Research workbench
VPS35/VPS29 arch of metazoan membrane-assembled RETROMER:SNX3 complex modelled with human proteins
Analyse VPS35/VPS29 arch of metazoan membrane-assembled RETROMER:SNX3 complex modelled… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BLN
- Type
- protein
- Length
- 1,902 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
- Q9UBQ0, Q96QK1
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Vacuolar protein sorting-associated protein 29 | protein | 182 | 15% helix, 33% strand | Q9UBQ0 |
| A, C | Vacuolar protein sorting-associated protein 35 | protein | 769 | 72% helix, 1% strand | Q96QK1 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.87 | 0.87 | 140 | empty |
| 2 | 1176 | 0.84 | 0.84 | 135 | empty |
| 3 | 877 | 0.81 | 0.83 | 103 | empty |
| 4 | 247 | 0.80 | 0.92 | 47 | empty |
| 5 | 185 | 0.80 | 0.94 | 42 | empty |
Interfaces
3 interfaces between chains.
- D–C · 1053 Ų buried · 4 hydrogen bonds · protein-protein
- B–A · 1037 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7BLN · VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex modelled with human… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9UBQ0 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 29… · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.92
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 Q9UBQ0
- Every structure of UniProt Q96QK1
- Elsewhere: RCSB PDB 7BLN · PDBe 7BLN · UniProt Q9UBQ0 · UniProt Q96QK1
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