Research workbench

Rabbit CAV1.1-diltiazem complex

Analyse Rabbit CAV1.1-diltiazem complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JPB
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, P19517, P13806
Ligands: 3PE, PC1, C9F, ETA, NAG, BMA, CA
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 45% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Voltage-dependent L-type calcium channel subunit alpha-1S	protein	1274	59% helix, 2% strand	P07293
E	Voltage-dependent calcium channel gamma-1 subunit	protein	169	53% helix, 7% strand	P19518
B	Voltage-dependent L-type calcium channel subunit beta-1	protein	100	28% helix, 25% strand	P19517
C	Voltage-dependent L-type calcium channel subunit beta-1	protein	178	43% helix, 15% strand	P19517
F	Voltage-dependent calcium channel subunit alpha-2/DELTA-1	protein	973	27% helix, 23% strand	P13806

Ligands and binding sites

3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains A, E
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains A, E
C9F · [(2~{S},3~{S})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate · ligand · chains A
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	1162	0.84	0.84	69	CA, C9F
2	1037	0.81	0.82	103	3PE
3	1145	0.81	0.82	104	empty
4	636	0.80	0.85	72	empty
5	878	0.79	0.81	87	empty

Interfaces

4 interfaces between chains.

A–F · 1857 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 1642 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1255 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 900 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 glycan, 11 disulfide (N-glycosylation, disulfide).

Compared structures

6JPB · Rabbit Cav1.1-Diltiazem Complex · the same entry in another collection · chain F against F, 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 0.87

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 P07293
Every structure of UniProt P19518
Every structure of UniProt P19517
Every structure of UniProt P13806
Elsewhere: RCSB PDB 6JPB · PDBe 6JPB · UniProt P07293 · UniProt P19518 · UniProt P19517 · UniProt P13806

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