Research workbench
Structure of the escrt-II endosomal trafficking complex
Analyse Structure of the escrt-II endosomal trafficking complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U5T
- Type
- protein
- Length
- 738 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Appears to be functionally related to SNF7; Defective in vacuolar protein sorting…
- UniProt
- Q12483, Q06696, P47142
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Appears to be functionally related to SNF7 | protein | 213 | 54% helix, 8% strand | Q12483 |
| B | Defective in vacuolar protein sorting | protein | 169 | 41% helix, 14% strand | Q06696 |
| C, D | Hypothetical 23.6 kda protein in YUH1-URA8 intergenic region | protein | 178 | 37% helix, 8% strand | P47142 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.77 | 0.83 | 63 | empty |
| 2 | 321 | 0.68 | 0.82 | 51 | empty |
| 3 | 238 | 0.52 | 0.75 | 24 | empty |
| 4 | 187 | 0.49 | 0.76 | 31 | empty |
| 5 | 74 | 0.33 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1280 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 821 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 724 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 229 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 119 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1U5T · Structure of the ESCRT-II endosomal trafficking complex · the same entry in another collection · chain C against C, 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 B against A, TM-score 0.95
- 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 0.93
- 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 Q06696
- Every structure of UniProt P47142
- Elsewhere: RCSB PDB 1U5T · PDBe 1U5T · UniProt Q12483 · UniProt Q06696 · UniProt P47142
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