Research workbench
Crystal structure of thermotoga maritima sodium pumping membrane integral pyrophosphatase at 4 a in complex with phosphate and magnesium
Analyse Crystal structure of thermotoga maritima sodium pumping membrane integral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AV6
- Type
- protein
- Length
- 1,297 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K(+)-stimulated pyrophosphate-energized sodium pump
- EC
- 3.6.1.1
- UniProt
- Q9S5X0
- Ligands
- MG, K, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | K(+)-stimulated pyrophosphate-energized sodium pump (EC 3.6.1.1) | protein | 655 | 82% helix, 0% strand | Q9S5X0 |
| B | K(+)-stimulated pyrophosphate-energized sodium pump (EC 3.6.1.1) | protein | 642 | 83% helix, 0% strand | Q9S5X0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.78 | 0.98 | 19 | empty |
| 2 | 53 | 0.70 | 0.98 | 25 | empty |
| 3 | 158 | 0.69 | 0.88 | 39 | empty |
| 4 | 52 | 0.68 | 0.97 | 22 | empty |
| 5 | 266 | 0.61 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2825 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4AV6 · Crystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9S5X0 · AlphaFold monomer V2.0 prediction for K(+)-stimulated pyrophosphate- energized sodium… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9S5X0
- Elsewhere: RCSB PDB 4AV6 · PDBe 4AV6 · UniProt Q9S5X0
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