MolNFT v1 · #126335 · protein
Crystal structure of thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with tungstate and magnesium
5LZR · K(+)-stimulated pyrophosphate-energized sodium pump: “Crystal structure of thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with…”. X-ray diffraction, 2 ligands (MG, WO4), 20 pockets (best druggability…
- PDB
- 5LZR
- Type
- protein
- Length
- 1,387 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, WO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | K(+)-stimulated pyrophosphate-energized sodium pump (EC 3.6.1.1) | protein | 690 | 83% helix, 2% strand | Q9S5X0 |
| B | K(+)-stimulated pyrophosphate-energized sodium pump (EC 3.6.1.1) | protein | 697 | 82% helix, 2% strand | Q9S5X0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- WO4 · Tungstate(vi)ion · ion · 2 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.75 | 0.98 | 19 | empty |
| 2 | 658 | 0.74 | 0.80 | 87 | WO4, MG |
| 3 | 564 | 0.71 | 0.80 | 69 | WO4, MG |
| 4 | 75 | 0.66 | 0.92 | 21 | empty |
| 5 | 196 | 0.64 | 0.84 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2944 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5LZR · 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 0.97
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 5LZR · PDBe 5LZR · UniProt Q9S5X0
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