SMTL ID : 7miy.1

Human N-type voltage-gated calcium channel Cav2.2 at 3.1 Angstrom resolution

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: 4 residues within 4Å: Chain C: 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: 3 residues within 4Å: Chain C: A.83, P.611, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain C: E.567, N.568, L.591, A.893, 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: 10 residues within 4Å: Chain C: Q.108, W.113, E.115, N.468, T.470, T.477, L.479, K.480, N.481, L.485 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.115

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

NAG.6: 1 residues within 4Å: Chain A: N.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.256 NAG.18: 3 residues within 4Å: Chain C: K.88, N.92, E.199 No protein-ligand interaction detected (PLIP) NAG.19: 3 residues within 4Å: Chain C: F.780, N.781, K.782 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.781, C:K.782, 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: 5 residues within 4Å: Chain A: D.122 Chain C: D.259, 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

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 9 residues within 4Å: Chain A: F.617, I.620, P.650, I.653, L.654, M.1390, S.1393, I.1394, V.1397 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.617, A:F.617, A:I.620, A:P.650, A:P.650, A:I.653, A:L.654, A:L.654, A:V.1397 Y01.11: 7 residues within 4Å: Chain A: T.496, L.497, A.500, H.503, F.1294, V.1351, L.1352 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.496, A:A.500, A:F.1294, A:V.1351, A:L.1352 Salt bridges: A:H.503 Y01.12: 9 residues within 4Å: Chain A: I.1165, A.1168, A.1169, R.1179, F.1611, F.1641, L.1642 Ligands: CLR.13, 3PE.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.1165, A:I.1165, A:A.1168, A:F.1611, A:F.1641, A:L.1642 Salt bridges: A:R.1179, A:R.1179

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 7 residues within 4Å: Chain A: F.1292, F.1296, I.1299, E.1391, L.1392, F.1395 Ligands: PT5.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1292, A:F.1296, A:I.1299, A:E.1391, A:F.1395, A:F.1395 Hydrogen bonds: A:E.1391 CLR.10: 6 residues within 4Å: Chain A: N.299, L.301, V.1486, M.1489, M.1490, F.1492 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.301, A:V.1486, A:M.1490, A:F.1492, A:F.1492 CLR.13: 6 residues within 4Å: Chain A: L.1162, I.1165, P.1178, R.1179, A.1182 Ligands: Y01.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1162, A:I.1165, A:P.1178, A:R.1179, A:R.1179, A:A.1182 CLR.14: 3 residues within 4Å: Chain A: D.1682, F.1683, F.1686 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.1682, A:F.1683, A:F.1683, A:F.1686, A:F.1686, A:F.1686

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

3PE.15: 12 residues within 4Å: Chain A: N.329, T.330, W.333, A.1607, F.1610, T.1640, L.1642, Q.1643, L.1645, M.1646, F.1649 Ligands: Y01.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.333, A:W.333, A:A.1607, A:F.1610, A:F.1610, A:L.1642, A:L.1645, A:F.1649 Hydrogen bonds: A:Q.1643 3PE.16: 14 residues within 4Å: Chain A: F.232, M.236, F.237, I.240, F.244, Y.245, K.248, A.327, W.331, N.332, L.334, Y.335, F.1566, L.1569 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.232, A:F.237, A:I.240, A:W.331, A:W.331, A:L.334, A:Y.335, A:L.1569, A:L.1569

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: 19 residues within 4Å: Chain A: S.544, S.545, F.546, N.547, L.580, L.583, R.584, K.587, W.592, L.595, R.596, V.599, L.602, I.609, F.704, V.1401, V.1402, F.1406 Ligands: CLR.9 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.546, A:L.580, A:L.583, A:W.592, A:L.595, A:V.599, A:V.599, A:L.602, A:I.609, A:F.704, A:V.1401, A:V.1402, A:F.1406 Hydrogen bonds: A:S.544, A:F.546, A:K.587, A:W.592 Salt bridges: A:R.584, 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
Voltage-dependent L-type calcium channel subunit beta-3: B
Voltage-dependent calcium channel subunit alpha-2/delta-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

Membrane

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

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

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

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