MolNFT v1 · #153771 · protein

Rabbit CAV1.1-nifedipine complex

6JP5 · Voltage-dependent L-type calcium channel subunit alpha-1S: “Rabbit CAV1.1-nifedipine complex”. Electron microscopy, 7 ligands (3PE, C5U, PC1), 20 pockets (best druggability 0.84). MolNFT v1 #153771 on GenesisL1: 3D structure…

PDB: 6JP5
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, P13806, P19517
Ligands: 3PE, C5U, PC1, ETA, NAG, BMA, CA
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 46% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Voltage-dependent L-type calcium channel subunit alpha-1S	protein	1274	62% helix, 2% strand	P07293
E	Voltage-dependent calcium channel gamma-1 subunit	protein	169	53% helix, 6% strand	P19518
F	Voltage-dependent calcium channel subunit alpha-2/DELTA-1	protein	973	27% helix, 23% strand	P13806
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

Ligands and binding sites

3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains A, E
C5U · dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate · ligand · chains A
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains A, E
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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1112	0.84	0.84	61	CA, C5U
2	1072	0.80	0.81	98	3PE
3	666	0.80	0.85	71	empty
4	868	0.78	0.81	89	empty
5	888	0.77	0.79	93	empty

Interfaces

4 interfaces between chains.

A–F · 1829 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 1703 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 1220 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 901 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 glycan, 12 disulfide (N-glycosylation, disulfide).

Compared structures

6JP5 · Rabbit Cav1.1-Nifedipine Complex · the same entry in another collection · chain C against C, 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 0.98
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 P13806
Every structure of UniProt P19517
Elsewhere: RCSB PDB 6JP5 · PDBe 6JP5 · UniProt P07293 · UniProt P19518 · UniProt P13806 · UniProt P19517

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