SMTL ID : 7mix.1

Human N-type voltage-gated calcium channel Cav2.2 in the presence of ziconotide at 3.0 Angstrom resolution

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: 5 residues within 4Å: Chain C: Q.112, R.114, N.120, 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: 4 residues within 4Å: Chain C: A.83, T.610, P.611, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain C: N.568, L.591, A.893, F.894, 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: 12 residues within 4Å: Chain C: Q.108, W.113, E.115, E.182, N.468, T.470, K.476, T.477, L.479, K.480, N.481, L.485 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.115, A:R.1320

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

NAG.6: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP) NAG.18: 6 residues within 4Å: Chain C: D.85, K.88, L.89, N.92, E.199, D.200 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.85 NAG.19: 3 residues within 4Å: Chain C: F.780, N.781, K.782 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.782

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: E.314, E.663, E.1365, G.1654 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.314, A:E.663, A:E.1365 CA.20: 4 residues within 4Å: Chain A: D.122 Chain C: S.261, S.263, T.331 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:S.261, C:S.263, C:T.331, A:D.122

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 12 residues within 4Å: Chain A: L.613, L.616, F.617, I.620, P.650, I.653, L.654, M.1390, S.1393, I.1394, V.1397 Chain C: N.393 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.616, A:F.617, A:I.620, A:I.653, A:I.653, A:L.654, A:M.1390, A:I.1394, A:V.1397 Hydrogen bonds: C:N.393 Y01.11: 8 residues within 4Å: Chain A: T.496, L.497, A.500, H.503, F.1294, N.1350, V.1351, L.1352 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.496, A:L.497, A:A.500, A:H.503, A:F.1294, A:V.1351

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 12 residues within 4Å: Chain A: F.572, L.577, F.1292, F.1296, I.1299, L.1303, E.1391, L.1392, I.1394, F.1395, V.1398 Ligands: PT5.17 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.577, A:F.1292, A:F.1296, A:I.1299, A:L.1303, A:E.1391, A:I.1394, A:F.1395, A:V.1398, A:V.1398 Hydrogen bonds: A:E.1391 CLR.10: 5 residues within 4Å: Chain A: N.299, V.1486, M.1489, M.1490, F.1492 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.1486, A:M.1490, A:F.1492, A:F.1492 CLR.12: 5 residues within 4Å: Chain A: I.1165, A.1169, R.1179, L.1642 Ligands: CLR.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1165, A:L.1642 CLR.13: 6 residues within 4Å: Chain A: L.1162, I.1165, P.1178, R.1179, L.1186 Ligands: CLR.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.1165, A:P.1178, A:R.1179 CLR.14: 4 residues within 4Å: Chain A: S.1666, S.1681, D.1682, F.1686 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.1682, A:F.1686 Hydrogen bonds: A:S.1666

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

3PE.15: 10 residues within 4Å: Chain A: N.329, T.330, W.333, F.345, T.1640, L.1642, Q.1643, L.1645, F.1649, M.1699 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.333, A:W.333, A:L.1642, A:F.1649, A:F.1649 Hydrogen bonds: A:Q.1643 3PE.16: 15 residues within 4Å: Chain A: M.236, F.237, I.240, F.244, Y.245, K.248, A.327, W.331, N.332, L.334, Y.335, N.1563, F.1566, L.1569, A.1573 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.237, A:F.237, A:I.240, A:F.244, A:W.331, A:Y.335, A:L.1569, A:A.1573 Hydrogen bonds: A:A.327, A:N.1563 Salt bridges: A:K.248

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)

PT5.17: 15 residues within 4Å: Chain A: S.544, S.545, F.546, L.583, R.584, K.587, W.592, L.595, R.596, L.598, V.599, L.602, F.1292, F.1406 Ligands: CLR.9 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.546, A:L.583, A:W.592, A:L.595, A:L.598, A:V.599, A:L.602, A:F.1292, A:F.1406, A:F.1406 Hydrogen bonds: A:S.545, A:S.545, A:F.546, A:R.596 Salt bridges: A:R.584, A:K.587, A:K.587

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, S. et al., Structure of human Ca v 2.2 channel blocked by the painkiller ziconotide. Nature (2021)

Release Date

2021-07-07

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent N-type calcium channel subunit alpha-1B

Omega-conotoxin MVIIA

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

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

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