MolNFT v1 · #183373 · protein
Rb-loaded cryo-EM structure of the E1-ATP kdpfabc complex.
7NNP · Potassium-transporting ATPase potassium-binding subunit: “Rb-loaded cryo-EM structure of the E1-ATP kdpfabc complex.”. Electron microscopy, 3 ligands (CDL, ACP, RB), 20 pockets (best druggability 0.80). MolNFT v1 #183373 on…
- PDB
- 7NNP
- Type
- protein
- Length
- 1,456 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium-transporting ATPase potassium-binding subunit; Potassium-transporting ATPase…
- EC
- 7.2.2.6
- UniProt
- A0A2S5ZPF1, A0A037YI39, P36937, A0A024L5I2
- Ligands
- CDL, ACP, RB
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium-transporting ATPase potassium-binding subunit | protein | 557 | 63% helix, 3% strand | A0A2S5ZPF1 |
| C | Potassium-transporting ATPase kdpc subunit | protein | 190 | 47% helix, 9% strand | A0A037YI39 |
| D | Potassium-transporting ATPase kdpf subunit | protein | 27 | 81% helix, 0% strand | P36937 |
| B | Potassium-transporting ATPase ATP-binding subunit (EC 7.2.2.6) | protein | 682 | 51% helix, 14% strand | A0A024L5I2 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 2 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains B
- RB · Rubidium ion · metal · 8 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 | 401 | 0.80 | 0.89 | 60 | RB |
| 2 | 428 | 0.77 | 0.86 | 52 | ACP |
| 3 | 337 | 0.72 | 0.84 | 38 | empty |
| 4 | 50 | 0.65 | 0.95 | 15 | empty |
| 5 | 335 | 0.64 | 0.80 | 45 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4096 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2357 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 746 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 274 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7NNP · Rb-loaded cryo-EM structure of the E1-ATP KdpFABC complex. · the same entry in another collection · chain A against A, TM-score 1.00
- P36937 · AlphaFold monomer V2.0 prediction for potassium-transporting ATPase kdpf subunit (P36937) · a predicted model of the same protein · chain D against A, TM-score 0.77
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 A0A2S5ZPF1
- Every structure of UniProt A0A037YI39
- Every structure of UniProt P36937
- Every structure of UniProt A0A024L5I2
- Elsewhere: RCSB PDB 7NNP · PDBe 7NNP · UniProt A0A2S5ZPF1 · UniProt A0A037YI39 · UniProt P36937 · UniProt A0A024L5I2
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