SMTL ID : 7vfw.1

Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to CaV2.2-blocker1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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 B: L.591, N.895, F.982 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 10 residues within 4Å: Chain B: 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 B: D.43, L.44, T.46, L.47, I.816, S.820, W.821, E.823, N.824, K.827 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.46

15 x R16: HEXADECANE(Non-covalent)

R16.4: 4 residues within 4Å: Chain A: S.1681, D.1682, F.1686 Ligands: R16.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.1682, A:F.1686, A:F.1686 R16.5: 6 residues within 4Å: Chain A: L.1352, W.1353, L.1355, F.1359, Y.1685, F.1693 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1352, A:W.1353, A:W.1353, A:W.1353, A:F.1359, A:Y.1685, A:F.1693 R16.7: 2 residues within 4Å: Chain A: I.653, V.1397 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1397, A:V.1397 R16.8: 9 residues within 4Å: Chain A: F.237, F.244, Y.245, W.331, N.332, L.334, P.338, I.1562, F.1566 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.237, A:F.244, A:W.331, A:P.338, A:F.1566, A:F.1566 R16.9: 5 residues within 4Å: Chain A: L.630, Q.676, K.681, F.684, S.685 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.630, A:Q.676 R16.10: 6 residues within 4Å: Chain A: L.301, F.302, I.304, M.683, F.684 Ligands: Y01.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.301, A:L.301, A:F.302, A:I.304, A:M.683, A:F.684 R16.11: 2 residues within 4Å: Chain A: G.165, W.166 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.166, A:W.166 R16.13: 2 residues within 4Å: Chain A: F.1492 Ligands: Y01.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1492 R16.14: 2 residues within 4Å: Chain A: P.1600, Y.1601 No protein-ligand interaction detected (PLIP) R16.15: 2 residues within 4Å: Chain A: F.1611 Ligands: Y01.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1611 R16.16: 2 residues within 4Å: Chain A: L.1186 Ligands: Y01.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1186 R16.17: 7 residues within 4Å: Chain A: N.329, W.333, I.337, L.1642, L.1645, M.1646, F.1649 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.333, A:I.337, A:L.1642, A:L.1645, A:L.1645, A:M.1646, A:F.1649 R16.18: 5 residues within 4Å: Chain A: N.1245, K.1248, V.1252, F.1683 Ligands: R16.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.1252, A:F.1683, A:F.1683 R16.19: 3 residues within 4Å: Chain A: L.577, F.1296, E.1391 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.577, A:F.1296, A:F.1296, A:E.1391 R16.20: 6 residues within 4Å: Chain A: L.1218, F.1272, Y.1613, I.1616, F.1683, F.1686 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1218, A:L.1218, A:F.1272, A:Y.1613, A:I.1616, A:F.1683, A:F.1686

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 8 residues within 4Å: Chain A: T.496, L.497, A.500, M.501, H.503, N.1350, V.1351, L.1352 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.501, A:L.1352 Salt bridges: A:H.503 Y01.12: 7 residues within 4Å: Chain A: N.299, I.300, L.301, V.1486, F.1492 Ligands: R16.10, R16.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.300, A:L.301, A:V.1486, A:F.1492, A:F.1492 Y01.21: 7 residues within 4Å: Chain A: I.1165, A.1168, R.1179, F.1611, F.1641 Ligands: R16.15, R16.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.1165, A:I.1165, A:F.1611, A:F.1641, A:F.1641 Salt bridges: A:R.1174, 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)

PT5.22: 16 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, V.1288, F.1292, F.1406 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.546, A:L.580, A:L.583, A:W.592, A:W.592, A:L.595, A:V.599, A:L.602, A:V.1288, A:F.1292, A:F.1406, A:F.1406, A:F.1406 Hydrogen bonds: A:S.544, A:S.545, A:S.545, A:F.546, A:N.547, A:R.584, A:R.584, A:R.596, A:R.596 Salt bridges: A:K.532, A:R.584, A:K.587, A:K.587, A:R.596

1 x 6I7: 5-(4-chlorophenyl)-1-(2-methoxyphenyl)-3-(2,2,6,6-tetramethyloxan-4-yl)pyrazole(Non-covalent)

6I7.23: 11 residues within 4Å: Chain A: L.348, L.1286, Y.1289, F.1359, V.1408, F.1411, V.1412, F.1693, S.1696, F.1697, L.1700 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.348, A:F.1359, A:F.1411, A:F.1411, A:V.1412, A:F.1693, A:L.1700

2 x CA: CALCIUM ION(Non-covalent)

CA.24: 4 residues within 4Å: Chain A: E.314, E.663, E.1365, G.1654 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.314, A:E.663, A:E.1365, A:E.1365 CA.25: 4 residues within 4Å: Chain A: D.122 Chain B: S.261, S.263, T.331 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:S.263, B:T.331, A:D.122

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

NAG.26: 3 residues within 4Å: Chain B: L.89, N.92, E.199 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.89 Hydrogen bonds: B:N.92, B:E.199 NAG.27: 1 residues within 4Å: Chain B: N.324 No protein-ligand interaction detected (PLIP) NAG.28: 2 residues within 4Å: Chain B: N.346, N.348 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.346 NAG.29: 4 residues within 4Å: Chain B: T.587, F.588, R.589, N.604 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.587 NAG.30: 4 residues within 4Å: Chain B: E.80, A.83, R.84, N.613 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.83, B:R.84 Hydrogen bonds: B:E.80, B:R.84, B:N.613 NAG.31: 4 residues within 4Å: Chain B: N.675, T.677, E.678, L.681 No protein-ligand interaction detected (PLIP) NAG.32: 1 residues within 4Å: Chain B: N.888 No protein-ligand interaction detected (PLIP) NAG.33: 6 residues within 4Å: Chain B: V.107, R.114, N.120, N.184, W.185, S.187 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.107 Hydrogen bonds: B:R.114, B:N.120, B: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
Voltage-dependent calcium channel subunit alpha-2/delta-1: B
Voltage-dependent L-type calcium channel subunit beta-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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 calcium channel subunit alpha-2/delta-1

Voltage-dependent L-type calcium channel subunit beta-1

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