MolNFT v1 · #119928 · protein

Structure of the mammalian voltage-gated calcium channel CAV1.1 complex at near atomic resolution

5GJV · Voltage-dependent L-type calcium channel subunit alpha-1S: “Structure of the mammalian voltage-gated calcium channel CAV1.1 complex at near atomic resolution”. Electron microscopy, 5 ligands (PC1, ETA, NAG), 20 pockets (best…

PDB: 5GJV
Type: protein
Length: 2,661 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 L-type…
UniProt: P07293, P19517, P19518, P13806
Ligands: PC1, ETA, NAG, BMA, CA
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 5 distinct chains · 48% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Voltage-dependent L-type calcium channel subunit alpha-1S	protein	1276	63% helix, 2% strand	P07293
B	Voltage-dependent L-type calcium channel subunit beta-1	protein	100	33% helix, 25% strand	P19517
C	Voltage-dependent L-type calcium channel subunit beta-1	protein	178	48% helix, 16% strand	P19517
E	Voltage-dependent calcium channel gamma-1 subunit	protein	166	61% helix, 11% strand	P19518
F	Voltage-dependent calcium channel subunit alpha-2/DELTA-1	protein	941	27% helix, 21% strand	P13806

Ligands and binding sites

PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 14 copies · 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	767	0.82	0.85	69	empty
2	1032	0.81	0.82	105	empty
3	667	0.81	0.85	73	empty
4	580	0.80	0.85	64	PC1, CA
5	231	0.77	0.91	36	empty

Interfaces

4 interfaces between chains.

A–F · 1858 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 1603 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1035 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 878 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 glycan, 11 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).

Compared structures

5GJV · Structure of the mammalian voltage-gated calcium channel Cav1.1 complex at near atomic… · the same entry in another collection · chain F against F, TM-score 1.00
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 0.99
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 0.99
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 0.97
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 0.91

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 P19517
Every structure of UniProt P19518
Every structure of UniProt P13806
Elsewhere: RCSB PDB 5GJV · PDBe 5GJV · UniProt P07293 · UniProt P19517 · UniProt P19518 · UniProt P13806

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