MolNFT v1 · #189437 · protein
Human N-type voltage gated calcium channel CAV2.2-ALPHA2/DELTA1-BETA1 complex, bound to ziconotide
7VFU · Voltage-dependent N-type calcium channel subunit alpha-1B: “Human N-type voltage gated calcium channel CAV2.2-ALPHA2/DELTA1-BETA1 complex, bound to ziconotide”. Electron microscopy, 6 ligands (R16, Y01, PT5), 20 pockets (best…
- PDB
- 7VFU
- Type
- protein
- Length
- 2,409 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, Q02641, P54289
- Ligands
- R16, Y01, PT5, NAG, BMA, CA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Voltage-dependent N-type calcium channel subunit alpha-1B | protein | 1266 | 68% helix, 2% strand | Q00975 |
| E | Omega-conotoxin mviia | protein | 25 | 12% helix, 12% strand | P05484 |
| D | Voltage-dependent L-type calcium channel subunit beta-1 | protein | 163 | 49% helix, 15% strand | Q02641 |
| B | Voltage-dependent calcium channel subunit alpha-2/DELTA-1 | protein | 955 | 31% helix, 22% strand | P54289 |
Ligands and binding sites
- R16 · Hexadecane · ligand · 18 copies · chains A
- Y01 · Cholesterol hemisuccinate · ligand · 3 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 · 14 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
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 | 1013 | 0.86 | 0.87 | 113 | empty |
| 2 | 1139 | 0.86 | 0.86 | 78 | R16 |
| 3 | 853 | 0.78 | 0.81 | 92 | empty |
| 4 | 201 | 0.77 | 0.92 | 30 | empty |
| 5 | 1164 | 0.74 | 0.77 | 82 | R16, PT5 |
Interfaces
3 interfaces between chains.
- A–D · 1318 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1236 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1229 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 7VFU · Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to… · the same entry in another collection · chain B against B, TM-score 1.00
- P54289 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q02641 · AlphaFold monomer V2.0 prediction for voltage-dependent L-type calcium channel subunit… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 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 0.93
- P05484 · AlphaFold monomer V2.0 prediction for omega-conotoxin mviia (P05484) · a predicted model of the same protein · chain E against A, TM-score 0.72
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 Q02641
- Every structure of UniProt P54289
- Elsewhere: RCSB PDB 7VFU · PDBe 7VFU · UniProt Q00975 · UniProt P05484 · UniProt Q02641 · UniProt P54289
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