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Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (semet labeled)
Analyse Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (semet… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F0M
- Type
- protein
- Length
- 912 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
- SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 35 | protein | 458 | 73% helix, 0% strand | Q96QK1 |
| B | Vacuolar protein sorting-associated protein 26A | protein | 293 | 3% helix, 60% strand | O75436 |
| C | Sorting nexin-3 | protein | 150 | 37% helix, 19% strand | O60493 |
| D | Natural resistance-associated macrophage protein 2 | protein | 11 | 0% helix, 45% strand | P49281 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.69 | 0.79 | 62 | EDO |
| 2 | 209 | 0.54 | 0.78 | 29 | empty |
| 3 | 199 | 0.52 | 0.78 | 25 | empty |
| 4 | 122 | 0.48 | 0.79 | 25 | SO4, EDO |
| 5 | 118 | 0.41 | 0.75 | 24 | GOL |
Interfaces
5 interfaces between chains.
- B–C · 1077 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 904 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 864 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 603 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 119 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5F0M · Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (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 0.43
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 5F0M · PDBe 5F0M · UniProt Q96QK1 · UniProt O75436 · UniProt O60493 · UniProt P49281
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