Research workbench
Cryoem structure of kdpfabc in E1-ATP state
Analyse Cryoem structure of kdpfabc in E1-ATP state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LC3
- Type
- protein
- Length
- 1,445 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
- P03959, P03960, P03961, P36937
- Ligands
- 9Y0, ACP, K, MG
- Pockets
- 17 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium-transporting ATPase potassium-binding subunit | protein | 557 | 64% helix, 3% strand | P03959 |
| B | Potassium-transporting ATPase ATP-binding subunit (EC 7.2.2.6) | protein | 673 | 56% helix, 16% strand | P03960 |
| C | Potassium-transporting ATPase kdpc subunit | protein | 188 | 48% helix, 10% strand | P03961 |
| D | Potassium-transporting ATPase kdpf subunit | protein | 27 | 81% helix, 0% strand | P36937 |
Ligands and binding sites
- 9Y0 · (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate · ligand · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains B
- K · Potassium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.80 | 0.88 | 52 | MG, ACP |
| 2 | 311 | 0.78 | 0.88 | 58 | empty |
| 3 | 374 | 0.70 | 0.82 | 54 | empty |
| 4 | 303 | 0.65 | 0.81 | 52 | empty |
| 5 | 79 | 0.61 | 0.89 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4043 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2397 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 714 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 259 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7LC3 · CryoEM Structure of KdpFABC in E1-ATP state · the same entry in another collection · chain D against D, TM-score 1.00
- P03959 · AlphaFold monomer V2.0 prediction for potassium-transporting ATPase potassium-binding… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P03961 · AlphaFold monomer V2.0 prediction for potassium-transporting ATPase kdpc subunit (P03961) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P03960 · AlphaFold monomer V2.0 prediction for potassium-transporting ATPase ATP-binding subunit… · a predicted model of the same protein · chain B against A, TM-score 0.84
- 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 0.72
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 P03959
- Every structure of UniProt P03960
- Every structure of UniProt P03961
- Every structure of UniProt P36937
- Elsewhere: RCSB PDB 7LC3 · PDBe 7LC3 · UniProt P03959 · UniProt P03960 · UniProt P03961 · UniProt P36937
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