MolNFT v1 · #119929 · protein
Structure of the mammalian voltage-gated calcium channel CAV1.1 complex for classii MAP
5GJW · Voltage-dependent L-type calcium channel subunit alpha-1S: “Structure of the mammalian voltage-gated calcium channel CAV1.1 complex for classii MAP”. Electron microscopy, 4 ligands (ETA, NAG, BMA), 20 pockets (best druggability…
- PDB
- 5GJW
- Type
- protein
- Length
- 2,676 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 L-type…
- UniProt
- P07293, P19517, P19518, P13806
- Ligands
- ETA, NAG, BMA, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Voltage-dependent L-type calcium channel subunit alpha-1S | protein | 1291 | 65% helix, 2% strand | P07293 |
| B | Voltage-dependent L-type calcium channel subunit beta-1 | protein | 100 | 23% helix, 24% strand | P19517 |
| C | Voltage-dependent L-type calcium channel subunit beta-1 | protein | 178 | 47% helix, 16% strand | P19517 |
| E | Voltage-dependent calcium channel gamma-1 subunit | protein | 166 | 59% helix, 11% strand | P19518 |
| F | Voltage-dependent calcium channel subunit alpha-2/DELTA-1 | protein | 941 | 28% helix, 18% strand | P13806 |
Ligands and binding sites
- 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 | 827 | 0.84 | 0.86 | 70 | CA |
| 2 | 1060 | 0.82 | 0.83 | 110 | empty |
| 3 | 1159 | 0.81 | 0.82 | 108 | empty |
| 4 | 521 | 0.79 | 0.85 | 53 | empty |
| 5 | 356 | 0.76 | 0.86 | 49 | empty |
Interfaces
4 interfaces between chains.
- A–F · 1897 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1624 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1219 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 877 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 11 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 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 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 0.99
- 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 0.97
- 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 0.91
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 P19517
- Every structure of UniProt P19518
- Every structure of UniProt P13806
- Elsewhere: RCSB PDB 5GJW · PDBe 5GJW · UniProt P07293 · UniProt P19517 · UniProt P19518 · UniProt P13806
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