Research workbench
Thermus thermophilus V/A-type ATPASE/SYNTHASE, rotational state 1
Analyse Thermus thermophilus V/A-type ATPASE/SYNTHASE, rotational state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QUM
- Type
- protein
- Length
- 5,874 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
- 7.1.2.2
- UniProt
- Q56403, Q56404, O87880, P74903, Q5SIT5, P74901, P74902, Q5SIT6, Q5SIT7
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 15 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | V-type ATP synthase alpha chain (EC 7.1.2.2) | protein | 578 | 32% helix, 22% strand | Q56403 |
| D | V-type ATP synthase beta chain | protein | 470 | 33% helix, 20% strand | Q56404 |
| E | V-type ATP synthase beta chain | protein | 469 | 32% helix, 20% strand | Q56404 |
| F | V-type ATP synthase beta chain | protein | 470 | 31% helix, 23% strand | Q56404 |
| G | V-type ATP synthase subunit D | protein | 207 | 76% helix, 7% strand | O87880 |
| H | V-type ATP synthase subunit F | protein | 104 | 39% helix, 13% strand | P74903 |
| I | V-type ATP synthase, subunit (vapc-therm) | protein | 103 | 94% helix, 0% strand | Q5SIT5 |
| J | V-type ATP synthase subunit E | protein | 186 | 73% helix, 7% strand | P74901 |
| K | V-type ATP synthase, subunit (vapc-therm) | protein | 99 | 95% helix, 0% strand | Q5SIT5 |
| L | V-type ATP synthase subunit E | protein | 187 | 70% helix, 8% strand | P74901 |
| M | V-type ATP synthase subunit C | protein | 320 | 60% helix, 0% strand | P74902 |
| N | V-type ATP synthase subunit I | protein | 649 | 58% helix, 7% strand | Q5SIT6 |
| O, P, R, S, T, U, V, W, Y, Z | V-type ATP synthase, subunit K | protein | 73 | 90% helix, 0% strand | Q5SIT7 |
| Q | V-type ATP synthase, subunit K | protein | 74 | 86% helix, 0% strand | Q5SIT7 |
| X | V-type ATP synthase, subunit K | protein | 72 | 90% helix, 0% strand | Q5SIT7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, F, G
- MG · Magnesium ion · metal · chains A, F
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 | 1103 | 0.88 | 0.90 | 129 | empty |
| 2 | 524 | 0.87 | 0.94 | 97 | empty |
| 3 | 637 | 0.84 | 0.89 | 58 | empty |
| 4 | 562 | 0.84 | 0.90 | 75 | empty |
| 5 | 612 | 0.83 | 0.88 | 73 | empty |
Interfaces
56 interfaces between chains.
- A–F · 3432 Ų buried · 48 hydrogen bonds · protein-protein
- C–E · 2981 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 2472 Ų buried · 32 hydrogen bonds · protein-protein
- K–L · 2239 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 2111 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- Q56404 · AlphaFold monomer V2.0 prediction for V-type ATP synthase beta chain (Q56404) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q56403 · AlphaFold monomer V2.0 prediction for V-type ATP synthase alpha chain (Q56403) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P74901 · AlphaFold monomer V2.0 prediction for V-type ATP synthase subunit E (P74901) · a predicted model of the same protein · chain J against A, TM-score 0.92
- O87880 · AlphaFold monomer V2.0 prediction for V-type ATP synthase subunit D (O87880) · a predicted model of the same protein · chain G against A, TM-score 0.90
- P74902 · AlphaFold monomer V2.0 prediction for V-type ATP synthase subunit C (P74902) · a predicted model of the same protein · chain M against A, TM-score 0.82
- P74903 · AlphaFold monomer V2.0 prediction for V-type ATP synthase subunit F (P74903) · a predicted model of the same protein · chain H against A, TM-score 0.70
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
- Every structure of UniProt Q5SIT6
- Every structure of UniProt Q5SIT7
- Elsewhere: RCSB PDB 6QUM · PDBe 6QUM · UniProt Q56403 · UniProt Q56404 · UniProt O87880 · UniProt P74903 · UniProt Q5SIT5 · UniProt P74901 · UniProt P74902 · UniProt Q5SIT6 · UniProt Q5SIT7
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