Research workbench
Crystal structure of thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sodium ion
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
- 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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