MolNFT v1 · #162056 · protein
Structure of membrane bound pyrophosphatase from thermotoga maritima in complex with imidodiphosphate and N-[(2-amino-6-benzothiazolyl) methyl]-1H-indole-2-carboxamide (atc)
6QXA · K(+)-stimulated pyrophosphate-energized sodium pump: “Structure of membrane bound pyrophosphatase from thermotoga maritima in complex with imidodiphosphate and…”. X-ray diffraction, 6 ligands (2PN, GQB, D1D), 20 pockets (best…
- PDB
- 6QXA
- Type
- protein
- Length
- 2,884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K(+)-stimulated pyrophosphate-energized sodium pump
- EC
- 7.2.3.-
- UniProt
- Q9S5X0
- Ligands
- 2PN, GQB, D1D, MG, NA, K
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 82% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | K(+)-stimulated pyrophosphate-energized sodium pump (EC 7.2.3.-) | protein | 725 | 82% helix, 2% strand | Q9S5X0 |
| B | K(+)-stimulated pyrophosphate-energized sodium pump (EC 7.2.3.-) | protein | 715 | 83% helix, 1% strand | Q9S5X0 |
| D | K(+)-stimulated pyrophosphate-energized sodium pump (EC 7.2.3.-) | protein | 719 | 82% helix, 1% strand | Q9S5X0 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 4 copies · chains A, B, C, D
- GQB · ~{N}-[(2-azanyl-3~{H}-1,3-benzothiazol-6-yl)methyl]-1~{H}-indole-2-carboxamide · ligand · 3 copies · chains A, C
- D1D · (4S,5S)-1,2-dithiane-4,5-diol · ligand · chains C
- MG · Magnesium ion · metal · 20 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B, D
- K · Potassium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.82 | 0.96 | 55 | MG, 2PN, K |
| 2 | 170 | 0.80 | 0.96 | 51 | MG, 2PN, K |
| 3 | 134 | 0.79 | 0.97 | 43 | MG, 2PN |
| 4 | 157 | 0.79 | 0.96 | 46 | MG, 2PN, K |
| 5 | 165 | 0.61 | 0.82 | 19 | empty |
Interfaces
2 interfaces between chains.
- C–D · 3265 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 3239 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6QXA · Structure of membrane bound pyrophosphatase from Thermotoga maritima in complex with… · 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 6QXA · PDBe 6QXA · UniProt Q9S5X0
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