Research workbench
Mouse retromer sub-structure: VPS35/VPS35 flat dimer
Analyse Mouse retromer sub-structure: VPS35/VPS35 flat dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VAB
- Type
- protein
- Length
- 938 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 29; Vacuolar protein sorting-associated…
- UniProt
- Q9QZ88, Q9EQH3
- Pockets
- 18 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Vacuolar protein sorting-associated protein 29 | protein | 182 | 13% helix, 32% strand | Q9QZ88 |
| B | Vacuolar protein sorting-associated protein 35 | protein | 276 | 72% helix, 0% strand | Q9EQH3 |
| D | Vacuolar protein sorting-associated protein 35 | protein | 298 | 67% helix, 1% strand | Q9EQH3 |
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.72 | 0.77 | 73 | empty |
| 2 | 774 | 0.71 | 0.78 | 75 | empty |
| 3 | 381 | 0.68 | 0.81 | 70 | empty |
| 4 | 587 | 0.68 | 0.78 | 68 | empty |
| 5 | 574 | 0.68 | 0.78 | 66 | empty |
Interfaces
3 interfaces between chains.
- C–D · 277 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 239 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VAB · Mouse retromer sub-structure: VPS35/VPS35 flat dimer · the same entry in another collection · chain A against A, TM-score 1.00
- Q9QZ88 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 29… · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q9EQH3 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 35… · a predicted model of the same protein · chain D against A, TM-score 0.92
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 Q9QZ88
- Every structure of UniProt Q9EQH3
- Elsewhere: RCSB PDB 6VAB · PDBe 6VAB · UniProt Q9QZ88 · UniProt Q9EQH3
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