SMTL ID : 8fd7.1

Structure of the human L-type voltage-gated calcium channel Cav1.2 complexed with gabapentin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: L.593, F.896, N.897 No protein-ligand interaction detected (PLIP)

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: R.116, N.122, N.186, W.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.116, A:R.116, A:N.186, A:N.186 NAG.4: 5 residues within 4Å: Chain A: D.87, K.90, L.91, N.94, E.201 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.90 Hydrogen bonds: A:E.201 NAG.5: 8 residues within 4Å: Chain A: Q.110, N.470, T.472, T.479, K.482, N.483, L.487 Ligands: NAG.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.487 Hydrogen bonds: A:Q.110, A:T.479, A:K.482, A:K.482, A:N.483 NAG.6: 2 residues within 4Å: Chain A: W.115 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: N.677, T.679, E.680 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.677 NAG.8: 4 residues within 4Å: Chain A: D.45, L.49, N.826 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.49 NAG.9: 3 residues within 4Å: Chain A: L.49, T.52 Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain A: N.890 No protein-ligand interaction detected (PLIP)

1 x GBN: [1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID(Non-covalent)

GBN.3: 10 residues within 4Å: Chain A: W.207, V.209, Y.219, Y.238, R.243, W.245, Y.452, D.454, A.455, D.493 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.207, A:V.209, A:Y.219, A:A.455 Hydrogen bonds: A:Y.238, A:Y.238, A:D.454, A:A.455, A:D.493 Salt bridges: A:R.243

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.11: 4 residues within 4Å: Chain A: S.263, S.265, T.333 Chain B: D.151 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.263, A:S.265, A:T.333 CA.18: 1 residues within 4Å: Ligands: WO9.13 No protein-ligand interaction detected (PLIP) CA.19: 4 residues within 4Å: Chain B: E.363, E.706, E.1115, G.1415 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.363

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 1 residues within 4Å: Chain A: W.448 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.448

1 x WO9: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl heptadecanoate(Non-covalent)

WO9.13: 11 residues within 4Å: Chain B: V.275, M.353, L.354, F.357, T.361, V.396, T.704, I.738, N.741, F.1114 Ligands: CA.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.275, B:V.396, B:I.738

1 x YSW: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl dodecanoate(Non-covalent)

YSW.14: 5 residues within 4Å: Chain B: A.235, F.239, Y.719, P.725, V.729 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.235, B:F.239

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.15: 1 residues within 4Å: Chain B: F.1247 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.1247, B:F.1247 CLR.16: 5 residues within 4Å: Chain B: A.542, H.545, N.1100, V.1101, L.1102 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.542, B:H.545, B:N.1100, B:V.1101, B:L.1102, B:L.1102 CLR.17: 6 residues within 4Å: Chain B: N.348, F.349, I.1234, A.1237, M.1238, H.1240 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.349, B:I.1234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., Structural basis for Ca V alpha 2 delta :gabapentin binding. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-03-22

Peptides

Voltage-dependent calcium channel subunit alpha-2/delta-1: A
Voltage-dependent L-type calcium channel subunit alpha-1C: B
Voltage-dependent L-type calcium channel subunit beta-3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
K

C
C

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent calcium channel subunit alpha-2/delta-1

Voltage-dependent L-type calcium channel subunit alpha-1C

Voltage-dependent L-type calcium channel subunit beta-3

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