Research workbench
Crystal structure of the peripheral stalk of thermus thermophilus H+- ATPASE/SYNTHASE
Analyse Crystal structure of the peripheral stalk of thermus thermophilus H+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K5B
- Type
- protein
- Length
- 569 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase, subunit (vapc-therm); V-type ATP synthase subunit E
- UniProt
- Q5SIT5, P74901
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, B | V-type ATP synthase, subunit (vapc-therm) | protein | 100 | 89% helix, 0% strand | Q5SIT5 |
| E | V-type ATP synthase subunit E | protein | 184 | 59% helix, 7% strand | P74901 |
| A | V-type ATP synthase subunit E | protein | 185 | 70% helix, 6% strand | P74901 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.74 | 0.84 | 54 | empty |
| 2 | 182 | 0.62 | 0.83 | 32 | empty |
Interfaces
3 interfaces between chains.
- G–E · 2457 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 2367 Ų buried · 16 hydrogen bonds · protein-protein
- G–B · 220 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3K5B · Crystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase · the same entry in another collection · chain G against G, TM-score 1.00
- P74901 · AlphaFold monomer V2.0 prediction for V-type ATP synthase subunit E (P74901) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q5SIT5
- Every structure of UniProt P74901
- Elsewhere: RCSB PDB 3K5B · PDBe 3K5B · UniProt Q5SIT5 · UniProt P74901
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