SMTL ID : 6mvy.1 (1 other biounit)

NavAb voltage-gated sodium channel, residues 1-226, crystallized in the presence of Class 1B Anti-arrhythmic drug Lidocaine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

PX4.1: 7 residues within 4Å: Chain A: L.169, F.170, Y.209, Y.211, A.212, V.214 Chain C: I.115 Ligand excluded by PLIP PX4.2: 14 residues within 4Å: Chain A: M.206, P.210, W.213 Chain C: M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.227 Ligands: PX4.3 Ligand excluded by PLIP PX4.3: 15 residues within 4Å: Chain B: I.40, 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 Ligands: PX4.2 Ligand excluded by PLIP PX4.4: 7 residues within 4Å: Chain A: P.93, W.94, F.97, V.138, S.139, I.142, S.143 Ligand excluded by PLIP PX4.6: 7 residues within 4Å: Chain B: L.169, F.170, Y.209, Y.211, A.212, V.214 Chain D: I.115 Ligand excluded by PLIP PX4.7: 14 residues within 4Å: Chain B: M.206, P.210, W.213 Chain D: M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.227 Ligands: PX4.8 Ligand excluded by PLIP PX4.8: 15 residues within 4Å: Chain A: I.40, 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 Ligands: PX4.7 Ligand excluded by PLIP PX4.9: 7 residues within 4Å: Chain B: P.93, W.94, F.97, V.138, S.139, I.142, S.143 Ligand excluded by PLIP PX4.11: 7 residues within 4Å: Chain B: I.115 Chain C: L.169, F.170, Y.209, Y.211, A.212, V.214 Ligand excluded by PLIP PX4.12: 14 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 Chain C: M.206, P.210, W.213 Ligands: PX4.13 Ligand excluded by PLIP PX4.13: 15 residues within 4Å: Chain B: T.156, L.157, Y.160, T.180, L.181, G.182 Chain D: I.40, G.44, I.45, G.48, L.49, S.52, T.54, L.127 Ligands: PX4.12 Ligand excluded by PLIP PX4.14: 7 residues within 4Å: Chain C: P.93, W.94, F.97, V.138, S.139, I.142, S.143 Ligand excluded by PLIP PX4.16: 7 residues within 4Å: Chain A: I.115 Chain D: L.169, F.170, Y.209, Y.211, A.212, V.214 Ligand excluded by PLIP PX4.17: 14 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 Chain D: M.206, P.210, W.213 Ligands: PX4.18 Ligand excluded by PLIP PX4.18: 15 residues within 4Å: Chain A: T.156, L.157, Y.160, T.180, L.181, G.182 Chain C: I.40, G.44, I.45, G.48, L.49, S.52, T.54, L.127 Ligands: PX4.17 Ligand excluded by PLIP PX4.19: 7 residues within 4Å: Chain D: P.93, W.94, F.97, V.138, S.139, I.142, S.143 Ligand excluded by PLIP

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: F.174, P.175, E.176, W.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.176, A:E.176, A:W.177 SO4.10: 4 residues within 4Å: Chain B: F.174, P.175, E.176, W.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.176, B:E.176, B:W.177 SO4.15: 4 residues within 4Å: Chain C: F.174, P.175, E.176, W.177 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.176, C:E.176, C:W.177 SO4.20: 4 residues within 4Å: Chain D: F.174, P.175, E.176, W.177 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.176, D:E.176, D:W.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gamal El-Din, T.M. et al., Fenestrations control resting-state block of a voltage-gated sodium channel. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-12-05

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

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