Research workbench
Cryo-EM structure of kdpfabc in E2PI state with MGF4
Analyse Cryo-EM structure of kdpfabc in E2PI state with MGF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BGY
- Type
- protein
- Length
- 1,450 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
- PEV, 9Y0, MF4, MG
- Pockets
- 16 · best druggability 0.77
Structure
electron microscopy · 4 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium-transporting ATPase potassium-binding subunit | protein | 557 | 64% helix, 2% strand | P03959 |
| B | Potassium-transporting ATPase ATP-binding subunit (EC 7.2.2.6) | protein | 674 | 52% helix, 13% strand | P03960 |
| C | Potassium-transporting ATPase kdpc subunit | protein | 190 | 46% helix, 7% strand | P03961 |
| D | Potassium-transporting ATPase kdpf subunit | protein | 29 | 76% helix, 0% strand | P36937 |
Ligands and binding sites
- PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains A
- 9Y0 · (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate · ligand · chains A, B
- MF4 · Tetrafluoromagnesate(2-) · ligand · chains B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.77 | 0.98 | 25 | empty |
| 2 | 340 | 0.72 | 0.83 | 29 | empty |
| 3 | 763 | 0.71 | 0.77 | 87 | empty |
| 4 | 277 | 0.71 | 0.84 | 31 | 9Y0 |
| 5 | 306 | 0.65 | 0.81 | 45 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4125 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 1996 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 810 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7BGY · Cryo-EM Structure of KdpFABC in E2Pi state with MgF4 · 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
- 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 0.79
- 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 0.61
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 7BGY · PDBe 7BGY · UniProt P03959 · UniProt P03960 · UniProt P03961 · UniProt P36937
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