SMTL ID : 6nt3.1

Cryo-EM structure of a human-cockroach hybrid Nav channel.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA.1: 7 residues within 4Å: Chain A: F.346, T.356, W.360, N.384, C.397, L.398, Q.399 No protein-ligand interaction detected (PLIP)

2 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: 1 residues within 4Å: Chain A: N.366 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.362 No protein-ligand interaction detected (PLIP)

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.4: 1 residues within 4Å: Chain A: N.1082 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1082 NAG.5: 2 residues within 4Å: Chain A: H.1086, N.1088 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1088 NAG.6: 2 residues within 4Å: Chain A: E.1068, N.1069 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1069 NAG.7: 1 residues within 4Å: Chain A: N.354 No protein-ligand interaction detected (PLIP)

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 5 residues within 4Å: Chain A: W.445, I.447, I.451, F.1358, G.1394 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.445, A:I.451, A:F.1358 Hydrogen bonds: A:S.386, A:W.445

4 x 76F: (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate(Non-covalent)

76F.9: 3 residues within 4Å: Chain A: L.333, S.1314, T.1316 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.333 Hydrogen bonds: A:S.1314, A:S.1314, A:T.1316 76F.10: 8 residues within 4Å: Chain A: K.975, W.976, F.1010, F.1013, S.1017, V.1030, I.1036, I.1451 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.975, A:F.1013, A:I.1036, A:I.1451 Hydrogen bonds: A:S.1017 Salt bridges: A:K.975 76F.11: 4 residues within 4Å: Chain A: I.1044, H.1100, L.1158, R.1438 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1044, A:L.1158 Salt bridges: A:H.1100, A:R.1438, A:R.1438, A:R.1438 76F.12: 5 residues within 4Å: Chain A: T.414, W.417, F.419, W.769, I.772 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.419, A:F.419, A:I.772, A:I.772

1 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.13: 6 residues within 4Å: Chain A: P.254, W.255, W.289, V.302, F.709, V.781 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.709, A:F.709, A:V.781

1 x AJP: Digitonin(Non-covalent)

AJP.14: 10 residues within 4Å: Chain A: F.1050, M.1053, L.1057, R.1128, T.1138, N.1139, Y.1141, L.1144, Y.1145, F.1148 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1050, A:L.1144, A:F.1148 Hydrogen bonds: A:R.1128, A:T.1138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clairfeuille, T. et al., Cryo-EM structures of a human-cockroach hybrid Nav channel in the presence and absence of the alpha-scorpion toxin AaH2. Science (2019)

Release Date

2019-02-20

Peptides

Sodium channel protein type 9 subunit alpha, Sodium channel protein PaFPC1, chimeric construct: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 9 subunit alpha, Sodium channel protein PaFPC1, chimeric construct

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