Research workbench
Crystal structure of alix in complex with the sivagmtan-1 aydparkll late domain
Analyse Crystal structure of alix in complex with the sivagmtan-1 aydparkll late domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XS8
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 6-interacting protein; Sivagmtan-1 gag P6
- UniProt
- Q8WUM4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death 6-interacting protein | protein | 697 | 69% helix, 1% strand | Q8WUM4 |
| B | Sivagmtan-1 gag P6 | protein | 9 | 44% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.71 | 0.90 | 26 | empty |
| 2 | 401 | 0.58 | 0.75 | 43 | empty |
| 3 | 236 | 0.55 | 0.77 | 22 | empty |
| 4 | 79 | 0.34 | 0.75 | 14 | empty |
| 5 | 78 | 0.31 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2XS8 · Crystal Structure of ALIX in complex with the SIVagmTan-1 AYDPARKLL Late Domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WUM4 · AlphaFold monomer V2.0 prediction for programmed cell death 6-interacting protein (Q8WUM4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8WUM4
- Elsewhere: RCSB PDB 2XS8 · PDBe 2XS8 · UniProt Q8WUM4
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