SMTL ID : 6vxo.1

NaChBac-Nav1.7VSDII chimera in nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 11 residues within 4Å: Chain A: L.34, I.42, Y.45, R.47, I.48 Chain D: I.156, Y.159, L.180, Q.181, L.184 Ligands: POV.6 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.156, D:Y.159, D:L.180, D:Q.181, A:L.34, A:I.42 Salt bridges: A:R.47 POV.2: 12 residues within 4Å: Chain A: F.205, A.206, P.209, W.210, W.212, L.213 Chain B: Q.181, L.182, L.184, L.185, F.188 Ligands: POV.8 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.210, A:W.212, A:W.212, A:W.212, A:L.213, B:L.185, B:F.188 Hydrogen bonds: B:Q.181 POV.3: 12 residues within 4Å: Chain A: L.153, F.157, F.161, E.207, V.208, P.209, W.210, S.211, L.213 Chain B: L.95, S.113, V.114 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.153, A:F.157, A:F.157, A:F.161, A:F.161, A:W.210, A:W.210, A:L.213, B:L.95 Hydrogen bonds: B:S.113 POV.4: 11 residues within 4Å: Chain A: I.156, Y.159, L.180, Q.181, L.184 Chain B: L.34, I.42, Y.45, R.47, I.48 Ligands: POV.10 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.156, A:Y.159, A:L.180, A:Q.181, B:L.34, B:I.42 Salt bridges: B:R.47 POV.5: 12 residues within 4Å: Chain B: L.153, F.157, F.161, E.207, V.208, P.209, W.210, S.211, L.213 Chain C: L.95, S.113, V.114 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:L.95, B:L.153, B:F.157, B:F.157, B:F.161, B:F.161, B:W.210, B:W.210, B:L.213 Hydrogen bonds: C:S.113 POV.6: 12 residues within 4Å: Chain C: F.205, A.206, P.209, W.210, W.212, L.213 Chain D: Q.181, L.182, L.184, L.185, F.188 Ligands: POV.1 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.210, C:W.212, C:W.212, C:W.212, C:L.213, D:L.185, D:F.188 Hydrogen bonds: D:Q.181 POV.7: 12 residues within 4Å: Chain C: L.153, F.157, F.161, E.207, V.208, P.209, W.210, S.211, L.213 Chain D: L.95, S.113, V.114 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.153, C:F.157, C:F.157, C:F.161, C:F.161, C:W.210, C:W.210, C:L.213, D:L.95 Hydrogen bonds: D:S.113 POV.8: 11 residues within 4Å: Chain B: I.156, Y.159, L.180, Q.181, L.184 Chain C: L.34, I.42, Y.45, R.47, I.48 Ligands: POV.2 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.156, B:Y.159, B:L.180, B:Q.181, C:L.34, C:I.42 Salt bridges: C:R.47 POV.9: 12 residues within 4Å: Chain B: F.205, A.206, P.209, W.210, W.212, L.213 Chain C: Q.181, L.182, L.184, L.185, F.188 Ligands: POV.12 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.185, C:F.188, B:W.210, B:W.212, B:W.212, B:W.212, B:L.213 Hydrogen bonds: C:Q.181 POV.10: 12 residues within 4Å: Chain A: Q.181, L.182, L.184, L.185, F.188 Chain D: F.205, A.206, P.209, W.210, W.212, L.213 Ligands: POV.4 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:W.210, D:W.212, D:W.212, D:W.212, D:W.212, D:L.213, A:L.185, A:F.188 Hydrogen bonds: A:Q.181 POV.11: 12 residues within 4Å: Chain A: L.95, S.113, V.114 Chain D: L.153, F.157, F.161, E.207, V.208, P.209, W.210, S.211, L.213 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: A:L.95, D:L.153, D:F.157, D:F.157, D:F.161, D:F.161, D:W.210, D:W.210, D:L.213 Hydrogen bonds: A:S.113 POV.12: 11 residues within 4Å: Chain C: I.156, Y.159, L.180, Q.181, L.184 Chain D: L.34, I.42, Y.45, R.47, I.48 Ligands: POV.9 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.34, D:I.42, C:I.156, C:Y.159, C:L.180, C:Q.181 Salt bridges: D:R.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, S. et al., Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na+channels in nanodisc. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-06-24

Peptides

NaChBac-Nav1.7VSDII chimera: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

Membrane

We predict this structure to be a membrane protein.
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NaChBac-Nav1.7VSDII chimera

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