SMTL ID : 6p6y.1

Crystal structure of voltage-gated sodium channel NavAb V100C/Q150C disulfide crosslinked mutant in the activated state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-tetramer

Ligands

8 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.1: 13 residues within 4Å: Chain A: V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Chain D: I.137, A.140 Ligands: CPS.2 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.151, A:L.230, A:A.233, A:I.234, A:D.237, A:A.238, A:I.241, D:I.137 Hydrogen bonds: A:V.144, A:G.147 CPS.2: 11 residues within 4Å: Chain A: A.140, S.143, V.144, A.238, I.241, L.242, K.245 Chain C: A.233, V.236, D.237 Ligands: CPS.1 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.144, A:A.238, A:I.241, A:L.242, C:V.236 Hydrogen bonds: A:S.143, A:S.143, A:K.245 CPS.8: 13 residues within 4Å: Chain B: V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Chain C: I.137, A.140 Ligands: CPS.9 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.151, B:L.230, B:A.233, B:I.234, B:D.237, B:A.238, B:I.241, C:I.137 Hydrogen bonds: B:V.144, B:G.147 CPS.9: 11 residues within 4Å: Chain B: A.140, S.143, V.144, A.238, I.241, L.242, K.245 Chain D: A.233, V.236, D.237 Ligands: CPS.8 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:V.236, B:V.144, B:A.238, B:I.241, B:L.242 Hydrogen bonds: B:S.143, B:S.143, B:K.245 CPS.15: 13 residues within 4Å: Chain A: I.137, A.140 Chain C: V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.16 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.151, C:L.230, C:A.233, C:I.234, C:D.237, C:A.238, C:I.241, A:I.137 Hydrogen bonds: C:V.144, C:G.147 CPS.16: 11 residues within 4Å: Chain B: A.233, V.236, D.237 Chain C: A.140, S.143, V.144, A.238, I.241, L.242, K.245 Ligands: CPS.15 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.144, C:A.238, C:I.241, C:L.242, B:V.236 Hydrogen bonds: C:S.143, C:S.143, C:K.245 CPS.22: 13 residues within 4Å: Chain B: I.137, A.140 Chain D: V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.23 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.151, D:L.230, D:A.233, D:I.234, D:D.237, D:A.238, D:I.241, B:I.137 Hydrogen bonds: D:V.144, D:G.147 CPS.23: 11 residues within 4Å: Chain A: A.233, V.236, D.237 Chain D: A.140, S.143, V.144, A.238, I.241, L.242, K.245 Ligands: CPS.22 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:V.144, D:A.238, D:I.241, D:L.242, A:V.236 Hydrogen bonds: D:S.143, D:S.143, D:K.245

20 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.3: 14 residues within 4Å: Chain A: A.153, T.156, L.157, Y.160, T.180, L.181, G.182 Chain D: V.41, I.45, G.48, S.52, T.54, L.127 Ligands: PX4.5 Ligand excluded by PLIP PX4.4: 7 residues within 4Å: Chain A: I.115 Chain C: F.162, M.165, R.173, Y.209, Y.211, A.212 Ligand excluded by PLIP PX4.5: 16 residues within 4Å: Chain A: M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.227, L.230 Chain C: M.206, P.210, W.213, F.221 Ligands: PX4.3 Ligand excluded by PLIP PX4.6: 8 residues within 4Å: Chain A: P.93, W.94, F.97, F.125, S.139, I.142 Chain C: F.158, V.222 Ligand excluded by PLIP PX4.7: 5 residues within 4Å: Chain A: M.227 Chain C: F.221, T.224 Ligands: PX4.21, PX4.28 Ligand excluded by PLIP PX4.10: 14 residues within 4Å: Chain B: A.153, T.156, L.157, Y.160, T.180, L.181, G.182 Chain C: V.41, I.45, G.48, S.52, T.54, L.127 Ligands: PX4.12 Ligand excluded by PLIP PX4.11: 7 residues within 4Å: Chain B: I.115 Chain D: F.162, M.165, R.173, Y.209, Y.211, A.212 Ligand excluded by PLIP PX4.12: 16 residues within 4Å: Chain B: M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.227, L.230 Chain D: M.206, P.210, W.213, F.221 Ligands: PX4.10 Ligand excluded by PLIP PX4.13: 8 residues within 4Å: Chain B: P.93, W.94, F.97, F.125, S.139, I.142 Chain D: F.158, V.222 Ligand excluded by PLIP PX4.14: 5 residues within 4Å: Chain B: M.227 Chain D: F.221, T.224 Ligands: PX4.21, PX4.28 Ligand excluded by PLIP PX4.17: 14 residues within 4Å: Chain A: V.41, I.45, G.48, S.52, T.54, L.127 Chain C: A.153, T.156, L.157, Y.160, T.180, L.181, G.182 Ligands: PX4.19 Ligand excluded by PLIP PX4.18: 7 residues within 4Å: Chain B: F.162, M.165, R.173, Y.209, Y.211, A.212 Chain C: I.115 Ligand excluded by PLIP PX4.19: 16 residues within 4Å: Chain B: M.206, P.210, W.213, F.221 Chain C: M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.227, L.230 Ligands: PX4.17 Ligand excluded by PLIP PX4.20: 8 residues within 4Å: Chain B: F.158, V.222 Chain C: P.93, W.94, F.97, F.125, S.139, I.142 Ligand excluded by PLIP PX4.21: 5 residues within 4Å: Chain B: F.221, T.224 Chain C: M.227 Ligands: PX4.7, PX4.14 Ligand excluded by PLIP PX4.24: 14 residues within 4Å: Chain B: V.41, I.45, G.48, S.52, T.54, L.127 Chain D: A.153, T.156, L.157, Y.160, T.180, L.181, G.182 Ligands: PX4.26 Ligand excluded by PLIP PX4.25: 7 residues within 4Å: Chain A: F.162, M.165, R.173, Y.209, Y.211, A.212 Chain D: I.115 Ligand excluded by PLIP PX4.26: 16 residues within 4Å: Chain A: M.206, P.210, W.213, F.221 Chain D: M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.227, L.230 Ligands: PX4.24 Ligand excluded by PLIP PX4.27: 8 residues within 4Å: Chain A: F.158, V.222 Chain D: P.93, W.94, F.97, F.125, S.139, I.142 Ligand excluded by PLIP PX4.28: 5 residues within 4Å: Chain A: F.221, T.224 Chain D: M.227 Ligands: PX4.7, PX4.14 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wisedchaisri, G. et al., Resting-State Structure and Gating Mechanism of a Voltage-Gated Sodium Channel. Cell (2019)

Release Date

2019-08-14

Peptides

Ion transport protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Membrane

We predict this structure to be a membrane protein.
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Ion transport protein