Research workbench
Cryo-EM structure of the kdpfabc complex in an E1 outward-facing state (state 1)
Analyse Cryo-EM structure of the kdpfabc complex in an E1 outward-facing state (state 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HRA
- 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
- 3.6.3.12
- UniProt
- P03959, P03961, P36937, P03960
- Ligands
- K
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium-transporting ATPase potassium-binding subunit | protein | 557 | 55% helix, 3% strand | P03959 |
| C | Potassium-transporting ATPase kdpc subunit | protein | 187 | 44% helix, 9% strand | P03961 |
| D | Potassium-transporting ATPase kdpf subunit | protein | 27 | 78% helix, 0% strand | P36937 |
| B | Potassium-transporting ATPase ATP-binding subunit (EC 3.6.3.12) | protein | 679 | 46% helix, 10% strand | P03960 |
Ligands and binding sites
- K · Potassium ion · metal · 3 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.78 | 0.88 | 59 | K |
| 2 | 393 | 0.69 | 0.81 | 51 | empty |
| 3 | 331 | 0.66 | 0.81 | 47 | empty |
| 4 | 70 | 0.58 | 0.89 | 22 | empty |
| 5 | 148 | 0.57 | 0.82 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4037 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2460 Ų buried · 8 hydrogen bonds · protein-protein
- D–B · 708 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 301 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6HRA · Cryo-EM structure of the KdpFABC complex in an E1 outward-facing state (state 1) · the same entry in another collection · chain B against B, 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 0.97
- 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 0.90
- 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 0.68
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 P03961
- Every structure of UniProt P36937
- Every structure of UniProt P03960
- Elsewhere: RCSB PDB 6HRA · PDBe 6HRA · UniProt P03959 · UniProt P03961 · UniProt P36937 · UniProt P03960
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