SMTL ID : 6mvv.1

NavAb voltage-gated sodium channel, I217C/F203A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

PX4.1: 11 residues within 4Å: Chain A: M.155, T.156, T.180, G.182, E.183, F.185, Y.186, F.189 Chain B: M.206, P.210, W.213 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.155, A:F.185, A:F.185, A:F.185, A:F.189 PX4.4: 13 residues within 4Å: Chain B: I.152, M.155, T.156, F.159, G.182, E.183, F.185, Y.186, F.189, M.227 Chain C: M.206, P.210, W.213 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.152, B:M.155, B:F.185, B:F.189, C:W.213 Hydrogen bonds: B:Y.186 Salt bridges: B:E.183 PX4.5: 10 residues within 4Å: Chain A: I.115, L.122 Chain B: L.169, F.170, R.173, V.208, Y.209, P.210, Y.211, V.214 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.169, B:Y.211, B:V.214, A:I.115, A:L.122 PX4.7: 14 residues within 4Å: Chain C: I.152, M.155, T.156, F.159, G.182, E.183, F.185, Y.186, F.189, M.227 Chain D: M.206, P.210, W.213, I.217 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.152, C:I.152, C:M.155, C:F.159, C:F.185, C:F.185, C:F.189, C:F.189 pi-Cation interactions: D:W.213 PX4.8: 8 residues within 4Å: Chain B: E.114, I.115 Chain C: L.169, F.170, R.173, Y.209, Y.211, A.212 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.169, C:F.170, C:F.170, C:Y.209, C:Y.209 PX4.10: 9 residues within 4Å: Chain A: M.206, P.210, W.213 Chain D: T.156, F.159, T.180, G.182, E.183, F.185 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.156, D:F.159, D:F.185 Salt bridges: D:E.183

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: S.52 Chain B: T.180 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.52, B:T.180 PO4.3: 2 residues within 4Å: Chain A: Y.209, Y.211 No protein-ligand interaction detected (PLIP) PO4.6: 1 residues within 4Å: Chain B: S.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.52 PO4.9: 4 residues within 4Å: Chain C: S.52, K.53, T.54 Chain D: T.180 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.53, C:T.54, C:T.54, C:T.54 PO4.11: 2 residues within 4Å: Chain D: S.52, T.54 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.54, D:T.54

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
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Ion transport protein