MolNFT v1 · #176547 · protein
Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase
7DQE · V-type sodium ATPase catalytic subunit a: “Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase”. X-ray diffraction, 3 ligands (ADP, MG, SO4), 20 pockets (best druggability 0.86).…
- PDB
- 7DQE
- Type
- protein
- Length
- 3,106 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type sodium ATPase catalytic subunit a; V-type sodium ATPase subunit B
- EC
- 7.2.2.1
- UniProt
- Q08636, Q08637
- Ligands
- ADP, MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | V-type sodium ATPase catalytic subunit a (EC 7.2.2.1) | protein | 584 | 36% helix, 23% strand | Q08636 |
| D | V-type sodium ATPase subunit B | protein | 446 | 37% helix, 23% strand | Q08637 |
| E, F | V-type sodium ATPase subunit B | protein | 454 | 33% helix, 25% strand | Q08637 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 3 copies · chains A, D, B, E, C
- SO4 · Sulfate ion · ion · chains A, 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 | 1047 | 0.86 | 0.87 | 127 | MG, ADP |
| 2 | 824 | 0.85 | 0.87 | 104 | MG, ADP |
| 3 | 649 | 0.84 | 0.88 | 67 | empty |
| 4 | 1097 | 0.84 | 0.85 | 95 | empty |
| 5 | 286 | 0.83 | 0.95 | 40 | empty |
Interfaces
6 interfaces between chains.
- C–F · 3077 Ų buried · 35 hydrogen bonds · protein-protein
- B–E · 2785 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 2663 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2157 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1804 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7DQE · Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus… · the same entry in another collection · chain F against F, TM-score 1.00
- Q08637 · AlphaFold monomer V2.0 prediction for V-type sodium ATPase subunit B (Q08637) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q08636 · AlphaFold monomer V2.0 prediction for V-type sodium ATPase catalytic subunit a (Q08636) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q08636
- Every structure of UniProt Q08637
- Elsewhere: RCSB PDB 7DQE · PDBe 7DQE · UniProt Q08636 · UniProt Q08637
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