Research workbench
Crystal structure of VPS4-VPS20 complex from S.CEREVISIAE
Analyse Crystal structure of VPS4-VPS20 complex from S.CEREVISIAE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FVL
- Type
- protein
- Length
- 211 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated…
- UniProt
- P52917, Q04272
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 4 | protein | 83 | 82% helix, 0% strand | P52917 |
| B | Vacuolar protein sorting-associated protein 4 | protein | 78 | 88% helix, 0% strand | P52917 |
| C | Vacuolar protein sorting-associated protein 20 | protein | 24 | 42% helix, 0% strand | Q04272 |
| D | Vacuolar protein sorting-associated protein 20 | protein | 26 | 38% helix, 0% strand | Q04272 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.56 | 0.80 | 28 | empty |
| 2 | 50 | 0.32 | 0.78 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–D · 970 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 860 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 351 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 294 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 163 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5FVL · Crystal structure of Vps4-Vps20 complex from S.cerevisiae · the same entry in another collection · chain D against D, TM-score 1.00
- P52917 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 4… · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q04272 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 20… · a predicted model of the same protein · chain C against A, TM-score 0.57
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 P52917
- Every structure of UniProt Q04272
- Elsewhere: RCSB PDB 5FVL · PDBe 5FVL · UniProt P52917 · UniProt Q04272
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