Research workbench
Human L-type voltage-gated calcium channel CAV1.3 in the presence of cinnarizine at 3.1 ångström resolution
Analyse Human L-type voltage-gated calcium channel CAV1.3 in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UHF
- Type
- protein
- Length
- 2,502 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Voltage-dependent L-type calcium channel subunit alpha-1D; Voltage-dependent calcium…
- UniProt
- Q01668, P54289, P54284
- Ligands
- N90, Y01, 3PE, NAG, 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-1D | protein | 1230 | 61% helix, 2% strand | Q01668 |
| D | Voltage-dependent calcium channel subunit alpha-2/DELTA-1 | protein | 948 | 31% helix, 25% strand | P54289 |
| C | Voltage-dependent L-type calcium channel subunit beta-3 | protein | 324 | 34% helix, 15% strand | P54284 |
Ligands and binding sites
- N90 · 1-(diphenylmethyl)-4-[(2E)-3-phenylprop-2-en-1-yl]piperazine · ligand · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains D, A
- CA · Calcium ion · metal · 2 copies · chains A, D
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 | 1169 | 0.84 | 0.84 | 80 | N90 |
| 2 | 1057 | 0.78 | 0.80 | 104 | empty |
| 3 | 980 | 0.77 | 0.79 | 99 | NAG |
| 4 | 741 | 0.76 | 0.81 | 78 | empty |
| 5 | 227 | 0.75 | 0.90 | 35 | empty |
Interfaces
2 interfaces between chains.
- A–D · 1335 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 986 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7UHF · Human L-type voltage-gated calcium channel Cav1.3 in the presence of cinnarizine at 3.1… · the same entry in another collection · chain A against A, TM-score 1.00
- P54289 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel subunit… · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q01668 · 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
- P54284 · 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 0.87
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 Q01668
- Every structure of UniProt P54289
- Every structure of UniProt P54284
- Elsewhere: RCSB PDB 7UHF · PDBe 7UHF · UniProt Q01668 · UniProt P54289 · UniProt P54284
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