SMTL ID : 8x91.1

P/Q type calcium channel in complex with omega-conotoxin MVIIC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-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: 4 residues within 4Å: Chain C: 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: 1 residues within 4Å: Chain C: N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain C: E.80, A.83, R.84, T.610, P.611, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.568, L.591, N.895, 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: 8 residues within 4Å: Chain C: Q.108, W.113, E.115, N.468, T.470, K.480, N.481, L.485 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain C: N.92, E.199 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.199 NAG.11: 1 residues within 4Å: Chain D: N.326 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.326

3 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain C: S.261, S.263, T.331 Chain D: D.168 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:S.261, C:S.263, C:T.331, D:D.168 CA.10: 5 residues within 4Å: Chain D: E.361, E.710, E.1502, G.1797, E.1798 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.361 CA.21: 1 residues within 4Å: Chain D: E.1502 No protein-ligand interaction detected (PLIP)

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.8: 12 residues within 4Å: Chain D: L.707, T.708, N.744, L.747, Y.1426, F.1496, S.1499, T.1500, P.1541, F.1542, V.1545, S.1841 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.1496, D:F.1542, D:V.1545 Hydrogen bonds: D:L.707 CLR.13: 7 residues within 4Å: Chain D: F.619, L.624, F.1429, F.1433, E.1528, M.1529, F.1532 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.619, D:F.1429, D:F.1433, D:F.1433, D:F.1532, D:F.1532 CLR.14: 4 residues within 4Å: Chain D: N.346, I.1623, M.1626, F.1629 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.1623, D:M.1626, D:F.1629, D:F.1629 CLR.17: 5 residues within 4Å: Chain D: I.1301, A.1302, R.1315, F.1322 Ligands: Y01.16 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.1301, D:A.1302, D:F.1322, D:F.1322 CLR.18: 8 residues within 4Å: Chain D: N.1382, S.1386, V.1389, V.1392, L.1393, V.1755, N.1826, F.1828 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.1389, D:V.1389, D:V.1392, D:V.1755, D:F.1828

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)

PT5.9: 14 residues within 4Å: Chain D: S.591, F.593, L.627, L.630, K.634, W.639, L.642, R.643, V.646, L.650, M.653, I.656, V.1539, F.1543 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.630, D:L.642, D:V.646, D:L.650, D:I.656, D:V.1539, D:F.1543, D:F.1543, D:F.1543 Hydrogen bonds: D:S.592 Salt bridges: D:K.634

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.12: 10 residues within 4Å: Chain C: N.393 Chain D: L.663, F.664, I.667, P.697, I.700, M.701, M.1527, I.1531, V.1534 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.663, D:F.664, D:P.697, D:I.700, D:M.1527, D:I.1531, D:V.1534, D:V.1534 Hydrogen bonds: C:N.393 Y01.15: 6 residues within 4Å: Chain D: A.547, I.548, H.550, N.552, P.554, V.1488 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.547, D:V.1488 Salt bridges: D:H.550 Y01.16: 9 residues within 4Å: Chain D: I.1301, A.1304, A.1305, R.1315, F.1746, F.1784, F.1785 Ligands: CLR.17, 3PE.19 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.1746, D:F.1784, D:F.1785, D:F.1785 Salt bridges: D:R.1315

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

3PE.19: 10 residues within 4Å: Chain D: N.376, W.380, I.384, A.1742, F.1745, T.1783, F.1785, M.1789, F.1792 Ligands: Y01.16 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.380, D:I.384, D:F.1745, D:F.1785, D:F.1785, D:M.1789, D:F.1792 Hydrogen bonds: D:Q.1786 3PE.20: 12 residues within 4Å: Chain D: F.283, F.290, Y.291, K.294, S.374, W.378, N.379, L.381, N.1698, S.1700, F.1701, R.1703 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.283, D:F.290, D:F.290, D:Y.291, D:W.378, D:W.378, D:W.378, D:W.378, D:W.378, D:L.381, D:F.1701, D:F.1701 Hydrogen bonds: D:S.374, D:N.379, D:S.1700, D:R.1703

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
X

C
B

D
A

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent L-type calcium channel subunit beta-3

Omega-conotoxin MVIIC

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

Voltage-dependent P/Q-type calcium channel subunit alpha-1A

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