-associated protein 29 | protein | 179 | 14% helix, 34% strand | Q9QZ88 |
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.83 | 0.84 | 167 | empty |
| 2 | 556 | 0.80 | 0.86 | 104 | empty |
| 3 | 1023 | 0.78 | 0.80 | 130 | empty |
| 4 | 639 | 0.74 | 0.81 | 94 | empty |
| 5 | 441 | 0.71 | 0.82 | 69 | empty |
Interfaces
2 interfaces between chains.
- A–C · 327 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VAC · Mouse retromer (VPS26/VPS35/VPS29) heterotrimer · the same entry in another collection · chain A against A, TM-score 1.00
- P40336 · 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
- Q9QZ88 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 29… · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q9EQH3 · 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 0.94
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 Q9EQH3
- Every structure of UniProt P40336
- Every structure of UniProt Q9QZ88
- Elsewhere: RCSB PDB 6VAC · PDBe 6VAC · UniProt Q9EQH3 · UniProt P40336 · UniProt Q9QZ88
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