Research workbench
Rabbit CAV1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9 ångström resolution
Analyse Rabbit CAV1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JPX
- Type
- protein
- Length
- 2,258 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, POV, 6UB, CA
- Pockets
- 20 · best druggability 0.86
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 | 1116 | 60% helix, 3% strand | P07293 |
| E | Voltage-dependent calcium channel gamma-1 subunit | protein | 169 | 55% helix, 8% strand | P19518 |
| F | Voltage-dependent calcium channel subunit alpha-2/DELTA-1 | protein | 973 | 28% helix, 25% 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
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · chains A
- 6UB · amlodipine · 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 | 939 | 0.86 | 0.87 | 70 | POV, 6UB |
| 2 | 557 | 0.80 | 0.86 | 59 | empty |
| 3 | 865 | 0.79 | 0.82 | 82 | 3PE |
| 4 | 921 | 0.79 | 0.81 | 96 | empty |
| 5 | 284 | 0.77 | 0.89 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–F · 1943 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 1603 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 7JPX · Rabbit Cav1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9 Angstrom… · 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 0.99
- 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 7JPX · PDBe 7JPX · UniProt P07293 · UniProt P19518 · UniProt P13806
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