MolNFT v1 · #138412 · protein
Crystal structure of a KV1.2-2.1 chimera K+ channel V406W mutant in an inactivated state
5WIE · Voltage-gated potassium channel subunit beta-2: “Crystal structure of a KV1.2-2.1 chimera K+ channel V406W mutant in an inactivated state”. X-ray diffraction, 3 ligands (PGW, NAP, K), 11 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5WIE
- Type
- protein
- Length
- 1,370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Voltage-gated potassium channel subunit beta-2; Potassium voltage-gated channel subfamily…
- EC
- 1.1.1.-
- UniProt
- P62483, P63142, P63141
- Ligands
- PGW, NAP, K
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Voltage-gated potassium channel subunit beta-2 (EC 1.1.1.-) | protein | 326 | 51% helix, 16% strand | P62483 |
| B | Potassium voltage-gated channel subfamily a member 2, potassium voltage-gated channel subfamily a member 2 | protein | 390 | 61% helix, 5% strand | P63142, P63141 |
| H | Potassium voltage-gated channel subfamily a member 2, potassium voltage-gated channel subfamily a member 2 | protein | 328 | 66% helix, 5% strand | P63142, P63141 |
Ligands and binding sites
- PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 6 copies · chains B, H
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, G
- K · Potassium ion · metal · 8 copies · chains B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.73 | 0.87 | 37 | NAP |
| 2 | 231 | 0.73 | 0.88 | 39 | NAP |
| 3 | 252 | 0.62 | 0.81 | 32 | empty |
| 4 | 112 | 0.47 | 0.79 | 17 | empty |
| 5 | 99 | 0.39 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- G–H · 486 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 455 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5WIE · Crystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant in an inactivated state · the same entry in another collection · chain A against A, 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 H against A, TM-score 0.98
- P63141 · AlphaFold monomer V2.0 prediction for potassium voltage-gated channel subfamily a member… · a predicted model of the same protein · chain H against A, TM-score 0.98
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 P63141
- Elsewhere: RCSB PDB 5WIE · PDBe 5WIE · UniProt P62483 · UniProt P63142 · UniProt P63141
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