MolNFT v1 · #176545 · protein
Crystal structure of nucleotide-free mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase
7DQC · V-type sodium ATPase catalytic subunit a: “Crystal structure of nucleotide-free mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #176545 on…
- PDB
- 7DQC
- Type
- protein
- Length
- 3,104 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
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | V-type sodium ATPase catalytic subunit a (EC 7.2.2.1) | protein | 586 | 35% helix, 24% strand | Q08636 |
| D | V-type sodium ATPase subunit B | protein | 448 | 34% helix, 23% strand | Q08637 |
| E | V-type sodium ATPase subunit B | protein | 450 | 33% helix, 25% strand | Q08637 |
| C | V-type sodium ATPase catalytic subunit a (EC 7.2.2.1) | protein | 584 | 34% helix, 24% strand | Q08636 |
| F | V-type sodium ATPase subunit B | protein | 450 | 30% helix, 22% strand | Q08637 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.85 | 0.86 | 94 | empty |
| 2 | 993 | 0.85 | 0.86 | 90 | empty |
| 3 | 1076 | 0.84 | 0.85 | 86 | empty |
| 4 | 974 | 0.83 | 0.84 | 103 | empty |
| 5 | 1083 | 0.80 | 0.82 | 92 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2258 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 2102 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 1969 Ų buried · 31 hydrogen bonds · protein-protein
- B–F · 1436 Ų buried · 18 hydrogen bonds · protein-protein
- D–C · 1435 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7DQC · Crystal structure of nucleotide-free 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 0.98
- Q08636 · AlphaFold monomer V2.0 prediction for V-type sodium ATPase catalytic subunit a (Q08636) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 7DQC · PDBe 7DQC · UniProt Q08636 · UniProt Q08637
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