SMTL ID : 8diw.1

Crystal structure of NavAb E96P as a basis for the human Nav1.7 Inherited Erythromelalgia S211P mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 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: 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, I.217, F.221 Ligands: PX4.4 Ligand excluded by PLIP PX4.2: 11 residues within 4Å: Chain A: P.93, W.94, F.97, F.125, V.138, S.139, I.142 Chain C: L.154, F.158, V.222, F.225 Ligand excluded by PLIP PX4.3: 10 residues within 4Å: Chain A: P.114, I.115 Chain C: F.162, L.169, R.173, Y.209, P.210, Y.211, A.212, 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, V.41, G.44, I.45, G.48, L.49, S.52, T.54, L.127 Ligands: PX4.1 Ligand excluded by PLIP PX4.5: 6 residues within 4Å: Chain A: F.221, T.224 Chain D: M.192, M.227 Ligands: PX4.19, PX4.26 Ligand excluded by PLIP PX4.8: 17 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, I.217, F.221 Ligands: PX4.11 Ligand excluded by PLIP PX4.9: 11 residues within 4Å: Chain B: P.93, W.94, F.97, F.125, V.138, S.139, I.142 Chain D: L.154, F.158, V.222, F.225 Ligand excluded by PLIP PX4.10: 10 residues within 4Å: Chain B: P.114, I.115 Chain D: F.162, L.169, R.173, Y.209, P.210, Y.211, A.212, 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, V.41, G.44, I.45, G.48, L.49, S.52, T.54, L.127 Ligands: PX4.8 Ligand excluded by PLIP PX4.12: 6 residues within 4Å: Chain B: F.221, T.224 Chain C: M.192, M.227 Ligands: PX4.19, PX4.26 Ligand excluded by PLIP PX4.15: 17 residues within 4Å: Chain B: M.206, P.210, W.213, I.217, 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: PX4.18 Ligand excluded by PLIP PX4.16: 11 residues within 4Å: Chain B: L.154, F.158, V.222, F.225 Chain C: P.93, W.94, F.97, F.125, V.138, 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, F.215 Chain C: P.114, I.115 Ligand excluded by PLIP PX4.18: 17 residues within 4Å: Chain A: I.40, V.41, G.44, I.45, G.48, L.49, 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: 6 residues within 4Å: Chain A: M.192, M.227 Chain C: F.221, T.224 Ligands: PX4.5, PX4.12 Ligand excluded by PLIP PX4.22: 17 residues within 4Å: Chain A: M.206, P.210, W.213, I.217, 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: PX4.25 Ligand excluded by PLIP PX4.23: 11 residues within 4Å: Chain A: L.154, F.158, V.222, F.225 Chain D: P.93, W.94, F.97, F.125, V.138, 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, F.215 Chain D: P.114, I.115 Ligand excluded by PLIP PX4.25: 17 residues within 4Å: Chain B: I.40, V.41, G.44, I.45, G.48, L.49, 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: 6 residues within 4Å: Chain B: M.192, M.227 Chain D: F.221, T.224 Ligands: PX4.5, PX4.12 Ligand excluded by PLIP

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

CPS.6: 7 residues within 4Å: Chain A: A.140, S.143, A.238, I.241 Chain C: D.237 Ligands: CPS.7, CPS.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.241, A:I.241 Hydrogen bonds: A:S.143, A:S.143 CPS.7: 13 residues within 4Å: Chain A: V.144, G.147, M.148, V.151, A.233, I.234, D.237, A.238, I.241 Chain D: I.137, A.140 Ligands: CPS.6, CPS.27 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.144, A:V.151, A:I.234, A:A.238, A:I.241 Hydrogen bonds: A:V.144, A:G.147 CPS.13: 7 residues within 4Å: Chain B: A.140, S.143, A.238, I.241 Chain D: D.237 Ligands: CPS.14, CPS.28 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.241, B:I.241 Hydrogen bonds: B:S.143, B:S.143 CPS.14: 13 residues within 4Å: Chain B: V.144, G.147, M.148, V.151, A.233, I.234, D.237, A.238, I.241 Chain C: I.137, A.140 Ligands: CPS.13, CPS.20 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.144, B:V.151, B:I.234, B:A.238, B:I.241 Hydrogen bonds: B:V.144, B:G.147 CPS.20: 7 residues within 4Å: Chain B: D.237 Chain C: A.140, S.143, A.238, I.241 Ligands: CPS.14, CPS.21 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.241, C:I.241 Hydrogen bonds: C:S.143, C:S.143 CPS.21: 13 residues within 4Å: Chain A: I.137, A.140 Chain C: V.144, G.147, M.148, V.151, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.6, CPS.20 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.144, C:V.151, C:I.234, C:A.238, C:I.241 Hydrogen bonds: C:V.144, C:G.147 CPS.27: 7 residues within 4Å: Chain A: D.237 Chain D: A.140, S.143, A.238, I.241 Ligands: CPS.7, CPS.28 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.241, D:I.241 Hydrogen bonds: D:S.143, D:S.143 CPS.28: 13 residues within 4Å: Chain B: I.137, A.140 Chain D: V.144, G.147, M.148, V.151, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.13, CPS.27 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.144, D:V.151, D:I.234, D:A.238, D:I.241 Hydrogen bonds: D:V.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 voltage sensors of sodium channel NaV1.7. J.Gen.Physiol. (2023)

Release Date

2023-10-25

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