Research workbench
The crystal structure of endosomal complex escrt-II (VPS22/VPS25/VPS36)
Analyse The crystal structure of endosomal complex escrt-II (VPS22/VPS25/VPS36) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W7P
- Type
- protein
- Length
- 748 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VPS22, YPL002C; VPS25, YJR102C; VPS36P, YLR417W
- UniProt
- Q12483, P47142, Q06696
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VPS22, YPL002C | protein | 213 | 60% helix, 10% strand | Q12483 |
| B, C | VPS25, YJR102C | protein | 182 | 43% helix, 14% strand | P47142 |
| D | VPS36P, YLR417W | protein | 171 | 44% helix, 14% strand | Q06696 |
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 | 652 | 0.75 | 0.81 | 57 | empty |
| 2 | 195 | 0.71 | 0.88 | 33 | empty |
| 3 | 57 | 0.55 | 0.88 | 19 | empty |
| 4 | 181 | 0.53 | 0.79 | 27 | empty |
| 5 | 79 | 0.53 | 0.84 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1290 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 836 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 780 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1W7P · The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36) · the same entry in another collection · chain A against A, TM-score 1.00
- Q06696 · AlphaFold monomer V2.0 prediction for vacuolar protein-sorting- associated protein 36… · a predicted model of the same protein · chain D against A, TM-score 0.94
- P47142 · AlphaFold monomer V2.0 prediction for vacuolar protein-sorting- associated protein 25… · a predicted model of the same protein · chain B against A, TM-score 0.91
- Q12483 · AlphaFold monomer V2.0 prediction for vacuolar-sorting protein SNF8 (Q12483) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 Q12483
- Every structure of UniProt P47142
- Every structure of UniProt Q06696
- Elsewhere: RCSB PDB 1W7P · PDBe 1W7P · UniProt Q12483 · UniProt P47142 · UniProt Q06696
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