MolNFT v1 · #147390 · protein
The voltage-activated KV1.2-2.1 paddle chimera channel in lipid nanodiscs
6EBK · Voltage-gated potassium channel subunit beta-2: “The voltage-activated KV1.2-2.1 paddle chimera channel in lipid nanodiscs”. Electron microscopy, 1 ligand (NAP), 20 pockets (best druggability 0.85). MolNFT v1 #147390 on GenesisL1…
- PDB
- 6EBK
- Type
- protein
- Length
- 2,848 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Voltage-gated potassium channel subunit beta-2; Potassium voltage-gated channel subfamily…
- UniProt
- P62483, P63142, Q63099
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Voltage-gated potassium channel subunit beta-2 | protein | 325 | 47% helix, 15% strand | P62483 |
| B, D, F, H | Potassium voltage-gated channel subfamily a member 2, potassium voltage-gated channel subfamily B member 2 chimera | protein | 387 | 56% helix, 5% strand | P63142, Q63099 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.85 | 0.87 | 80 | empty |
| 2 | 732 | 0.83 | 0.86 | 40 | empty |
| 3 | 859 | 0.82 | 0.84 | 44 | empty |
| 4 | 308 | 0.74 | 0.86 | 57 | NAP |
| 5 | 303 | 0.73 | 0.86 | 45 | NAP |
Interfaces
18 interfaces between chains.
- B–H · 2405 Ų buried · 26 hydrogen bonds · protein-protein
- F–H · 2405 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 2396 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2391 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 967 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6EBK · The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid nanodiscs · the same entry in another collection · chain H against H, TM-score 1.00
- P62483 · AlphaFold monomer V2.0 prediction for voltage-gated potassium channel subunit beta-2… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P63142 · AlphaFold monomer V2.0 prediction for potassium voltage-gated channel subfamily a member… · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q63099 · AlphaFold monomer V2.0 prediction for potassium voltage-gated channel subfamily B member… · a predicted model of the same protein · chain B against A, TM-score 0.73
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 P62483
- Every structure of UniProt P63142
- Every structure of UniProt Q63099
- Elsewhere: RCSB PDB 6EBK · PDBe 6EBK · UniProt P62483 · UniProt P63142 · UniProt Q63099
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