Research workbench
Crystal structure of the nucleotide-free mutant A3B3
Analyse Crystal structure of the nucleotide-free mutant A3B3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZEA
- Type
- protein
- Length
- 6,235 residues
- Chains
- 12
- 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
- 3.6.3.15
- UniProt
- Q08636, Q08637
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 587 | 37% helix, 23% strand | Q08636 |
| B, H | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 586 | 34% helix, 22% strand | Q08636 |
| C, I | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 584 | 34% helix, 22% strand | Q08636 |
| D, K | V-type sodium ATPase subunit B | protein | 454 | 36% helix, 24% strand | Q08637 |
| E | V-type sodium ATPase subunit B | protein | 452 | 36% helix, 23% strand | Q08637 |
| F | V-type sodium ATPase subunit B | protein | 451 | 36% helix, 20% strand | Q08637 |
| J, L | V-type sodium ATPase subunit B | protein | 455 | 36% helix, 22% strand | Q08637 |
Ligands and binding sites
- GOL · Glycerol · additive · 17 copies · chains A, E, C, D, G, H, K
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 | 1066 | 0.84 | 0.85 | 91 | empty |
| 2 | 1100 | 0.84 | 0.85 | 105 | empty |
| 3 | 929 | 0.84 | 0.86 | 88 | empty |
| 4 | 1047 | 0.84 | 0.85 | 87 | empty |
| 5 | 1033 | 0.84 | 0.85 | 90 | empty |
Interfaces
14 interfaces between chains.
- I–L · 2244 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 2120 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2117 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 2070 Ų buried · 25 hydrogen bonds · protein-protein
- G–J · 2065 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5ZEA · Crystal structure of the nucleotide-free mutant A3B3 · the same entry in another collection · chain L against L, 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 Q08636
- Every structure of UniProt Q08637
- Elsewhere: RCSB PDB 5ZEA · PDBe 5ZEA · UniProt Q08636 · UniProt Q08637
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