SMTL ID : 7w7f.1

Cryo-EM structure of human NaV1.3/beta1/beta2-ICA121431

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.280, W.315, N.339, C.352 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: 3 residues within 4Å: Chain C: N.1379, N.1380, 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: 1 residues within 4Å: Chain A: N.110 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.114 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain A: N.135 No protein-ligand interaction detected (PLIP) NAG.7: 6 residues within 4Å: Chain C: N.1366, T.1368, F.1373, D.1377, L.1387, Q.1390 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.1373 Hydrogen bonds: C:N.1366, C:Q.1390

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

6OU.8: 1 residues within 4Å: Ligands: 8DE.9 No protein-ligand interaction detected (PLIP) 6OU.10: 5 residues within 4Å: Chain C: A.1224, F.1225, D.1227, R.1233, F.1695 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.1224, C:F.1225, C:F.1225, C:F.1695 6OU.11: 13 residues within 4Å: Chain C: L.1343, W.1346, G.1404, A.1405, Y.1407, L.1408, P.1744, S.1745, I.1748, F.1749, V.1752, I.1756 Ligands: 6OU.22 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.1343, C:W.1346, C:Y.1407, C:L.1408, C:I.1748, C:F.1749, C:F.1749, C:V.1752, C:I.1756, C:I.1756 Hydrogen bonds: C:S.1745 6OU.12: 5 residues within 4Å: Chain C: T.146, F.894, F.930, F.933, Y.1443 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.146, C:F.894, C:Y.1443 Hydrogen bonds: C:S.148, C:Y.1443 6OU.13: 10 residues within 4Å: Chain C: G.362, S.370, W.371, F.373, Q.957, T.958, L.961, I.962 Ligands: 6OU.14, 6OU.15 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.373, C:L.961, C:I.962 Hydrogen bonds: C:Q.957 6OU.14: 6 residues within 4Å: Chain C: F.369, V.1541, T.1547 Ligands: 6OU.13, 6OU.15, 6OU.17 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.369, C:V.1541 6OU.15: 3 residues within 4Å: Chain C: I.962 Ligands: 6OU.13, 6OU.14 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.962 6OU.16: 3 residues within 4Å: Chain C: L.1538, T.1542, Y.1553 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.1538, C:T.1542 6OU.17: 2 residues within 4Å: Chain C: I.252 Ligands: 6OU.14 No protein-ligand interaction detected (PLIP) 6OU.18: 3 residues within 4Å: Chain C: I.1530, I.1534, C.1537 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.1530 6OU.20: 6 residues within 4Å: Chain C: T.399, Y.400, F.403, L.406, T.1618, V.1622 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.399, C:Y.400, C:F.403, C:L.406, C:V.1622 6OU.21: 4 residues within 4Å: Chain C: S.1302, T.1305, F.1672, S.1675 No protein-ligand interaction detected (PLIP) 6OU.22: 2 residues within 4Å: Chain C: Y.1407 Ligands: 6OU.11 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.1407 6OU.23: 2 residues within 4Å: Chain C: W.1272, N.1326 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.1272, C:W.1272 6OU.24: 1 residues within 4Å: Chain C: I.830 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.830 6OU.25: 3 residues within 4Å: Chain C: Y.1443, L.1446 Ligands: 6OU.26 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.1446 6OU.26: 2 residues within 4Å: Chain C: I.1450 Ligands: 6OU.25 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.1450

1 x 8DE: 2,2-diphenyl-~{N}-[4-(1,3-thiazol-2-ylsulfamoyl)phenyl]ethanamide(Non-covalent)

8DE.9: 11 residues within 4Å: Chain C: S.1559, N.1562, L.1563, S.1600, G.1603, M.1604, E.1608, R.1624, R.1627, R.1630 Ligands: 6OU.8 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.1563, C:E.1608 Hydrogen bonds: C:N.1562, C:R.1624, C:R.1627, C:R.1630, C:R.1630

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

9Z9.19: 9 residues within 4Å: Chain C: M.401, I.402, V.405, G.1659, F.1663, M.1666, G.1696, M.1699, F.1703 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.402, C:F.1663, C:M.1699, C:F.1703

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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