Research workbench
V/A-type ATPase/synthase from Thermus thermophilus, rotational state 3.
Analyse V/A-type ATPase/synthase from Thermus thermophilus, rotational state 3. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y60
- Type
- protein
- Length
- 5,852 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 7.5
- Source
- Thermus thermophilus HB8
- 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, Q5SIT6, Q5SIT7
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 7.5 · 9 distinct chains · 52% helix, 8% 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, 17% strand | Q56403 |
| D, E, F | V-type ATP synthase beta chain | protein | 459 | 29% helix, 14% strand | Q56404 |
| G | V-type ATP synthase subunit D | protein | 210 | 69% helix, 5% strand | O87880 |
| H | V-type ATP synthase subunit F | protein | 100 | 40% helix, 2% strand | P74903 |
| I, K | V-type ATP synthase, subunit (VAPC-THERM) | protein | 100 | 93% helix, 0% strand | Q5SIT5 |
| J, L | V-type ATP synthase subunit E | protein | 185 | 71% helix, 5% strand | P74901 |
| M | V-type ATP synthase subunit C | protein | 320 | 68% helix, 0% strand | P74902 |
| N | V-type ATP synthase subunit I | protein | 632 | 59% helix, 6% strand | Q5SIT6 |
| O, P, Q, R, S, T, U, V, W, X, Y, Z | V-type ATP synthase, subunit K | protein | 76 | 80% helix, 0% strand | Q5SIT7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, F, B, D
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 | 783 | 0.81 | 0.85 | 120 | empty |
| 2 | 728 | 0.79 | 0.84 | 122 | empty |
| 3 | 403 | 0.74 | 0.85 | 81 | empty |
| 4 | 958 | 0.72 | 0.77 | 154 | empty |
| 5 | 685 | 0.72 | 0.79 | 133 | empty |
Interfaces
39 interfaces between chains.
- B–D · 677 Ų buried · 7 hydrogen bonds · protein-protein
- I–J · 561 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 558 Ų buried · 1 hydrogen bond · protein-protein
- W–X · 474 Ų buried · 2 hydrogen bonds · protein-protein
- U–V · 473 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5Y60 · V/A-type ATPASE/SYNTHASE from thermus thermophilus, rotational state 3. · 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 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 5Y60 · PDBe 5Y60 · UniProt Q56403 · UniProt Q56404 · UniProt O87880 · UniProt P74903 · UniProt Q5SIT5 · UniProt P74901 · UniProt P74902 · UniProt Q5SIT6 · UniProt Q5SIT7
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