Research workbench
The membrane-embedded vo domain of V/A-ATPase from thermus thermophilus
Analyse The membrane-embedded vo domain of V/A-ATPase from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LY9
- Type
- protein
- Length
- 1,894 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase subunit I; V-type ATP synthase, subunit K; V-type ATP synthase…
- UniProt
- Q5SIT6, Q5SIT7, P74902, Q5SIT5, P74901
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 8 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | V-type ATP synthase subunit I | protein | 649 | 62% helix, 4% strand | Q5SIT6 |
| O, T, U, X, Y, Z | V-type ATP synthase, subunit K | protein | 73 | 90% helix, 0% strand | Q5SIT7 |
| P | V-type ATP synthase, subunit K | protein | 76 | 88% helix, 0% strand | Q5SIT7 |
| Q, R, S, W | V-type ATP synthase, subunit K | protein | 74 | 86% helix, 0% strand | Q5SIT7 |
| V | V-type ATP synthase, subunit K | protein | 72 | 86% helix, 0% strand | Q5SIT7 |
| M | V-type ATP synthase subunit C | protein | 321 | 67% helix, 0% strand | P74902 |
| K | V-type ATP synthase, subunit (vapc-therm) | protein | 22 | 91% helix, 0% strand | Q5SIT5 |
| L | V-type ATP synthase subunit E | protein | 20 | 90% helix, 0% strand | P74901 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.85 | 0.89 | 90 | empty |
| 2 | 175 | 0.81 | 0.96 | 32 | empty |
| 3 | 70 | 0.74 | 0.98 | 19 | empty |
| 4 | 987 | 0.74 | 0.76 | 54 | empty |
| 5 | 79 | 0.72 | 0.96 | 15 | empty |
Interfaces
37 interfaces between chains.
- O–P · 1651 Ų buried · 8 hydrogen bonds · protein-protein
- U–V · 1591 Ų buried · 5 hydrogen bonds · protein-protein
- T–U · 1588 Ų buried · 4 hydrogen bonds · protein-protein
- O–Z · 1583 Ų buried · 10 hydrogen bonds · protein-protein
- Q–R · 1575 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6LY9 · The membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus · 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 Q5SIT6
- Every structure of UniProt Q5SIT7
- Every structure of UniProt P74902
- Every structure of UniProt Q5SIT5
- Every structure of UniProt P74901
- Elsewhere: RCSB PDB 6LY9 · PDBe 6LY9 · UniProt Q5SIT6 · UniProt Q5SIT7 · UniProt P74902 · UniProt Q5SIT5 · UniProt P74901
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