Research workbench
Rabbit CAV1.1 in the presence of 100 micromolar (R)-(+)-bay K8644 in nanodiscs at 3.2 ångström resolution
Analyse Rabbit CAV1.1 in the presence of 100 micromolar (R)-(+)-bay K8644 in nanodiscs… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JPW
- Type
- protein
- Length
- 2,257 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Voltage-dependent L-type calcium channel subunit alpha-1S; Voltage-dependent calcium…
- UniProt
- P07293, P19518, P13806
- Ligands
- 3PE, PC1, VFY, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Voltage-dependent L-type calcium channel subunit alpha-1S | protein | 1115 | 60% helix, 3% strand | P07293 |
| E | Voltage-dependent calcium channel gamma-1 subunit | protein | 169 | 54% helix, 8% strand | P19518 |
| F | Voltage-dependent calcium channel subunit alpha-2/DELTA-1 | protein | 973 | 29% helix, 24% strand | P13806 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 9 copies · chains A, E
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains A, E
- VFY · methyl (4~{R})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate · ligand · chains A
- CA · Calcium ion · metal · chains A
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 | 1094 | 0.84 | 0.85 | 69 | VFY |
| 2 | 752 | 0.84 | 0.87 | 87 | empty |
| 3 | 1157 | 0.82 | 0.83 | 132 | empty |
| 4 | 286 | 0.78 | 0.90 | 53 | empty |
| 5 | 677 | 0.74 | 0.80 | 64 | empty |
Interfaces
2 interfaces between chains.
- A–F · 1785 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1690 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7JPW · Rabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644 in nanodiscs at 3.2… · the same entry in another collection · chain A against A, TM-score 1.00
- P13806 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel subunit… · a predicted model of the same protein · chain F against A, TM-score 1.00
- P07293 · AlphaFold monomer V2.0 prediction for voltage-dependent L-type calcium channel subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P19518 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-1 subunit… · a predicted model of the same protein · chain E against A, TM-score 0.89
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 P07293
- Every structure of UniProt P19518
- Every structure of UniProt P13806
- Elsewhere: RCSB PDB 7JPW · PDBe 7JPW · UniProt P07293 · UniProt P19518 · UniProt P13806
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