SMTL ID : 7vfv.1

Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to PD173212

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

16 x R16: HEXADECANE(Non-covalent)

R16.4: 5 residues within 4Å: Chain A: S.1681, D.1682, F.1686 Ligands: R16.6, R16.19 Ligand excluded by PLIP R16.5: 5 residues within 4Å: Chain A: M.1293, L.1352, W.1353, F.1359 Ligands: R16.6 Ligand excluded by PLIP R16.6: 6 residues within 4Å: Chain A: W.1353, D.1682, F.1686, V.1689 Ligands: R16.4, R16.5 Ligand excluded by PLIP R16.8: 2 residues within 4Å: Chain A: I.653, V.1397 Ligand excluded by PLIP R16.9: 9 residues within 4Å: Chain A: F.237, F.244, Y.245, W.331, N.332, L.334, P.338, I.1562, F.1566 Ligand excluded by PLIP R16.10: 5 residues within 4Å: Chain A: L.630, Q.676, K.681, F.684, S.685 Ligand excluded by PLIP R16.11: 6 residues within 4Å: Chain A: L.301, F.302, I.304, M.683, F.684 Ligands: Y01.13 Ligand excluded by PLIP R16.12: 2 residues within 4Å: Chain A: G.165, W.166 Ligand excluded by PLIP R16.14: 2 residues within 4Å: Chain A: F.1492 Ligands: Y01.13 Ligand excluded by PLIP R16.15: 3 residues within 4Å: Chain A: P.1600, Y.1601 Ligands: Y01.22 Ligand excluded by PLIP R16.16: 2 residues within 4Å: Chain A: F.1611 Ligands: Y01.22 Ligand excluded by PLIP R16.17: 2 residues within 4Å: Chain A: L.1186 Ligands: Y01.22 Ligand excluded by PLIP R16.18: 7 residues within 4Å: Chain A: N.329, W.333, I.337, L.1642, L.1645, M.1646, F.1649 Ligand excluded by PLIP R16.19: 6 residues within 4Å: Chain A: N.1245, K.1248, V.1252, L.1256, F.1683 Ligands: R16.4 Ligand excluded by PLIP R16.20: 3 residues within 4Å: Chain A: L.577, F.1296, E.1391 Ligand excluded by PLIP R16.21: 6 residues within 4Å: Chain A: L.1218, W.1219, Y.1613, I.1616, F.1683, F.1686 Ligand excluded by PLIP

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 7 residues within 4Å: Chain A: T.496, 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 Y01.13: 7 residues within 4Å: Chain A: N.299, I.300, L.301, V.1486, F.1492 Ligands: R16.11, R16.14 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 Y01.22: 9 residues within 4Å: Chain A: I.1165, A.1169, R.1179, F.1611, F.1641, L.1642 Ligands: R16.15, R16.16, R16.17 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.1165, A:I.1165, A:A.1169, A:F.1611, A:F.1641, 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)

PT5.23: 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 6IX: (2~{S})-~{N}-[(2~{S})-1-(~{tert}-butylamino)-1-oxidanylidene-3-(4-phenylmethoxyphenyl)propan-2-yl]-2-[(4-~{tert}-butylphenyl)methyl-methyl-amino]-4-methyl-pentanamide(Covalent)

6IX.24: 18 residues within 4Å: Chain A: M.313, F.345, L.348, L.352, L.1286, Y.1289, F.1359, S.1362, T.1363, F.1403, V.1408, F.1411, A.1652, I.1692, F.1693, S.1696, L.1700, F.1703 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.348, A:L.352, A:L.1286, A:Y.1289, A:Y.1289, A:T.1363, A:V.1408, A:F.1411, A:F.1411, A:F.1411, A:I.1692, A:F.1693, A:F.1693, A:L.1700, A:L.1700, A:F.1703

2 x CA: CALCIUM ION(Non-covalent)

CA.25: 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.26: 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.27: 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.28: 1 residues within 4Å: Chain B: N.324 No protein-ligand interaction detected (PLIP) NAG.29: 2 residues within 4Å: Chain B: N.346, N.348 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.346 NAG.30: 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.31: 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.32: 4 residues within 4Å: Chain B: N.675, T.677, E.678, L.681 No protein-ligand interaction detected (PLIP) NAG.33: 1 residues within 4Å: Chain B: N.888 No protein-ligand interaction detected (PLIP) NAG.34: 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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