Research workbench
Rabbit CAV1.1-verapamil complex
Analyse Rabbit CAV1.1-verapamil complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JPA
- Type
- protein
- Length
- 2,694 residues
- Chains
- 5
- 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, P19517, P13806
- Ligands
- 3PE, PC1, 4YH, 9Z9, ETA, NAG, BMA, CA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Voltage-dependent L-type calcium channel subunit alpha-1S | protein | 1274 | 65% helix, 3% strand | P07293 |
| E | Voltage-dependent calcium channel gamma-1 subunit | protein | 169 | 53% helix, 6% strand | P19518 |
| B | Voltage-dependent L-type calcium channel subunit beta-1 | protein | 100 | 25% helix, 26% strand | P19517 |
| C | Voltage-dependent L-type calcium channel subunit beta-1 | protein | 178 | 44% helix, 15% strand | P19517 |
| F | Voltage-dependent calcium channel subunit alpha-2/DELTA-1 | protein | 973 | 27% helix, 23% strand | P13806 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains A, E
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, E
- 4YH · (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl) pentanenitrile · ligand · 2 copies · chains A
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · chains A
- ETA · Ethanolamine · ligand · chains F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains F, A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains F
- CA · Calcium ion · metal · 3 copies · chains A, F
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 | 614 | 0.82 | 0.86 | 61 | 3PE, 9Z9, 4YH |
| 2 | 1027 | 0.80 | 0.81 | 89 | 3PE |
| 3 | 599 | 0.79 | 0.84 | 68 | empty |
| 4 | 841 | 0.77 | 0.80 | 79 | empty |
| 5 | 1058 | 0.76 | 0.78 | 61 | empty |
Interfaces
4 interfaces between chains.
- A–F · 1854 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1583 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1170 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 896 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 11 disulfide (N-glycosylation, disulfide).
Compared structures
- 6JPA · Rabbit Cav1.1-Verapamil Complex · the same entry in another collection · chain F against F, 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
- P19517 · AlphaFold monomer V2.0 prediction for voltage-dependent L-type calcium channel subunit… · a predicted model of the same protein · chain C against A, TM-score 0.97
- 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 P19517
- Every structure of UniProt P13806
- Elsewhere: RCSB PDB 6JPA · PDBe 6JPA · UniProt P07293 · UniProt P19518 · UniProt P19517 · UniProt P13806
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