SMTL ID : 8x93.1

P/Q type calcium channel in complex with omega-Agatoxin IVA

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: 3 residues within 4Å: Chain B: 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 B: 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: 4 residues within 4Å: Chain B: L.591, N.895, F.982, D.984 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: 10 residues within 4Å: Chain B: Q.108, W.113, E.115, E.182, N.468, T.470, T.477, K.480, N.481, L.485 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain B: S.261, S.263, T.331 Chain C: D.168 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.261, B:S.263, B:T.331, C:D.168 CA.10: 2 residues within 4Å: Chain C: E.1502 Ligands: CA.20 No protein-ligand interaction detected (PLIP) CA.20: 4 residues within 4Å: Chain C: E.361, E.710, E.1502 Ligands: CA.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.361, C:E.361, C:E.1502, C:E.1502

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

NAG.7: 4 residues within 4Å: Chain B: K.88, L.89, N.92, E.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.199 NAG.11: 1 residues within 4Å: Chain C: N.326 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.326

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.8: 11 residues within 4Å: Chain C: L.707, T.708, N.744, L.747, S.1499, T.1500, P.1541, F.1542, V.1545, I.1837, S.1841 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.747, C:T.1500, C:F.1542, C:V.1545 Hydrogen bonds: C:N.744 CLR.13: 8 residues within 4Å: Chain C: F.619, L.624, F.1433, V.1436, L.1440, E.1528, M.1529, F.1532 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.619, C:F.619, C:L.624, C:F.1433, C:L.1440, C:L.1440, C:E.1528, C:F.1532 CLR.14: 4 residues within 4Å: Chain C: N.346, I.347, M.1626, F.1629 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:M.1626, C:F.1629, C:F.1629 CLR.17: 4 residues within 4Å: Chain C: M.1298, R.1315, V.1318 Ligands: Y01.16 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.1315, C:V.1318, C:V.1318 CLR.18: 5 residues within 4Å: Chain C: S.1809, N.1826, E.1827, F.1828, F.1831 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:E.1827, C:F.1828, C:F.1831 Hydrogen bonds: C:S.1809, C:S.1809

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: 17 residues within 4Å: Chain C: S.592, F.593, L.627, L.630, R.631, K.634, W.639, L.642, R.643, L.645, V.646, L.650, M.653, I.656, V.1538, V.1539, F.1543 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.630, C:L.642, C:L.645, C:V.646, C:L.650, C:I.656, C:V.1538, C:V.1539, C:F.1543, C:F.1543, C:F.1543 Hydrogen bonds: C:S.592, C:W.639 Salt bridges: C:R.631, C:K.634, C:R.643

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.12: 11 residues within 4Å: Chain B: N.393 Chain C: F.664, I.667, P.697, I.700, M.701, M.1527, E.1528, S.1530, I.1531, V.1534 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.664, C:F.664, C:I.667, C:P.697, C:P.697, C:I.700, C:M.1527, C:I.1531, C:I.1531, C:V.1534 Hydrogen bonds: B:N.393 Y01.15: 8 residues within 4Å: Chain C: L.544, A.547, I.548, H.550, N.552, P.554, V.1488, L.1489 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.544, C:A.547, C:I.548, C:H.550, C:L.1489 Salt bridges: C:H.550 Y01.16: 8 residues within 4Å: Chain C: A.1304, A.1305, R.1315, F.1746, F.1784, F.1785 Ligands: CLR.17, 3PE.19 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.1746, C:F.1784, C:F.1785, C:F.1785 Salt bridges: C:R.1315

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

3PE.19: 10 residues within 4Å: Chain C: N.376, W.380, A.1742, F.1745, T.1783, F.1785, Q.1786, M.1789, F.1792 Ligands: Y01.16 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.380, C:W.380, C:W.380, C:F.1745, C:F.1745, C:F.1785, C:F.1785, C:F.1785, C:F.1792

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

Membrane

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

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

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

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