SMTL ID : 7w77.1

cryo-EM structure of human NaV1.3/beta1/beta2-bulleyaconitineA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 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: 5 residues within 4Å: Chain C: N.275, W.315, N.339, C.352, K.354 No protein-ligand interaction detected (PLIP)

1 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: 4 residues within 4Å: Chain C: N.1379, N.1380, S.1382, D.1383 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: V.91, N.93, F.107 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: G.33, N.110 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: E.84, R.89, N.114 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: F.54, Y.124, N.135, S.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.137 NAG.7: 6 residues within 4Å: Chain C: N.1366, T.1368, T.1369, F.1373, L.1387, Q.1390 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.1373, C:L.1387, C:Q.1390 Hydrogen bonds: C:N.1366, C:T.1368

3 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.8: 5 residues within 4Å: Chain C: H.781, P.783, N.1402, V.1403 Ligands: 6OU.22 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.1402, C:V.1403 9Z9.9: 8 residues within 4Å: Chain C: V.771, L.775, L.861, S.864, W.865, P.866, L.1340, I.1344 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.771, C:L.775, C:L.861, C:W.865, C:P.866, C:L.1340, C:I.1344 9Z9.19: 8 residues within 4Å: Chain C: D.342, M.401, I.402, V.405, M.1666, G.1696, M.1699, F.1703 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.402, C:F.1703

16 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)(Covalent)(Non-functional Binders)

6OU.10: 3 residues within 4Å: Chain C: A.1224, F.1225, R.1233 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.1225 6OU.11: 12 residues within 4Å: Chain C: L.1343, W.1346, G.1404, A.1405, Y.1407, L.1411, P.1744, S.1745, I.1748, V.1752, I.1756 Ligands: 6OU.22 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.1343, C:W.1346, C:Y.1407, C:Y.1407, C:L.1411, C:I.1748 6OU.12: 6 residues within 4Å: Chain C: T.146, F.929, F.930, F.933, Y.1443, L.1446 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:T.146, C:F.929, C:F.930, C:F.933, C:F.933, C:F.933, C:L.1446 Hydrogen bonds: C:Y.1443 6OU.13: 9 residues within 4Å: Chain C: S.370, W.371, F.373, L.374, Q.957, T.958, L.961, M.965 Ligands: 6OU.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.373, C:F.373, C:L.374 Hydrogen bonds: C:G.362, C:S.370, C:Q.957 6OU.14: 4 residues within 4Å: Chain C: T.368, V.1541, V.1545 Ligands: 6OU.17 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.1541 Hydrogen bonds: C:T.368 6OU.15: 3 residues within 4Å: Chain C: T.958 Ligands: 6OU.13, 6OU.17 No protein-ligand interaction detected (PLIP) 6OU.16: 2 residues within 4Å: Chain C: Y.1553, M.1554 No protein-ligand interaction detected (PLIP) 6OU.17: 7 residues within 4Å: Chain C: I.252, V.255, S.259, F.373, M.1544 Ligands: 6OU.14, 6OU.15 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.255, C:F.373 6OU.18: 2 residues within 4Å: Chain C: I.1534, C.1537 No protein-ligand interaction detected (PLIP) 6OU.20: 4 residues within 4Å: Chain C: L.268, T.399, T.1618, V.1622 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.268, C:V.1622 6OU.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 6OU.22: 3 residues within 4Å: Chain C: L.1343 Ligands: 9Z9.8, 6OU.11 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.1343 6OU.23: 4 residues within 4Å: Chain C: A.1271, W.1272, L.1312, V.1325 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.1312 6OU.24: 1 residues within 4Å: Chain C: G.823 No protein-ligand interaction detected (PLIP) 6OU.25: 2 residues within 4Å: Chain C: Y.1443, I.1450 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.1450 6OU.26: 5 residues within 4Å: Chain C: L.847, V.849, M.1352, Y.1443, I.1450 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.847, C:V.849, C:I.1450

1 x 966: [(1S,2R,3R,4R,5R,6S,8R,9S,13S,16S,17R,18R)-11-ethyl-5-hydroxy-6,16,18-trimethoxy-4-(4-methoxybenzoyl)-13-(methoxymethyl)-11-azahexacyclo[7.7.2.12,5.01,10.03,8.013,17]nonadecan-8-yl] acetate(Covalent)

966.27: 14 residues within 4Å: Chain C: F.377, M.380, T.381, S.412, V.416, I.419, L.420, L.940, C.941, G.942, M.968, N.972, F.979, F.1416 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.381, C:V.416, C:N.972 Hydrogen bonds: C:Y.1766

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., Structural basis for modulation of human Na V 1.3 by clinical drug and selective antagonist. Nat Commun (2022)

Release Date

2022-04-06

Peptides

Sodium channel subunit beta-1: A
Sodium channel subunit beta-2: B
Sodium channel protein type 3 subunit alpha: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

Membrane

We predict this structure to be a membrane protein.
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Sodium channel subunit beta-1

Sodium channel subunit beta-2

Sodium channel protein type 3 subunit alpha

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