Research workbench
V/A-type ATPASE/SYNTHASE from thermus thermophilus, peripheral domain, rotational state 1
Analyse V/A-type ATPASE/SYNTHASE from thermus thermophilus, peripheral domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y5Y
- Type
- protein
- Length
- 4,164 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase alpha chain; V-type ATP synthase beta chain; V-type ATP synthase…
- EC
- 3.6.3.14
- UniProt
- Q56403, Q56404, O87880, P74903, Q5SIT5, P74901, P74902
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 7 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 577 | 31% helix, 18% strand | Q56403 |
| D, E, F | V-type ATP synthase beta chain | protein | 459 | 32% helix, 17% strand | Q56404 |
| G | V-type ATP synthase subunit D | protein | 210 | 68% helix, 4% strand | O87880 |
| H | V-type ATP synthase subunit F | protein | 100 | 37% helix, 4% strand | P74903 |
| I, K | V-type ATP synthase, subunit (vapc-therm) | protein | 61 | 90% helix, 0% strand | Q5SIT5 |
| J, L | V-type ATP synthase subunit E | protein | 152 | 63% helix, 7% strand | P74901 |
| M | V-type ATP synthase subunit C | protein | 320 | 69% helix, 0% strand | P74902 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 959 | 0.90 | 0.92 | 147 | empty |
| 2 | 833 | 0.87 | 0.89 | 68 | empty |
| 3 | 893 | 0.86 | 0.88 | 93 | empty |
| 4 | 798 | 0.84 | 0.87 | 100 | empty |
| 5 | 608 | 0.84 | 0.89 | 80 | ADP |
Interfaces
22 interfaces between chains.
- A–F · 3437 Ų buried · 33 hydrogen bonds · protein-protein
- C–E · 3040 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 2551 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 2257 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 1754 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5Y5Y · V/A-type ATPase/synthase from Thermus thermophilus, peripheral domain, rotational state 1 · the same entry in another collection · chain M against M, 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 Q56403
- Every structure of UniProt Q56404
- Every structure of UniProt O87880
- Every structure of UniProt P74903
- Every structure of UniProt Q5SIT5
- Every structure of UniProt P74901
- Every structure of UniProt P74902
- Elsewhere: RCSB PDB 5Y5Y · PDBe 5Y5Y · UniProt Q56403 · UniProt Q56404 · UniProt O87880 · UniProt P74903 · UniProt Q5SIT5 · UniProt P74901 · UniProt P74902
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