Research workbench
VPS26 dimer region of metazoan membrane-assembled RETROMER:SNX3 complex modelled with human proteins
Analyse VPS26 dimer region of metazoan membrane-assembled RETROMER:SNX3 complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BLO
- Type
- protein
- Length
- 1,622 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 26A; Sorting nexin-3; C-term (residues…
- UniProt
- O75436, Q78ZM0, Q96QK1
- Ligands
- PIB
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, F | Vacuolar protein sorting-associated protein 26A | protein | 294 | 3% helix, 62% strand | O75436 |
| L, G | Sorting nexin-3 | protein | 155 | 41% helix, 18% strand | Q78ZM0 |
| N, H | C-term (residues 493-54) of wls (fitted sequence corresponds to HDMT1-II) | protein | 10 | 0% helix, 50% strand | — |
| A, C | Vacuolar protein sorting-associated protein 35 | protein | 352 | 76% helix, 0% strand | Q96QK1 |
Ligands and binding sites
- PIB · 2-(butanoyloxy)-1-{[(hydroxy{[2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl) oxy]methyl}ethyl butanoate · ligand · 2 copies · chains L, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.82 | 0.95 | 34 | empty |
| 2 | 293 | 0.80 | 0.91 | 54 | empty |
| 3 | 141 | 0.80 | 0.96 | 30 | empty |
| 4 | 1019 | 0.79 | 0.80 | 117 | empty |
| 5 | 221 | 0.79 | 0.92 | 44 | empty |
Interfaces
11 interfaces between chains.
- F–G · 1107 Ų buried · 6 hydrogen bonds · protein-protein
- J–L · 1106 Ų buried · 6 hydrogen bonds · protein-protein
- G–C · 868 Ų buried · 16 hydrogen bonds · protein-protein
- F–C · 867 Ų buried · 31 hydrogen bonds · protein-protein
- L–A · 814 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7BLO · VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with… · the same entry in another collection · chain C against C, 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 J 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 0.94
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 O75436
- Every structure of UniProt Q78ZM0
- Every structure of UniProt Q96QK1
- Elsewhere: RCSB PDB 7BLO · PDBe 7BLO · UniProt O75436 · UniProt Q78ZM0 · UniProt Q96QK1
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