MolNFT v1 · #183372 · protein
Cryo-EM structure of the kdpfabc complex in an E1-ATP conformation loaded with K+
7NNL · Potassium-transporting ATPase potassium-binding subunit: “Cryo-EM structure of the kdpfabc complex in an E1-ATP conformation loaded with K+”. Electron microscopy, 3 ligands (CDL, ACP, K), 20 pockets (best druggability 0.79). MolNFT…
- PDB
- 7NNL
- 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, K
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium-transporting ATPase potassium-binding subunit | protein | 557 | 62% helix, 3% strand | A0A2S5ZPF1 |
| C | Potassium-transporting ATPase kdpc subunit | protein | 190 | 46% 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 | 50% helix, 13% strand | A0A024L5I2 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 2 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains B
- K · Potassium ion · metal · 10 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.79 | 0.88 | 45 | ACP |
| 2 | 730 | 0.78 | 0.82 | 84 | K |
| 3 | 456 | 0.72 | 0.81 | 54 | empty |
| 4 | 85 | 0.60 | 0.88 | 24 | empty |
| 5 | 183 | 0.59 | 0.82 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4085 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2379 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 730 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 298 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 7NNL · Cryo-EM structure of the KdpFABC complex in an E1-ATP conformation loaded with K+ · 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 0.80
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 7NNL · PDBe 7NNL · UniProt A0A2S5ZPF1 · UniProt A0A037YI39 · UniProt P36937 · UniProt A0A024L5I2
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