SMTL ID : 6mwa.1

NavAb Voltage-gated Sodium Channel, residues 1-239

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

PX4.1: 15 residues within 4Å: Chain A: M.206, P.210, W.213, I.217 Chain D: M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.227 Ligands: PX4.2 Ligand excluded by PLIP PX4.2: 17 residues within 4Å: Chain B: V.41, G.44, I.45, G.48, L.49, S.52, T.54, L.127 Chain D: A.153, T.156, L.157, Y.160, T.180, L.181, G.182, F.185 Ligands: PX4.1 Ligand excluded by PLIP PX4.3: 15 residues within 4Å: Chain A: F.162, L.169, F.170, R.173, V.208, Y.209, Y.211, A.212, V.214, F.215 Chain D: F.97, I.115, L.119, L.122, F.125 Ligand excluded by PLIP PX4.4: 6 residues within 4Å: Chain A: P.93, W.94, F.97, F.125, S.139, I.142 Ligand excluded by PLIP PX4.8: 15 residues within 4Å: Chain B: M.206, P.210, W.213, I.217 Chain C: M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.227 Ligands: PX4.9 Ligand excluded by PLIP PX4.9: 17 residues within 4Å: Chain A: V.41, G.44, I.45, G.48, L.49, S.52, T.54, L.127 Chain C: A.153, T.156, L.157, Y.160, T.180, L.181, G.182, F.185 Ligands: PX4.8 Ligand excluded by PLIP PX4.10: 15 residues within 4Å: Chain B: F.162, L.169, F.170, R.173, V.208, Y.209, Y.211, A.212, V.214, F.215 Chain C: F.97, I.115, L.119, L.122, F.125 Ligand excluded by PLIP PX4.11: 6 residues within 4Å: Chain B: P.93, W.94, F.97, F.125, S.139, I.142 Ligand excluded by PLIP PX4.15: 15 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 C: M.206, P.210, W.213, I.217 Ligands: PX4.16 Ligand excluded by PLIP PX4.16: 17 residues within 4Å: Chain A: A.153, T.156, L.157, Y.160, T.180, L.181, G.182, F.185 Chain D: V.41, G.44, I.45, G.48, L.49, S.52, T.54, L.127 Ligands: PX4.15 Ligand excluded by PLIP PX4.17: 15 residues within 4Å: Chain A: F.97, I.115, L.119, L.122, F.125 Chain C: F.162, L.169, F.170, R.173, V.208, Y.209, Y.211, A.212, V.214, F.215 Ligand excluded by PLIP PX4.18: 6 residues within 4Å: Chain C: P.93, W.94, F.97, F.125, S.139, I.142 Ligand excluded by PLIP PX4.22: 15 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 D: M.206, P.210, W.213, I.217 Ligands: PX4.23 Ligand excluded by PLIP PX4.23: 17 residues within 4Å: Chain B: A.153, T.156, L.157, Y.160, T.180, L.181, G.182, F.185 Chain C: V.41, G.44, I.45, G.48, L.49, S.52, T.54, L.127 Ligands: PX4.22 Ligand excluded by PLIP PX4.24: 15 residues within 4Å: Chain B: F.97, I.115, L.119, L.122, F.125 Chain D: F.162, L.169, F.170, R.173, V.208, Y.209, Y.211, A.212, V.214, F.215 Ligand excluded by PLIP PX4.25: 6 residues within 4Å: Chain D: P.93, W.94, F.97, F.125, S.139, I.142 Ligand excluded by PLIP

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

SO4.5: 5 residues within 4Å: Chain A: R.173, F.174, P.175, E.176, W.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.174, A:E.176, A:W.177 SO4.12: 5 residues within 4Å: Chain B: R.173, F.174, P.175, E.176, W.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.174, B:E.176, B:W.177 SO4.19: 5 residues within 4Å: Chain C: R.173, F.174, P.175, E.176, W.177 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.174, C:E.176, C:W.177 SO4.26: 5 residues within 4Å: Chain D: R.173, F.174, P.175, E.176, W.177 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.174, D:E.176, D:W.177

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

CPS.6: 14 residues within 4Å: Chain A: S.143, V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Chain D: I.137 Ligands: CPS.7, CPS.28 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.144, A:V.151, A:L.230, A:I.234, A:D.237, A:I.241 Hydrogen bonds: A:V.144, A:G.147 CPS.7: 13 residues within 4Å: Chain A: A.140, S.143, V.144, I.234, A.238, I.241, L.242 Chain C: V.232, A.233, V.236, D.237 Ligands: CPS.6, CPS.20 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.144, A:I.234, A:A.238, A:I.241, C:V.236 Hydrogen bonds: A:S.143, A:S.143 CPS.13: 14 residues within 4Å: Chain B: S.143, V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Chain C: I.137 Ligands: CPS.14, CPS.21 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.144, B:V.151, B:L.230, B:I.234, B:D.237, B:I.241 Hydrogen bonds: B:V.144, B:G.147 CPS.14: 13 residues within 4Å: Chain B: A.140, S.143, V.144, I.234, A.238, I.241, L.242 Chain D: V.232, A.233, V.236, D.237 Ligands: CPS.13, CPS.27 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:V.144, B:I.234, B:A.238, B:I.241, D:V.236 Hydrogen bonds: B:S.143, B:S.143 CPS.20: 14 residues within 4Å: Chain A: I.137 Chain C: S.143, V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.7, CPS.21 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.144, C:V.151, C:L.230, C:I.234, C:D.237, C:I.241 Hydrogen bonds: C:V.144, C:G.147 CPS.21: 13 residues within 4Å: Chain B: V.232, A.233, V.236, D.237 Chain C: A.140, S.143, V.144, I.234, A.238, I.241, L.242 Ligands: CPS.13, CPS.20 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:V.236, C:V.144, C:I.234, C:A.238, C:I.241 Hydrogen bonds: C:S.143, C:S.143 CPS.27: 14 residues within 4Å: Chain B: I.137 Chain D: S.143, V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.14, CPS.28 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.144, D:V.151, D:L.230, D:I.234, D:D.237, D:I.241 Hydrogen bonds: D:V.144, D:G.147 CPS.28: 13 residues within 4Å: Chain A: V.232, A.233, V.236, D.237 Chain D: A.140, S.143, V.144, I.234, A.238, I.241, L.242 Ligands: CPS.6, CPS.27 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:V.144, D:I.234, D:A.238, D:I.241, A:V.236 Hydrogen bonds: D:S.143, D:S.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gamal El-Din, T.M. et al., Molecular dissection of multiphase inactivation of the bacterial sodium channel NaVAb. J. Gen. Physiol. (2019)

Release Date

2018-12-19

Peptides

Ion transport protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Membrane

We predict this structure to be a membrane protein.
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Ion transport protein