SMTL ID : 8dj1.1

Crystal structure of NavAb V126T as a basis for the human Nav1.7 Inherited Erythromelalgia S241T mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-tetramer

Ligands

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

PX4.1: 17 residues within 4Å: Chain A: I.152, M.155, T.156, F.159, G.182, E.183, F.185, Y.186, F.189, M.192, M.227 Chain C: M.206, P.210, W.213, I.217 Ligands: PX4.4, PX4.19 Ligand excluded by PLIP PX4.2: 7 residues within 4Å: Chain A: P.93, W.94, F.97, F.125, S.139, I.142 Chain C: V.222 Ligand excluded by PLIP PX4.3: 10 residues within 4Å: Chain A: I.115 Chain C: F.162, L.169, R.173, Y.209, P.210, Y.211, A.212, V.214, F.215 Ligand excluded by PLIP PX4.4: 17 residues within 4Å: Chain A: T.156, L.157, Y.160, T.180, L.181, G.182, F.185 Chain D: I.40, G.44, I.45, G.48, L.49, T.51, S.52, T.54, L.127 Ligands: PX4.1 Ligand excluded by PLIP PX4.5: 8 residues within 4Å: Chain A: L.194, F.221, T.224 Chain D: L.194, M.227 Ligands: PX4.19, PX4.22, PX4.26 Ligand excluded by PLIP PX4.8: 17 residues within 4Å: Chain B: I.152, M.155, T.156, F.159, G.182, E.183, F.185, Y.186, F.189, M.192, M.227 Chain D: M.206, P.210, W.213, I.217 Ligands: PX4.11, PX4.26 Ligand excluded by PLIP PX4.9: 7 residues within 4Å: Chain B: P.93, W.94, F.97, F.125, S.139, I.142 Chain D: V.222 Ligand excluded by PLIP PX4.10: 10 residues within 4Å: Chain B: I.115 Chain D: F.162, L.169, R.173, Y.209, P.210, Y.211, A.212, V.214, F.215 Ligand excluded by PLIP PX4.11: 17 residues within 4Å: Chain B: T.156, L.157, Y.160, T.180, L.181, G.182, F.185 Chain C: I.40, G.44, I.45, G.48, L.49, T.51, S.52, T.54, L.127 Ligands: PX4.8 Ligand excluded by PLIP PX4.12: 8 residues within 4Å: Chain B: L.194, F.221, T.224 Chain C: L.194, M.227 Ligands: PX4.15, PX4.19, PX4.26 Ligand excluded by PLIP PX4.15: 17 residues within 4Å: Chain B: M.206, P.210, W.213, I.217 Chain C: I.152, M.155, T.156, F.159, G.182, E.183, F.185, Y.186, F.189, M.192, M.227 Ligands: PX4.12, PX4.18 Ligand excluded by PLIP PX4.16: 7 residues within 4Å: Chain B: V.222 Chain C: P.93, W.94, F.97, F.125, S.139, I.142 Ligand excluded by PLIP PX4.17: 10 residues within 4Å: Chain B: F.162, L.169, R.173, Y.209, P.210, Y.211, A.212, V.214, F.215 Chain C: I.115 Ligand excluded by PLIP PX4.18: 17 residues within 4Å: Chain A: I.40, G.44, I.45, G.48, L.49, T.51, S.52, T.54, L.127 Chain C: T.156, L.157, Y.160, T.180, L.181, G.182, F.185 Ligands: PX4.15 Ligand excluded by PLIP PX4.19: 8 residues within 4Å: Chain A: L.194, M.227 Chain C: L.194, F.221, T.224 Ligands: PX4.1, PX4.5, PX4.12 Ligand excluded by PLIP PX4.22: 17 residues within 4Å: Chain A: M.206, P.210, W.213, I.217 Chain D: I.152, M.155, T.156, F.159, G.182, E.183, F.185, Y.186, F.189, M.192, M.227 Ligands: PX4.5, PX4.25 Ligand excluded by PLIP PX4.23: 7 residues within 4Å: Chain A: V.222 Chain D: P.93, W.94, F.97, F.125, S.139, I.142 Ligand excluded by PLIP PX4.24: 10 residues within 4Å: Chain A: F.162, L.169, R.173, Y.209, P.210, Y.211, A.212, V.214, F.215 Chain D: I.115 Ligand excluded by PLIP PX4.25: 17 residues within 4Å: Chain B: I.40, G.44, I.45, G.48, L.49, T.51, S.52, T.54, L.127 Chain D: T.156, L.157, Y.160, T.180, L.181, G.182, F.185 Ligands: PX4.22 Ligand excluded by PLIP PX4.26: 8 residues within 4Å: Chain B: L.194, M.227 Chain D: L.194, F.221, T.224 Ligands: PX4.5, PX4.8, PX4.12 Ligand excluded by PLIP

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

CPS.6: 8 residues within 4Å: Chain A: A.140, S.143, T.144, A.238, I.241, L.242 Chain C: D.237 Ligands: CPS.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.144, A:I.241, A:I.241, A:L.242 Hydrogen bonds: A:S.143, A:S.143 CPS.7: 13 residues within 4Å: Chain A: T.144, G.147, M.148, S.150, V.151, A.233, I.234, D.237, A.238, I.241 Chain D: K.136, I.137 Ligands: CPS.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.151, A:A.233, A:A.238, A:I.241 Hydrogen bonds: A:T.144, A:G.147 CPS.13: 8 residues within 4Å: Chain B: A.140, S.143, T.144, A.238, I.241, L.242 Chain D: D.237 Ligands: CPS.14 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.144, B:I.241, B:I.241, B:L.242 Hydrogen bonds: B:S.143, B:S.143 CPS.14: 13 residues within 4Å: Chain B: T.144, G.147, M.148, S.150, V.151, A.233, I.234, D.237, A.238, I.241 Chain C: K.136, I.137 Ligands: CPS.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.151, B:A.233, B:A.238, B:I.241 Hydrogen bonds: B:T.144, B:G.147 CPS.20: 8 residues within 4Å: Chain B: D.237 Chain C: A.140, S.143, T.144, A.238, I.241, L.242 Ligands: CPS.21 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.144, C:I.241, C:I.241, C:L.242 Hydrogen bonds: C:S.143, C:S.143 CPS.21: 13 residues within 4Å: Chain A: K.136, I.137 Chain C: T.144, G.147, M.148, S.150, V.151, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.20 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.151, C:A.233, C:A.238, C:I.241 Hydrogen bonds: C:T.144, C:G.147 CPS.27: 8 residues within 4Å: Chain A: D.237 Chain D: A.140, S.143, T.144, A.238, I.241, L.242 Ligands: CPS.28 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:T.144, D:I.241, D:I.241, D:L.242 Hydrogen bonds: D:S.143, D:S.143 CPS.28: 13 residues within 4Å: Chain B: K.136, I.137 Chain D: T.144, G.147, M.148, S.150, V.151, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.27 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.151, D:A.233, D:A.238, D:I.241 Hydrogen bonds: D:T.144, D:G.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wisedchaisri, G. et al., Structural basis for severe pain caused by mutations in the S4-S5 linkers of voltage-gated sodium channel Na V 1.7. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-04-12

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