Research workbench
Functional architecture of the retromer cargo-recognition complex
Analyse Functional architecture of the retromer cargo-recognition complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R17
- Type
- protein
- Length
- 940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 29; Vacuolar protein sorting-associated…
- UniProt
- Q9UBQ0, Q96QK1
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vacuolar protein sorting-associated protein 29 | protein | 183 | 15% helix, 33% strand | Q9UBQ0 |
| C | Vacuolar protein sorting-associated protein 35 | protein | 298 | 72% helix, 1% strand | Q96QK1 |
| D | Vacuolar protein sorting-associated protein 35 | protein | 276 | 79% helix, 0% strand | Q96QK1 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.75 | 0.82 | 51 | GOL |
| 2 | 435 | 0.72 | 0.82 | 51 | empty |
| 3 | 313 | 0.57 | 0.76 | 38 | empty |
| 4 | 273 | 0.55 | 0.76 | 35 | empty |
| 5 | 312 | 0.54 | 0.75 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1718 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1680 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 514 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2R17 · Functional architecture of the retromer cargo-recognition complex · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98
- Q96QK1 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 35… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 2R17 · PDBe 2R17 · UniProt Q9UBQ0 · UniProt Q96QK1
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