MolNFT v1 · #126334 · protein
Crystal structure of thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sodium ion
5LZQ · K(+)-stimulated pyrophosphate-energized sodium pump: “Crystal structure of thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with…”. X-ray diffraction, 3 ligands (2PN, MG, NA), 18 pockets (best…
- PDB
- 5LZQ
- Type
- protein
- Length
- 1,450 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
- 2PN, MG, NA
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | K(+)-stimulated pyrophosphate-energized sodium pump (EC 3.6.1.1) | protein | 725 | 82% helix, 2% strand | Q9S5X0 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 10 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.78 | 0.95 | 40 | MG, 2PN |
| 2 | 125 | 0.76 | 0.96 | 33 | MG, 2PN |
| 3 | 55 | 0.73 | 0.98 | 14 | empty |
| 4 | 173 | 0.62 | 0.83 | 18 | empty |
| 5 | 179 | 0.58 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3277 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5LZQ · 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 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 Q9S5X0
- Elsewhere: RCSB PDB 5LZQ · PDBe 5LZQ · UniProt Q9S5X0
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