Research workbench
Human N-type voltage-gated calcium channel CAV2.2 in the presence of ziconotide at 3.0 ångström resolution
Analyse Human N-type voltage-gated calcium channel CAV2.2 in the presence of ziconotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MIX
- Type
- protein
- Length
- 2,623 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Voltage-dependent N-type calcium channel subunit alpha-1B; Omega-conotoxin mviia…
- UniProt
- Q00975, P05484, P54289, P54284
- Ligands
- CLR, Y01, 3PE, PT5, NAG, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Voltage-dependent N-type calcium channel subunit alpha-1B | protein | 1326 | 67% helix, 2% strand | Q00975 |
| B | Omega-conotoxin mviia | protein | 25 | 12% helix, 20% strand | P05484 |
| D | Voltage-dependent calcium channel subunit alpha-2/DELTA-1 | protein | 948 | 30% helix, 25% strand | P54289 |
| C | Voltage-dependent L-type calcium channel subunit beta-3 | protein | 324 | 36% helix, 14% strand | P54284 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 5 copies · chains A
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains A, D
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A
- PT5 · (1S)-2-{[(R)-hydroxy{[(1r,2r,3s,4r,5r,6s)-2,3,6-trihydroxy-4,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy) methyl]ethyl (8E,11E)-icosa-5,8,11,14-tetraenoate · 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 | 1198 | 0.84 | 0.84 | 76 | empty |
| 2 | 852 | 0.83 | 0.86 | 88 | empty |
| 3 | 1048 | 0.82 | 0.84 | 117 | empty |
| 4 | 610 | 0.79 | 0.85 | 73 | empty |
| 5 | 371 | 0.78 | 0.88 | 68 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1489 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1137 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1010 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7MIX · Human N-type voltage-gated calcium channel Cav2.2 in the presence of ziconotide at 3.0… · the same entry in another collection · chain C against C, 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 1.00
- Q00975 · AlphaFold monomer V2.0 prediction for voltage-dependent N-type calcium channel subunit… · a predicted model of the same protein · chain A against A, TM-score 0.92
- 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
- P05484 · AlphaFold monomer V2.0 prediction for omega-conotoxin mviia (P05484) · a predicted model of the same protein · chain B against A, TM-score 0.76
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 Q00975
- Every structure of UniProt P05484
- Every structure of UniProt P54289
- Every structure of UniProt P54284
- Elsewhere: RCSB PDB 7MIX · PDBe 7MIX · UniProt Q00975 · UniProt P05484 · UniProt P54289 · UniProt P54284
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