Research workbench
Crystal structure of VPS4-VFA1 complex from S.CEREVISIAE at 1.66 a resolution.
Analyse Crystal structure of VPS4-VFA1 complex from S.CEREVISIAE at 1.66 a resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FVK
- Type
- protein
- Length
- 204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 4; VPS4-associated protein 1
- EC
- 3.6.4.6
- UniProt
- P52917, P40080
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vacuolar protein sorting-associated protein 4 (EC 3.6.4.6) | protein | 82 | 89% helix, 1% strand | P52917 |
| C | VPS4-associated protein 1 | protein | 21 | 33% helix, 5% strand | P40080 |
| D | VPS4-associated protein 1 | protein | 19 | 37% helix, 5% strand | P40080 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.48 | 0.81 | 20 | empty |
| 2 | 59 | 0.32 | 0.76 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–C · 931 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 878 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 304 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 139 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FVK · Crystal structure of Vps4-Vfa1 complex from S.cerevisiae at 1.66 A resolution. · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.92
- P40080 · AlphaFold monomer V2.0 prediction for VPS4-associated protein 1 (P40080) · a predicted model of the same protein · chain D against A, TM-score 0.48
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 P40080
- Elsewhere: RCSB PDB 5FVK · PDBe 5FVK · UniProt P52917 · UniProt P40080
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