Research workbench
Crystal structure of KV1.2-2.1 paddle chimera channel in complex with charybdotoxin in cs+
Analyse Crystal structure of KV1.2-2.1 paddle chimera channel in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JTC
- Type
- protein
- Length
- 1,438 residues
- Chains
- 5
- 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…
- UniProt
- P62483, P63142, P15387, P13487
- Ligands
- PGW, NAP, CS
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Voltage-gated potassium channel subunit beta-2 | protein | 326 | 50% helix, 16% strand | P62483 |
| B | Potassium voltage-gated channel subfamily a member 2, potassium voltage-gated channel subfamily B member 1 | protein | 386 | 62% helix, 5% strand | P63142, P15387 |
| H | Potassium voltage-gated channel subfamily a member 2, potassium voltage-gated channel subfamily B member 1 | protein | 363 | 51% helix, 5% strand | P63142, P15387 |
| Y | Potassium channel toxin alpha-ktx 1.1 | protein | 37 | 27% helix, 5% strand | P13487 |
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 · 17 copies · chains B, H
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, G
- CS · Cesium ion · metal · 8 copies · chains B, H, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.74 | 0.86 | 52 | NAP |
| 2 | 236 | 0.73 | 0.88 | 37 | NAP |
| 3 | 383 | 0.70 | 0.82 | 52 | empty |
| 4 | 120 | 0.46 | 0.78 | 20 | empty |
| 5 | 51 | 0.44 | 0.84 | 14 | empty |
Interfaces
3 interfaces between chains.
- G–H · 414 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 412 Ų buried · 5 hydrogen bonds · protein-protein
- H–Y · 207 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 4JTC · Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin in Cs+ · 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 B against A, TM-score 0.96
- P15387 · 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 0.75
- P13487 · AlphaFold monomer V2.0 prediction for potassium channel toxin alpha- ktx 1.1 (P13487) · a predicted model of the same protein · chain Y against A, TM-score 0.75
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 P15387
- Every structure of UniProt P13487
- Elsewhere: RCSB PDB 4JTC · PDBe 4JTC · UniProt P62483 · UniProt P63142 · UniProt P15387 · UniProt P13487
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