Research workbench
Thermus thermophilus V/A-ATPase, conformation 1
Analyse Thermus thermophilus V/A-ATPase, conformation 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GAR
- Type
- protein
- Length
- 5,878 residues
- Chains
- 26
- 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, Q72J73, P74901, Q72J66, Q72J74, P74903, P74902, H9ZQR4, P74900
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 10 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 577 | 31% helix, 20% strand | Q56403 |
| B | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 576 | 32% helix, 19% strand | Q56403 |
| D, E, F | V-type ATP synthase beta chain | protein | 457 | 29% helix, 16% strand | Q72J73 |
| G, H | V-type ATP synthase subunit E | protein | 184 | 63% helix, 3% strand | P74901 |
| I, J | V-type ATPase subunit G | protein | 100 | 85% helix, 0% strand | Q72J66 |
| K | V-type ATP synthase subunit D | protein | 210 | 67% helix, 3% strand | Q72J74 |
| L | V-type ATP synthase subunit F | protein | 100 | 35% helix, 6% strand | P74903 |
| M | V-type ATP synthase subunit C | protein | 320 | 68% helix, 0% strand | P74902 |
| N | ARCHAEAL/VACUOLAR-type H+-ATPase subunit I | protein | 619 | 61% helix, 6% strand | H9ZQR4 |
| O, P, Q, R, S, T, U, V, W, X, Y, Z | Vacuolar type ATP synthase subunit | protein | 80 | 79% helix, 0% strand | P74900 |
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 | 854 | 0.80 | 0.84 | 130 | empty |
| 2 | 971 | 0.76 | 0.79 | 157 | empty |
| 3 | 614 | 0.75 | 0.83 | 123 | empty |
| 4 | 879 | 0.74 | 0.79 | 139 | empty |
| 5 | 332 | 0.74 | 0.87 | 64 | empty |
Interfaces
47 interfaces between chains.
- C–F · 746 Ų buried · 10 hydrogen bonds · protein-protein
- U–V · 574 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 550 Ų buried · 6 hydrogen bonds · protein-protein
- Q–R · 546 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 515 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5GAR · Thermus thermophilus V/A-ATPase, conformation 1 · the same entry in another collection · chain K against K, 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 Q72J73
- Every structure of UniProt P74901
- Every structure of UniProt Q72J66
- Every structure of UniProt Q72J74
- Every structure of UniProt P74903
- Every structure of UniProt P74902
- Every structure of UniProt H9ZQR4
- Every structure of UniProt P74900
- Elsewhere: RCSB PDB 5GAR · PDBe 5GAR · UniProt Q56403 · UniProt Q72J73 · UniProt P74901 · UniProt Q72J66 · UniProt Q72J74 · UniProt P74903 · UniProt P74902 · UniProt H9ZQR4 · UniProt P74900
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