SMTL ID : 7vfu.1

Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to ziconotide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG-NAG-BMA.1: 3 residues within 4Å: Chain D: L.591, N.895, F.982 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 10 residues within 4Å: Chain D: Q.108, W.113, E.115, E.182, N.468, T.470, K.476, K.480, N.481, L.485 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 10 residues within 4Å: Chain D: D.43, L.44, T.46, L.47, I.816, S.820, W.821, E.823, N.824, K.827 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.46, D:T.46

18 x R16: HEXADECANE(Non-covalent)

R16.4: 6 residues within 4Å: Chain A: S.1666, S.1681, D.1682, F.1686 Ligands: R16.6, R16.21 Ligand excluded by PLIP R16.5: 8 residues within 4Å: Chain A: M.1290, M.1293, N.1350, L.1352, W.1353, L.1355, V.1689 Ligands: R16.6 Ligand excluded by PLIP R16.6: 7 residues within 4Å: Chain A: D.1682, Y.1685, F.1686, V.1689, F.1693 Ligands: R16.4, R16.5 Ligand excluded by PLIP R16.8: 8 residues within 4Å: Chain A: N.697, L.700, T.1363, P.1404, F.1405, N.1409, S.1696 Ligands: R16.9 Ligand excluded by PLIP R16.9: 8 residues within 4Å: Chain A: L.1279, L.1286, V.1408, V.1412, F.1693, F.1697, L.1700 Ligands: R16.8 Ligand excluded by PLIP R16.10: 7 residues within 4Å: Chain A: L.616, F.617, I.620, P.650, I.653, M.1390, V.1397 Ligand excluded by PLIP R16.11: 9 residues within 4Å: Chain A: F.237, F.244, Y.245, W.331, N.332, L.334, Y.335, P.338, L.1569 Ligand excluded by PLIP R16.12: 5 residues within 4Å: Chain A: L.630, Q.676, F.684, S.685, V.691 Ligand excluded by PLIP R16.13: 8 residues within 4Å: Chain A: L.301, F.302, I.304, V.679, M.683, S.686, F.687 Ligands: Y01.15 Ligand excluded by PLIP R16.14: 4 residues within 4Å: Chain A: G.165, W.166, L.200, K.214 Ligand excluded by PLIP R16.16: 5 residues within 4Å: Chain A: V.1486, M.1490, P.1496, Y.1499 Ligands: Y01.15 Ligand excluded by PLIP R16.17: 2 residues within 4Å: Chain A: P.1600, Y.1601 Ligand excluded by PLIP R16.18: 3 residues within 4Å: Chain A: A.1161, L.1265, Y.1601 Ligand excluded by PLIP R16.19: 1 residues within 4Å: Chain A: L.1186 Ligand excluded by PLIP R16.20: 6 residues within 4Å: Chain A: N.329, W.333, I.337, L.1642, L.1645, M.1646 Ligand excluded by PLIP R16.21: 6 residues within 4Å: Chain A: K.1248, V.1252, L.1256, F.1683 Ligands: R16.4, R16.23 Ligand excluded by PLIP R16.22: 5 residues within 4Å: Chain A: F.572, F.1292, F.1296, I.1299, E.1391 Ligand excluded by PLIP R16.23: 8 residues within 4Å: Chain A: L.1218, W.1219, I.1612, Y.1613, I.1616, F.1686, L.1694 Ligands: R16.21 Ligand excluded by PLIP

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 7 residues within 4Å: Chain A: T.496, L.497, A.500, M.501, H.503, N.1350, L.1352 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.496, A:L.497, A:A.500, A:M.501 Hydrogen bonds: A:H.503 Salt bridges: A:H.503 Y01.15: 9 residues within 4Å: Chain A: N.299, I.300, L.301, V.1486, M.1489, M.1490, F.1492 Ligands: R16.13, R16.16 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.300, A:L.301, A:L.301, A:V.1486, A:F.1492 Y01.24: 7 residues within 4Å: Chain A: I.1165, A.1168, A.1169, R.1179, F.1611, F.1641, L.1642 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.1165, A:I.1165, A:A.1168, A:A.1169, A:F.1611, A:F.1641, A:F.1641, A:L.1642, A:L.1642, A:L.1642 Salt bridges: A:R.1179, A:R.1179

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)

PT5.25: 21 residues within 4Å: Chain A: K.480, K.532, S.544, S.545, F.546, N.547, L.583, R.584, K.587, W.592, L.595, R.596, L.598, V.599, L.602, I.609, F.1292, V.1401, V.1402, F.1406, F.1407 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.583, A:L.595, A:L.598, A:V.599, A:I.609, A:F.1292, A:F.1292, A:V.1402, A:F.1406, A:F.1406, A:F.1406, A:F.1406, A:F.1407 Hydrogen bonds: A:S.544, A:S.545, A:F.546, A:N.547 Salt bridges: A:K.480, A:K.532, A:R.584, A:K.587, A:K.587

2 x CA: CALCIUM ION(Non-covalent)

CA.26: 4 residues within 4Å: Chain A: D.122 Chain D: S.261, S.263, T.331 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Metal complexes: A:D.122, D:S.263, D:T.331 CA.27: 4 residues within 4Å: Chain A: E.314, E.663, E.1365, E.1655 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.314, A:E.314, A:E.663, A:E.1365

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

NAG.28: 3 residues within 4Å: Chain D: L.89, N.92, E.199 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.89 Hydrogen bonds: D:N.92, D:E.199 NAG.29: 1 residues within 4Å: Chain D: N.324 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain D: N.346, N.348 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:N.346 NAG.31: 4 residues within 4Å: Chain D: T.587, F.588, R.589, N.604 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:T.587 NAG.32: 4 residues within 4Å: Chain D: E.80, A.83, R.84, N.613 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.83, D:R.84 Hydrogen bonds: D:E.80, D:R.84, D:N.613 NAG.33: 4 residues within 4Å: Chain D: N.675, T.677, E.678, L.681 No protein-ligand interaction detected (PLIP) NAG.34: 1 residues within 4Å: Chain D: N.888 No protein-ligand interaction detected (PLIP) NAG.35: 6 residues within 4Å: Chain D: V.107, R.114, N.120, N.184, W.185, S.187 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.107 Hydrogen bonds: D:R.114, D:N.120, D:S.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, Y. et al., Closed-state inactivation and pore-blocker modulation mechanisms of human Ca V 2.2. Cell Rep (2021)

Release Date

2021-11-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
D

D
B

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 L-type calcium channel subunit beta-1

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

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