SMTL ID : 5yua.1

Crystal structure of voltage-gated sodium channel NavAb in high-pH condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-functional Binders)

CA.1: 3 residues within 4Å: Ligands: CA.11, CA.21, CA.31 No protein-ligand interaction detected (PLIP) CA.11: 3 residues within 4Å: Ligands: CA.1, CA.21, CA.31 No protein-ligand interaction detected (PLIP) CA.21: 3 residues within 4Å: Ligands: CA.1, CA.11, CA.31 No protein-ligand interaction detected (PLIP) CA.31: 3 residues within 4Å: Ligands: CA.1, CA.11, CA.21 No protein-ligand interaction detected (PLIP)

8 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.2: 18 residues within 4Å: Chain A: M.134, M.178, T.179, L.180, T.210, M.213, I.214 Chain C: L.180, F.207, V.208, T.210, F.211 Ligands: PX4.7, PX4.10, LMT.12, LMT.22, PX4.25, LMT.32 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.207, C:V.208, C:T.210 Hydrogen bonds: A:M.178 LMT.3: 12 residues within 4Å: Chain A: F.148, M.151, L.155, R.159, Y.195, Y.197, V.200, F.201 Chain D: E.100, I.101 Ligands: PX4.38, PX4.39 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:I.101, A:F.148, A:L.155, A:F.201 Hydrogen bonds: D:E.100, A:Y.195, A:Y.197 LMT.12: 18 residues within 4Å: Chain B: M.134, M.178, T.179, L.180, T.210, M.213, I.214 Chain D: L.180, F.207, V.208, T.210, F.211 Ligands: LMT.2, PX4.17, PX4.20, LMT.22, LMT.32, PX4.35 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.207, D:V.208, D:T.210 Hydrogen bonds: B:M.178 LMT.13: 12 residues within 4Å: Chain B: F.148, M.151, L.155, R.159, Y.195, Y.197, V.200, F.201 Chain C: E.100, I.101 Ligands: PX4.28, PX4.29 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.148, B:L.155, B:F.201, C:I.101 Hydrogen bonds: B:Y.195, B:Y.197, C:E.100 LMT.22: 18 residues within 4Å: Chain B: L.180, F.207, V.208, T.210, F.211 Chain C: M.134, M.178, T.179, L.180, T.210, M.213, I.214 Ligands: LMT.2, LMT.12, PX4.15, PX4.27, PX4.30, LMT.32 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.207, B:V.208, B:T.210 Hydrogen bonds: C:M.178 LMT.23: 12 residues within 4Å: Chain A: E.100, I.101 Chain C: F.148, M.151, L.155, R.159, Y.195, Y.197, V.200, F.201 Ligands: PX4.8, PX4.9 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.148, C:L.155, C:F.201, A:I.101 Hydrogen bonds: C:Y.195, C:Y.197, A:E.100 LMT.32: 18 residues within 4Å: Chain A: L.180, F.207, V.208, T.210, F.211 Chain D: M.134, M.178, T.179, L.180, T.210, M.213, I.214 Ligands: LMT.2, PX4.5, LMT.12, LMT.22, PX4.37, PX4.40 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.207, A:V.208, A:T.210 Hydrogen bonds: D:M.178 LMT.33: 12 residues within 4Å: Chain B: E.100, I.101 Chain D: F.148, M.151, L.155, R.159, Y.195, Y.197, V.200, F.201 Ligands: PX4.18, PX4.19 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:I.101, D:F.148, D:L.155, D:F.201 Hydrogen bonds: B:E.100, D:Y.195, D:Y.197

4 x 1N7: CHAPSO(Non-covalent)

1N7.4: 7 residues within 4Å: Chain A: Q.119 Chain C: P.132, G.133, L.135, S.136, D.223 Ligands: PX4.30 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.135 Hydrogen bonds: C:S.136, C:S.136 1N7.14: 7 residues within 4Å: Chain B: Q.119 Chain D: P.132, G.133, L.135, S.136, D.223 Ligands: PX4.40 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.135 Hydrogen bonds: D:S.136, D:S.136 1N7.24: 7 residues within 4Å: Chain B: P.132, G.133, L.135, S.136, D.223 Chain C: Q.119 Ligands: PX4.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.135 Hydrogen bonds: B:S.136, B:S.136 1N7.34: 7 residues within 4Å: Chain A: P.132, G.133, L.135, S.136, D.223 Chain D: Q.119 Ligands: PX4.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.135 Hydrogen bonds: A:S.136, A:S.136

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

PX4.5: 21 residues within 4Å: Chain A: M.192, P.196, Y.197, W.199, F.207 Chain D: I.131, I.138, M.141, T.142, F.145, T.166, G.168, E.169, F.171, Y.172, F.175, M.213 Ligands: PX4.16, LMT.32, PX4.39, PX4.40 Ligand excluded by PLIP PX4.6: 16 residues within 4Å: Chain A: V.27, G.30, I.31, G.34, S.38, K.39, T.40, L.113 Chain C: T.142, L.143, Y.146, T.166, L.167, G.168, F.171 Ligands: PX4.15 Ligand excluded by PLIP PX4.7: 14 residues within 4Å: Chain A: P.79, W.80, F.83, F.111, T.115, S.125, I.128, S.129, I.131, P.132 Chain C: L.140 Ligands: LMT.2, PX4.8, PX4.10 Ligand excluded by PLIP PX4.8: 8 residues within 4Å: Chain A: P.79, W.80, F.83, F.111 Ligands: PX4.7, PX4.9, PX4.10, LMT.23 Ligand excluded by PLIP PX4.9: 10 residues within 4Å: Chain A: F.99, I.101 Chain C: P.196, Y.197, W.199, P.204 Ligands: PX4.8, PX4.10, LMT.23, PX4.25 Ligand excluded by PLIP PX4.10: 7 residues within 4Å: Chain A: L.135 Ligands: LMT.2, PX4.7, PX4.8, PX4.9, PX4.25, 1N7.34 Ligand excluded by PLIP PX4.15: 21 residues within 4Å: Chain B: M.192, P.196, Y.197, W.199, F.207 Chain C: I.131, I.138, M.141, T.142, F.145, T.166, G.168, E.169, F.171, Y.172, F.175, M.213 Ligands: PX4.6, LMT.22, PX4.29, PX4.30 Ligand excluded by PLIP PX4.16: 16 residues within 4Å: Chain B: V.27, G.30, I.31, G.34, S.38, K.39, T.40, L.113 Chain D: T.142, L.143, Y.146, T.166, L.167, G.168, F.171 Ligands: PX4.5 Ligand excluded by PLIP PX4.17: 14 residues within 4Å: Chain B: P.79, W.80, F.83, F.111, T.115, S.125, I.128, S.129, I.131, P.132 Chain D: L.140 Ligands: LMT.12, PX4.18, PX4.20 Ligand excluded by PLIP PX4.18: 8 residues within 4Å: Chain B: P.79, W.80, F.83, F.111 Ligands: PX4.17, PX4.19, PX4.20, LMT.33 Ligand excluded by PLIP PX4.19: 10 residues within 4Å: Chain B: F.99, I.101 Chain D: P.196, Y.197, W.199, P.204 Ligands: PX4.18, PX4.20, LMT.33, PX4.35 Ligand excluded by PLIP PX4.20: 7 residues within 4Å: Chain B: L.135 Ligands: LMT.12, PX4.17, PX4.18, PX4.19, 1N7.24, PX4.35 Ligand excluded by PLIP PX4.25: 21 residues within 4Å: Chain A: I.131, I.138, M.141, T.142, F.145, T.166, G.168, E.169, F.171, Y.172, F.175, M.213 Chain C: M.192, P.196, Y.197, W.199, F.207 Ligands: LMT.2, PX4.9, PX4.10, PX4.36 Ligand excluded by PLIP PX4.26: 16 residues within 4Å: Chain B: T.142, L.143, Y.146, T.166, L.167, G.168, F.171 Chain C: V.27, G.30, I.31, G.34, S.38, K.39, T.40, L.113 Ligands: PX4.35 Ligand excluded by PLIP PX4.27: 14 residues within 4Å: Chain B: L.140 Chain C: P.79, W.80, F.83, F.111, T.115, S.125, I.128, S.129, I.131, P.132 Ligands: LMT.22, PX4.28, PX4.30 Ligand excluded by PLIP PX4.28: 8 residues within 4Å: Chain C: P.79, W.80, F.83, F.111 Ligands: LMT.13, PX4.27, PX4.29, PX4.30 Ligand excluded by PLIP PX4.29: 10 residues within 4Å: Chain B: P.196, Y.197, W.199, P.204 Chain C: F.99, I.101 Ligands: LMT.13, PX4.15, PX4.28, PX4.30 Ligand excluded by PLIP PX4.30: 7 residues within 4Å: Chain C: L.135 Ligands: 1N7.4, PX4.15, LMT.22, PX4.27, PX4.28, PX4.29 Ligand excluded by PLIP PX4.35: 21 residues within 4Å: Chain B: I.131, I.138, M.141, T.142, F.145, T.166, G.168, E.169, F.171, Y.172, F.175, M.213 Chain D: M.192, P.196, Y.197, W.199, F.207 Ligands: LMT.12, PX4.19, PX4.20, PX4.26 Ligand excluded by PLIP PX4.36: 16 residues within 4Å: Chain A: T.142, L.143, Y.146, T.166, L.167, G.168, F.171 Chain D: V.27, G.30, I.31, G.34, S.38, K.39, T.40, L.113 Ligands: PX4.25 Ligand excluded by PLIP PX4.37: 14 residues within 4Å: Chain A: L.140 Chain D: P.79, W.80, F.83, F.111, T.115, S.125, I.128, S.129, I.131, P.132 Ligands: LMT.32, PX4.38, PX4.40 Ligand excluded by PLIP PX4.38: 8 residues within 4Å: Chain D: P.79, W.80, F.83, F.111 Ligands: LMT.3, PX4.37, PX4.39, PX4.40 Ligand excluded by PLIP PX4.39: 10 residues within 4Å: Chain A: P.196, Y.197, W.199, P.204 Chain D: F.99, I.101 Ligands: LMT.3, PX4.5, PX4.38, PX4.40 Ligand excluded by PLIP PX4.40: 7 residues within 4Å: Chain D: L.135 Ligands: PX4.5, 1N7.14, LMT.32, PX4.37, PX4.38, PX4.39 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Irie, K. et al., Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb. FEBS Lett. (2017)

Release Date

2017-12-27

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