SMTL ID : 8ha2.1

Crystal structure of voltage-gated sodium channel NavAb N49K/L176G mutant in calcium ion condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-tetramer

Ligands

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

LMT.1: 16 residues within 4Å: Chain A: M.134, M.178, T.179, T.210, M.213, I.214, V.217 Chain C: F.207, T.210, F.211 Ligands: PX4.6, CA.13, LMT.27, PX4.30, CA.39, LMT.40 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.207, C:T.210, C:F.211 Hydrogen bonds: A:T.210, A:M.213 LMT.2: 10 residues within 4Å: Chain A: F.148, L.155, F.156, Y.195, Y.197, A.198, V.200, F.201 Chain D: I.101 Ligands: PX4.46 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.148, A:L.155, A:F.156, A:Y.195, A:F.201 LMT.14: 16 residues within 4Å: Chain B: M.134, M.178, T.179, T.210, M.213, I.214, V.217 Chain D: F.207, T.210, F.211 Ligands: PX4.19, CA.26, LMT.27, LMT.40, PX4.43, CA.52 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.207, D:T.210, D:F.211 Hydrogen bonds: B:T.210, B:M.213 LMT.15: 10 residues within 4Å: Chain B: F.148, L.155, F.156, Y.195, Y.197, A.198, V.200, F.201 Chain C: I.101 Ligands: PX4.33 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.148, B:L.155, B:F.156, B:Y.195, B:F.201 LMT.27: 16 residues within 4Å: Chain B: F.207, T.210, F.211 Chain C: M.134, M.178, T.179, T.210, M.213, I.214, V.217 Ligands: LMT.1, LMT.14, PX4.17, CA.26, PX4.32, CA.39 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.207, B:T.210, B:F.211 Hydrogen bonds: C:T.210, C:M.213 LMT.28: 10 residues within 4Å: Chain A: I.101 Chain C: F.148, L.155, F.156, Y.195, Y.197, A.198, V.200, F.201 Ligands: PX4.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.148, C:L.155, C:F.156, C:Y.195, C:F.201 LMT.40: 16 residues within 4Å: Chain A: F.207, T.210, F.211 Chain D: M.134, M.178, T.179, T.210, M.213, I.214, V.217 Ligands: LMT.1, PX4.4, CA.13, LMT.14, PX4.45, CA.52 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.207, A:T.210, A:F.211 Hydrogen bonds: D:T.210, D:M.213 LMT.41: 10 residues within 4Å: Chain B: I.101 Chain D: F.148, L.155, F.156, Y.195, Y.197, A.198, V.200, F.201 Ligands: PX4.20 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.148, D:L.155, D:F.156, D:Y.195, D:F.201

4 x 1N7: CHAPSO(Non-covalent)

1N7.3: 7 residues within 4Å: Chain A: Q.119, M.120 Chain C: P.132, G.133, L.135, S.136 Ligands: PX4.34 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Q.119, C:L.135, C:L.135 Hydrogen bonds: A:Q.119 1N7.16: 7 residues within 4Å: Chain B: Q.119, M.120 Chain D: P.132, G.133, L.135, S.136 Ligands: PX4.47 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.135, D:L.135, B:Q.119 Hydrogen bonds: B:Q.119 1N7.29: 7 residues within 4Å: Chain B: P.132, G.133, L.135, S.136 Chain C: Q.119, M.120 Ligands: PX4.21 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Q.119, B:L.135, B:L.135 Hydrogen bonds: C:Q.119 1N7.42: 7 residues within 4Å: Chain A: P.132, G.133, L.135, S.136 Chain D: Q.119, M.120 Ligands: PX4.8 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Q.119, A:L.135, A:L.135 Hydrogen bonds: D:Q.119

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

PX4.4: 18 residues within 4Å: Chain A: M.192, W.199, I.203, F.207 Chain D: I.138, M.141, T.142, F.145, G.168, E.169, F.171, Y.172, F.175, M.178 Ligands: PX4.18, PX4.24, LMT.40, PX4.46 Ligand excluded by PLIP PX4.5: 10 residues within 4Å: Chain A: G.34, S.38, K.39, T.40 Chain C: T.142, Y.146, L.167, G.168 Ligands: PX4.11, PX4.17 Ligand excluded by PLIP PX4.6: 13 residues within 4Å: Chain A: P.79, W.80, F.83, F.111, S.125, I.128, S.129, I.131, P.132 Ligands: LMT.1, PX4.8, PX4.9, PX4.10 Ligand excluded by PLIP PX4.7: 5 residues within 4Å: Chain A: I.101 Chain C: Y.197 Ligands: LMT.28, PX4.30, PX4.50 Ligand excluded by PLIP PX4.8: 5 residues within 4Å: Chain A: P.132, L.135 Ligands: PX4.6, PX4.9, 1N7.42 Ligand excluded by PLIP PX4.9: 4 residues within 4Å: Chain A: S.129 Ligands: PX4.6, PX4.8, PX4.10 Ligand excluded by PLIP PX4.10: 9 residues within 4Å: Chain A: K.77, D.78, P.79, L.82, F.83, F.86, I.90 Ligands: PX4.6, PX4.9 Ligand excluded by PLIP PX4.11: 5 residues within 4Å: Chain A: T.40 Chain B: Y.197 Ligands: PX4.5, PX4.17, PX4.33 Ligand excluded by PLIP PX4.17: 18 residues within 4Å: Chain B: M.192, W.199, I.203, F.207 Chain C: I.138, M.141, T.142, F.145, G.168, E.169, F.171, Y.172, F.175, M.178 Ligands: PX4.5, PX4.11, LMT.27, PX4.33 Ligand excluded by PLIP PX4.18: 10 residues within 4Å: Chain B: G.34, S.38, K.39, T.40 Chain D: T.142, Y.146, L.167, G.168 Ligands: PX4.4, PX4.24 Ligand excluded by PLIP PX4.19: 13 residues within 4Å: Chain B: P.79, W.80, F.83, F.111, S.125, I.128, S.129, I.131, P.132 Ligands: LMT.14, PX4.21, PX4.22, PX4.23 Ligand excluded by PLIP PX4.20: 5 residues within 4Å: Chain B: I.101 Chain D: Y.197 Ligands: PX4.37, LMT.41, PX4.43 Ligand excluded by PLIP PX4.21: 5 residues within 4Å: Chain B: P.132, L.135 Ligands: PX4.19, PX4.22, 1N7.29 Ligand excluded by PLIP PX4.22: 4 residues within 4Å: Chain B: S.129 Ligands: PX4.19, PX4.21, PX4.23 Ligand excluded by PLIP PX4.23: 9 residues within 4Å: Chain B: K.77, D.78, P.79, L.82, F.83, F.86, I.90 Ligands: PX4.19, PX4.22 Ligand excluded by PLIP PX4.24: 5 residues within 4Å: Chain A: Y.197 Chain B: T.40 Ligands: PX4.4, PX4.18, PX4.46 Ligand excluded by PLIP PX4.30: 18 residues within 4Å: Chain A: I.138, M.141, T.142, F.145, G.168, E.169, F.171, Y.172, F.175, M.178 Chain C: M.192, W.199, I.203, F.207 Ligands: LMT.1, PX4.7, PX4.44, PX4.50 Ligand excluded by PLIP PX4.31: 10 residues within 4Å: Chain B: T.142, Y.146, L.167, G.168 Chain C: G.34, S.38, K.39, T.40 Ligands: PX4.37, PX4.43 Ligand excluded by PLIP PX4.32: 13 residues within 4Å: Chain C: P.79, W.80, F.83, F.111, S.125, I.128, S.129, I.131, P.132 Ligands: LMT.27, PX4.34, PX4.35, PX4.36 Ligand excluded by PLIP PX4.33: 5 residues within 4Å: Chain B: Y.197 Chain C: I.101 Ligands: PX4.11, LMT.15, PX4.17 Ligand excluded by PLIP PX4.34: 5 residues within 4Å: Chain C: P.132, L.135 Ligands: 1N7.3, PX4.32, PX4.35 Ligand excluded by PLIP PX4.35: 4 residues within 4Å: Chain C: S.129 Ligands: PX4.32, PX4.34, PX4.36 Ligand excluded by PLIP PX4.36: 9 residues within 4Å: Chain C: K.77, D.78, P.79, L.82, F.83, F.86, I.90 Ligands: PX4.32, PX4.35 Ligand excluded by PLIP PX4.37: 5 residues within 4Å: Chain C: T.40 Chain D: Y.197 Ligands: PX4.20, PX4.31, PX4.43 Ligand excluded by PLIP PX4.43: 18 residues within 4Å: Chain B: I.138, M.141, T.142, F.145, G.168, E.169, F.171, Y.172, F.175, M.178 Chain D: M.192, W.199, I.203, F.207 Ligands: LMT.14, PX4.20, PX4.31, PX4.37 Ligand excluded by PLIP PX4.44: 10 residues within 4Å: Chain A: T.142, Y.146, L.167, G.168 Chain D: G.34, S.38, K.39, T.40 Ligands: PX4.30, PX4.50 Ligand excluded by PLIP PX4.45: 13 residues within 4Å: Chain D: P.79, W.80, F.83, F.111, S.125, I.128, S.129, I.131, P.132 Ligands: LMT.40, PX4.47, PX4.48, PX4.49 Ligand excluded by PLIP PX4.46: 5 residues within 4Å: Chain A: Y.197 Chain D: I.101 Ligands: LMT.2, PX4.4, PX4.24 Ligand excluded by PLIP PX4.47: 5 residues within 4Å: Chain D: P.132, L.135 Ligands: 1N7.16, PX4.45, PX4.48 Ligand excluded by PLIP PX4.48: 4 residues within 4Å: Chain D: S.129 Ligands: PX4.45, PX4.47, PX4.49 Ligand excluded by PLIP PX4.49: 9 residues within 4Å: Chain D: K.77, D.78, P.79, L.82, F.83, F.86, I.90 Ligands: PX4.45, PX4.48 Ligand excluded by PLIP PX4.50: 5 residues within 4Å: Chain C: Y.197 Chain D: T.40 Ligands: PX4.7, PX4.30, PX4.44 Ligand excluded by PLIP

8 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.12: 3 residues within 4Å: Ligands: CA.25, CA.38, CA.51 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain D: T.179 Ligands: LMT.1, LMT.40 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.179 CA.25: 3 residues within 4Å: Ligands: CA.12, CA.38, CA.51 No protein-ligand interaction detected (PLIP) CA.26: 3 residues within 4Å: Chain C: T.179 Ligands: LMT.14, LMT.27 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.179 CA.38: 3 residues within 4Å: Ligands: CA.12, CA.25, CA.51 No protein-ligand interaction detected (PLIP) CA.39: 3 residues within 4Å: Chain A: T.179 Ligands: LMT.1, LMT.27 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.179 CA.51: 3 residues within 4Å: Ligands: CA.12, CA.25, CA.38 No protein-ligand interaction detected (PLIP) CA.52: 3 residues within 4Å: Chain B: T.179 Ligands: LMT.14, LMT.40 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Irie, K. et al., The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel. Nat Commun (2023)

Release Date

2023-07-26

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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