SMTL ID : 6p6x.1

Crystal structure of voltage-gated sodium channel NavAb G94C/Q150C mutant in the activated state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

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

PX4.1: 18 residues within 4Å: Chain A: I.152, M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, M.227, L.230 Chain C: M.206, P.210, W.213, F.221 Ligands: PX4.2, PX4.6, PX4.9 Ligand excluded by PLIP PX4.2: 18 residues within 4Å: Chain A: A.153, T.156, L.157, Y.160, T.180, G.182 Chain D: V.41, G.44, I.45, G.48, L.49, T.51, S.52, K.53, T.54, L.124 Ligands: PX4.1, CPS.43 Ligand excluded by PLIP PX4.3: 17 residues within 4Å: Chain A: I.115, L.119, L.122 Chain C: F.162, M.165, L.169, F.170, R.173, V.208, Y.209, Y.211, A.212, V.214, V.222 Ligands: PX4.4, PX4.6, PX4.8 Ligand excluded by PLIP PX4.4: 14 residues within 4Å: Chain A: P.93, W.94, F.97, F.125, V.128, V.138, S.139, I.142 Chain C: V.222 Ligands: PX4.3, PX4.6, PX4.7, PX4.8, PX4.9 Ligand excluded by PLIP PX4.5: 9 residues within 4Å: Chain A: P.146, L.149, S.150, A.153 Chain D: V.41, V.131, M.134 Ligands: PX4.6, CPS.44 Ligand excluded by PLIP PX4.6: 10 residues within 4Å: Chain A: I.142, I.145, P.146, L.149 Ligands: PX4.1, PX4.3, PX4.4, PX4.5, PX4.7, PX4.9 Ligand excluded by PLIP PX4.7: 2 residues within 4Å: Ligands: PX4.4, PX4.6 Ligand excluded by PLIP PX4.8: 4 residues within 4Å: Chain A: L.96, F.100 Ligands: PX4.3, PX4.4 Ligand excluded by PLIP PX4.9: 13 residues within 4Å: Chain A: I.145, M.148, I.152, F.189, M.192 Chain C: F.221, T.224, F.225 Ligands: PX4.1, PX4.4, PX4.6, PX4.31, PX4.42 Ligand excluded by PLIP PX4.12: 18 residues within 4Å: Chain B: I.152, M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, M.227, L.230 Chain D: M.206, P.210, W.213, F.221 Ligands: PX4.13, PX4.17, PX4.20 Ligand excluded by PLIP PX4.13: 18 residues within 4Å: Chain B: A.153, T.156, L.157, Y.160, T.180, G.182 Chain C: V.41, G.44, I.45, G.48, L.49, T.51, S.52, K.53, T.54, L.124 Ligands: PX4.12, CPS.32 Ligand excluded by PLIP PX4.14: 17 residues within 4Å: Chain B: I.115, L.119, L.122 Chain D: F.162, M.165, L.169, F.170, R.173, V.208, Y.209, Y.211, A.212, V.214, V.222 Ligands: PX4.15, PX4.17, PX4.19 Ligand excluded by PLIP PX4.15: 14 residues within 4Å: Chain B: P.93, W.94, F.97, F.125, V.128, V.138, S.139, I.142 Chain D: V.222 Ligands: PX4.14, PX4.17, PX4.18, PX4.19, PX4.20 Ligand excluded by PLIP PX4.16: 9 residues within 4Å: Chain B: P.146, L.149, S.150, A.153 Chain C: V.41, V.131, M.134 Ligands: PX4.17, CPS.33 Ligand excluded by PLIP PX4.17: 10 residues within 4Å: Chain B: I.142, I.145, P.146, L.149 Ligands: PX4.12, PX4.14, PX4.15, PX4.16, PX4.18, PX4.20 Ligand excluded by PLIP PX4.18: 2 residues within 4Å: Ligands: PX4.15, PX4.17 Ligand excluded by PLIP PX4.19: 4 residues within 4Å: Chain B: L.96, F.100 Ligands: PX4.14, PX4.15 Ligand excluded by PLIP PX4.20: 13 residues within 4Å: Chain B: I.145, M.148, I.152, F.189, M.192 Chain D: F.221, T.224, F.225 Ligands: PX4.12, PX4.15, PX4.17, PX4.31, PX4.42 Ligand excluded by PLIP PX4.23: 18 residues within 4Å: Chain B: M.206, P.210, W.213, F.221 Chain C: I.152, M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, M.227, L.230 Ligands: PX4.24, PX4.28, PX4.31 Ligand excluded by PLIP PX4.24: 18 residues within 4Å: Chain A: V.41, G.44, I.45, G.48, L.49, T.51, S.52, K.53, T.54, L.124 Chain C: A.153, T.156, L.157, Y.160, T.180, G.182 Ligands: CPS.10, PX4.23 Ligand excluded by PLIP PX4.25: 17 residues within 4Å: Chain B: F.162, M.165, L.169, F.170, R.173, V.208, Y.209, Y.211, A.212, V.214, V.222 Chain C: I.115, L.119, L.122 Ligands: PX4.26, PX4.28, PX4.30 Ligand excluded by PLIP PX4.26: 14 residues within 4Å: Chain B: V.222 Chain C: P.93, W.94, F.97, F.125, V.128, V.138, S.139, I.142 Ligands: PX4.25, PX4.28, PX4.29, PX4.30, PX4.31 Ligand excluded by PLIP PX4.27: 9 residues within 4Å: Chain A: V.41, V.131, M.134 Chain C: P.146, L.149, S.150, A.153 Ligands: CPS.11, PX4.28 Ligand excluded by PLIP PX4.28: 10 residues within 4Å: Chain C: I.142, I.145, P.146, L.149 Ligands: PX4.23, PX4.25, PX4.26, PX4.27, PX4.29, PX4.31 Ligand excluded by PLIP PX4.29: 2 residues within 4Å: Ligands: PX4.26, PX4.28 Ligand excluded by PLIP PX4.30: 4 residues within 4Å: Chain C: L.96, F.100 Ligands: PX4.25, PX4.26 Ligand excluded by PLIP PX4.31: 13 residues within 4Å: Chain B: F.221, T.224, F.225 Chain C: I.145, M.148, I.152, F.189, M.192 Ligands: PX4.9, PX4.20, PX4.23, PX4.26, PX4.28 Ligand excluded by PLIP PX4.34: 18 residues within 4Å: Chain A: M.206, P.210, W.213, F.221 Chain D: I.152, M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, M.227, L.230 Ligands: PX4.35, PX4.39, PX4.42 Ligand excluded by PLIP PX4.35: 18 residues within 4Å: Chain B: V.41, G.44, I.45, G.48, L.49, T.51, S.52, K.53, T.54, L.124 Chain D: A.153, T.156, L.157, Y.160, T.180, G.182 Ligands: CPS.21, PX4.34 Ligand excluded by PLIP PX4.36: 17 residues within 4Å: Chain A: F.162, M.165, L.169, F.170, R.173, V.208, Y.209, Y.211, A.212, V.214, V.222 Chain D: I.115, L.119, L.122 Ligands: PX4.37, PX4.39, PX4.41 Ligand excluded by PLIP PX4.37: 14 residues within 4Å: Chain A: V.222 Chain D: P.93, W.94, F.97, F.125, V.128, V.138, S.139, I.142 Ligands: PX4.36, PX4.39, PX4.40, PX4.41, PX4.42 Ligand excluded by PLIP PX4.38: 9 residues within 4Å: Chain B: V.41, V.131, M.134 Chain D: P.146, L.149, S.150, A.153 Ligands: CPS.22, PX4.39 Ligand excluded by PLIP PX4.39: 10 residues within 4Å: Chain D: I.142, I.145, P.146, L.149 Ligands: PX4.34, PX4.36, PX4.37, PX4.38, PX4.40, PX4.42 Ligand excluded by PLIP PX4.40: 2 residues within 4Å: Ligands: PX4.37, PX4.39 Ligand excluded by PLIP PX4.41: 4 residues within 4Å: Chain D: L.96, F.100 Ligands: PX4.36, PX4.37 Ligand excluded by PLIP PX4.42: 13 residues within 4Å: Chain A: F.221, T.224, F.225 Chain D: I.145, M.148, I.152, F.189, M.192 Ligands: PX4.9, PX4.20, PX4.34, PX4.37, PX4.39 Ligand excluded by PLIP

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

CPS.10: 6 residues within 4Å: Chain A: L.49, S.52, T.54, F.55, S.58 Ligands: PX4.24 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.49, A:T.54, A:F.55 Hydrogen bonds: A:S.52, A:S.52 CPS.11: 7 residues within 4Å: Chain A: S.30, K.34, I.37, A.130, P.132, Q.133 Ligands: PX4.27 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.34, A:I.37 Hydrogen bonds: A:Q.133, A:Q.133 CPS.21: 6 residues within 4Å: Chain B: L.49, S.52, T.54, F.55, S.58 Ligands: PX4.35 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.49, B:T.54, B:F.55 Hydrogen bonds: B:S.52, B:S.52 CPS.22: 7 residues within 4Å: Chain B: S.30, K.34, I.37, A.130, P.132, Q.133 Ligands: PX4.38 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.34, B:I.37 Hydrogen bonds: B:Q.133, B:Q.133 CPS.32: 6 residues within 4Å: Chain C: L.49, S.52, T.54, F.55, S.58 Ligands: PX4.13 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.49, C:T.54, C:F.55 Hydrogen bonds: C:S.52, C:S.52 CPS.33: 7 residues within 4Å: Chain C: S.30, K.34, I.37, A.130, P.132, Q.133 Ligands: PX4.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.34, C:I.37 Hydrogen bonds: C:Q.133, C:Q.133 CPS.43: 6 residues within 4Å: Chain D: L.49, S.52, T.54, F.55, S.58 Ligands: PX4.2 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.49, D:T.54, D:F.55 Hydrogen bonds: D:S.52, D:S.52 CPS.44: 7 residues within 4Å: Chain D: S.30, K.34, I.37, A.130, P.132, Q.133 Ligands: PX4.5 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:K.34, D:I.37 Hydrogen bonds: D:Q.133, D:Q.133

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