SMTL ID : 8x90.1

P/Q type calcium channel

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-NAG.1: 5 residues within 4Å: Chain B: V.107, R.114, E.121, N.184, W.185 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain B: N.346, N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: A.83, R.84, P.611, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.895, K.896, F.982 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG-NAG.3: 9 residues within 4Å: Chain B: Q.108, W.113, E.115, E.182, N.468, T.470, K.480, N.481, L.485 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.115, B:E.115

1 x PS1: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE](Non-covalent)

PS1.6: 19 residues within 4Å: Chain A: T.359, M.360, E.361, F.392, L.395, T.708, E.710, N.744, E.1502, V.1545, V.1549, A.1795, T.1796, G.1797, C.1840, M.1844, L.1845 Ligands: CLR.7, CA.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.392, A:F.392, A:L.395, A:V.1549, A:A.1795, A:M.1844 Hydrogen bonds: A:T.708, A:T.1796

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 10 residues within 4Å: Chain A: T.708, N.744, L.747, S.1499, T.1500, P.1541, F.1542, V.1545, S.1841 Ligands: PS1.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1542 CLR.12: 5 residues within 4Å: Chain A: L.624, F.1433, E.1528, M.1529, F.1532 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1433, A:F.1532 CLR.13: 3 residues within 4Å: Chain A: N.346, M.1626, F.1629 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.1626, A:F.1629, A:F.1629 CLR.16: 7 residues within 4Å: Chain A: I.1301, A.1302, A.1305, R.1315, V.1318, F.1322 Ligands: Y01.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1301, A:A.1302, A:A.1305, A:V.1318, A:V.1318, A:F.1322 CLR.17: 4 residues within 4Å: Chain A: N.1826, E.1827, F.1828, F.1831 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.1827, A:E.1827, A:F.1828, A:F.1831 Hydrogen bonds: A:N.1826

1 x PT5: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

PT5.8: 13 residues within 4Å: Chain A: S.591, S.592, F.593, L.630, K.634, W.639, L.642, R.643, V.646, L.649, I.656, V.1539, F.1543 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.630, A:L.642, A:L.649, A:I.656, A:V.1539, A:F.1543, A:F.1543, A:F.1543 Hydrogen bonds: A:S.591, A:S.592 Salt bridges: A:K.634

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: E.361, E.710, E.1502, G.1797 Ligands: PS1.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.361, A:E.361 CA.20: 4 residues within 4Å: Chain A: D.168 Chain B: S.261, S.263, T.331 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Metal complexes: A:D.168, B:S.261, B:S.263, B:T.331

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

NAG.10: 1 residues within 4Å: Chain A: N.326 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.326 NAG.21: 5 residues within 4Å: Chain B: D.85, K.88, L.89, N.92, E.199 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.89 Hydrogen bonds: B:E.199

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.11: 9 residues within 4Å: Chain A: L.663, F.664, P.697, I.700, M.701, M.1527, E.1528, I.1531, V.1534 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.663, A:F.664, A:P.697, A:P.697, A:I.700, A:M.1527, A:I.1531, A:V.1534, A:V.1534 Hydrogen bonds: A:E.1528 Y01.14: 5 residues within 4Å: Chain A: A.547, I.548, H.550, N.552, P.554 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.547, A:I.548 Salt bridges: A:H.550 Y01.15: 9 residues within 4Å: Chain A: I.1301, A.1304, A.1305, R.1315, F.1746, F.1784, F.1785 Ligands: CLR.16, 3PE.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1746, A:F.1784, A:F.1785, A:F.1785

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.18: 11 residues within 4Å: Chain A: N.376, W.380, I.384, A.1742, F.1745, T.1783, F.1785, Q.1786, L.1788, F.1792 Ligands: Y01.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.380, A:W.380, A:I.384, A:F.1745, A:F.1785, A:F.1785, A:L.1788, A:F.1792 3PE.19: 15 residues within 4Å: Chain A: F.283, I.286, F.290, Y.291, K.294, S.374, W.378, N.379, L.381, Y.382, L.1699, S.1700, F.1701, R.1703, L.1704 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.283, A:F.283, A:I.286, A:F.290, A:F.290, A:W.378, A:W.378, A:L.1699, A:L.1699, A:L.1704, A:L.1704 Hydrogen bonds: A:F.290, A:K.294, A:S.374, A:R.1703 Salt bridges: A:K.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z. et al., Structural basis for different omega-agatoxin IVA sensitivities of the P-type and Q-type Ca v 2.1 channels. Cell Res. (2024)

Release Date

2024-03-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent P/Q-type calcium channel subunit alpha-1A

Voltage-dependent calcium channel subunit alpha-2/delta-1

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

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