Research workbench
Crystal structure of RIDL(1-200) complexed with VPS29
Analyse Crystal structure of RIDL(1-200) complexed with VPS29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WYH
- Type
- protein
- Length
- 764 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 29; Interaptin
- UniProt
- Q9UBQ0, G8UZ99
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Vacuolar protein sorting-associated protein 29 | protein | 185 | 15% helix, 38% strand | Q9UBQ0 |
| B | Interaptin | protein | 196 | 54% helix, 2% strand | G8UZ99 |
| D | Interaptin | protein | 198 | 53% helix, 2% strand | G8UZ99 |
Ligands and binding sites
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.48 | 0.76 | 29 | empty |
| 2 | 51 | 0.48 | 0.86 | 12 | empty |
| 3 | 53 | 0.41 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 447 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 439 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 351 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5WYH · Crystal structure of RidL(1-200) complexed with VPS29 · 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
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 G8UZ99
- Elsewhere: RCSB PDB 5WYH · PDBe 5WYH · UniProt Q9UBQ0 · UniProt G8UZ99
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