Research workbench
Yeast vo motor in complex with 1 vopq molecule
Analyse Yeast vo motor in complex with 1 vopq molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PE4
- Type
- protein
- Length
- 3,295 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase subunit a, vacuolar isoform; V0 assembly protein 1; V-type proton…
- UniProt
- P32563, P53262, P32366, Q3E7B6, P0C5R9, P23968, P32842, P25515, A0A0L7YPA6
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 10 distinct chains · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type proton ATPase subunit a, vacuolar isoform | protein | 758 | 53% helix, 6% strand | P32563 |
| B | V0 assembly protein 1 | protein | 53 | 49% helix, 0% strand | P53262 |
| D | V-type proton ATPase subunit D | protein | 345 | 59% helix, 1% strand | P32366 |
| E | V-type proton ATPase subunit E | protein | 69 | 59% helix, 0% strand | Q3E7B6 |
| F | Uncharacterized protein YPR170W-B | protein | 74 | 54% helix, 0% strand | P0C5R9 |
| G | V-type proton ATPase subunit C'' | protein | 199 | 80% helix, 0% strand | P23968 |
| H | V-type proton ATPase subunit C' | protein | 158 | 76% helix, 0% strand | P32842 |
| I, J, K, L, M, N | V-type proton ATPase subunit C | protein | 159 | 74% helix, 0% strand | P25515 |
| O, P | V-type proton ATPase subunit C | protein | 158 | 75% helix, 0% strand | P25515 |
| Q | Cation transporter | protein | 369 | 39% helix, 4% strand | A0A0L7YPA6 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.82 | 0.83 | 71 | empty |
| 2 | 948 | 0.78 | 0.80 | 66 | empty |
| 3 | 697 | 0.76 | 0.81 | 56 | empty |
| 4 | 646 | 0.74 | 0.81 | 59 | empty |
| 5 | 884 | 0.74 | 0.78 | 66 | empty |
Interfaces
40 interfaces between chains.
- A–E · 2227 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 1899 Ų buried · 5 hydrogen bonds · protein-protein
- L–M · 1895 Ų buried · 5 hydrogen bonds · protein-protein
- M–N · 1868 Ų buried · 5 hydrogen bonds · protein-protein
- J–K · 1859 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6PE4 · Yeast Vo motor in complex with 1 VopQ molecule · the same entry in another collection · chain L against L, TM-score 1.00
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 P32563
- Every structure of UniProt P53262
- Every structure of UniProt P32366
- Every structure of UniProt Q3E7B6
- Every structure of UniProt P0C5R9
- Every structure of UniProt P23968
- Every structure of UniProt P32842
- Every structure of UniProt P25515
- Every structure of UniProt A0A0L7YPA6
- Elsewhere: RCSB PDB 6PE4 · PDBe 6PE4 · UniProt P32563 · UniProt P53262 · UniProt P32366 · UniProt Q3E7B6 · UniProt P0C5R9 · UniProt P23968 · UniProt P32842 · UniProt P25515 · UniProt A0A0L7YPA6
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