Research workbench
Crystal structure of subunit VPS25 of the endosomal trafficking complex escrt-II
Analyse Crystal structure of subunit VPS25 of the endosomal trafficking complex escrt-II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XB4
- Type
- protein
- Length
- 693 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical 23.6 kda protein in YUH1-URA8 intergenic region
- UniProt
- P47142
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical 23.6 kda protein in YUH1-URA8 intergenic region | protein | 180 | 40% helix, 17% strand | P47142 |
| B | Hypothetical 23.6 kda protein in YUH1-URA8 intergenic region | protein | 179 | 41% helix, 15% strand | P47142 |
| C | Hypothetical 23.6 kda protein in YUH1-URA8 intergenic region | protein | 180 | 38% helix, 17% strand | P47142 |
| D | Hypothetical 23.6 kda protein in YUH1-URA8 intergenic region | protein | 154 | 34% helix, 10% strand | P47142 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.72 | 0.75 | 88 | empty |
| 2 | 636 | 0.71 | 0.79 | 65 | empty |
| 3 | 88 | 0.39 | 0.77 | 21 | empty |
| 4 | 94 | 0.38 | 0.76 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 620 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 592 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 544 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1XB4 · Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II · the same entry in another collection · chain D against D, TM-score 1.00
- P47142 · AlphaFold monomer V2.0 prediction for vacuolar protein-sorting- associated protein 25… · 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 P47142
- Elsewhere: RCSB PDB 1XB4 · PDBe 1XB4 · UniProt P47142
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