SMTL ID : 6nt4.1

Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-mer

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: 6 residues within 4Å: Chain A: T.356, W.360, N.384, C.397, Q.399 Chain C: D.9 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.1088 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.1069 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: N.366, H.369 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.366 NAG.5: 2 residues within 4Å: Chain A: N.362 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain A: N.354 No protein-ligand interaction detected (PLIP)

5 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.7: 5 residues within 4Å: Chain A: S.385, W.445, H.446, I.452, Y.1311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.445, A:W.445, A:I.452 Salt bridges: A:H.446 76F.8: 5 residues within 4Å: Chain A: S.636, W.637, N.682, M.685, T.689 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.637, A:M.685 76F.9: 9 residues within 4Å: Chain A: K.975, W.976, F.1010, F.1013, T.1026, V.1030, V.1033, F.1037, I.1451 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.975, A:F.1010, A:F.1013, A:T.1026, A:V.1033, A:F.1037, A:I.1451 Hydrogen bonds: A:W.976 76F.10: 6 residues within 4Å: Chain A: I.1040, I.1044, W.1047, H.1100, N.1103, R.1438 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.1040, A:I.1044, A:W.1047 Hydrogen bonds: A:N.1103 Salt bridges: A:H.1100, A:R.1438, A:R.1438, A:R.1438 76F.11: 7 residues within 4Å: Chain A: G.416, W.417, F.419, F.423, W.769, I.772, P.773 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.417, A:F.419, A:F.419, A:F.423, A:W.769, A:W.769, A:I.772, A:I.772

1 x AJP: Digitonin(Non-covalent)

AJP.12: 8 residues within 4Å: Chain A: F.1050, M.1053, L.1057, E.1129, N.1139, Y.1141, M.1142, F.1148 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1050, A:L.1057, A:F.1148, A:F.1148 Hydrogen bonds: A:N.1139

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

LHG.13: 10 residues within 4Å: Chain A: P.254, W.255, L.258, W.289, R.299, V.302, S.306, I.309, I.708, F.709 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.258, A:V.302, A:I.309, A:I.708, A:F.709, A:F.709

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.14: 8 residues within 4Å: Chain A: S.386, W.445, I.447, L.448, F.1354, G.1394, I.1397, I.1398 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.445, A:W.445, A:I.447, A:L.448, A:F.1354, A:I.1397, A:I.1398 Hydrogen bonds: A:S.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clairfeuille, T. et al., Structural basis of alpha-scorpion toxin action on Na v channels. Science (2019)

Release Date

2019-02-20

Peptides

Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha,Sodium channel protein PaFPC1: A
Alpha-mammal toxin AaH2: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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

Alpha-mammal toxin AaH2

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