SMTL ID : 5vb2.1

Crystal structure of the NavAb voltage-gated sodium channel in a closed conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-tetramer

Ligands

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

CPS.1: 16 residues within 4Å: Chain A: S.143, V.144, G.147, M.148, S.150, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Chain D: I.137, A.140 Ligands: CPS.2, CPS.22 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:A.233, A:I.234, A:D.237, A:I.241, D:I.137 Hydrogen bonds: A:V.144, A:G.147 CPS.2: 13 residues within 4Å: Chain A: A.140, S.143, V.144, I.234, A.238, I.241, L.242 Chain B: V.232, A.233, V.236, D.237 Ligands: CPS.1, CPS.7 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.144, A:A.238, A:L.242, B:V.236, B:V.236 Hydrogen bonds: A:S.143 CPS.7: 15 residues within 4Å: Chain A: I.137, A.140 Chain B: S.143, V.144, G.147, M.148, V.151, L.230, A.233, I.234, D.237, A.238, I.241 Ligands: CPS.2, CPS.8 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.233, B:D.237, B:A.238, B:I.241, A:I.137 Hydrogen bonds: B:V.144, B:G.147 CPS.8: 13 residues within 4Å: Chain B: 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.7, CPS.15 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.144, B:I.241, B:L.242, C:V.236 CPS.14: 13 residues within 4Å: Chain C: 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.15, CPS.21 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.144, C:A.238, C:L.242, D:A.233, D:V.236, D:V.236 Hydrogen bonds: C:A.140 CPS.15: 15 residues within 4Å: Chain B: I.137, A.140 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.8, CPS.14 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.234, C:D.237, C:A.238, C:I.241, B:I.137 Hydrogen bonds: C:V.144, C:G.147 CPS.21: 15 residues within 4Å: Chain C: I.137, A.140 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.22 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.151, D:L.230, D:A.233, D:D.237, D:A.238, D:I.241, C:I.137 Hydrogen bonds: D:V.144, D:G.147 CPS.22: 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.1, CPS.21 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:A.233, A:V.236, A:V.236, D:V.144, D:A.238, D:I.241, D:L.242

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

PX4.3: 18 residues within 4Å: Chain A: M.206, P.210, Y.211, W.213, I.217, F.221 Chain D: I.152, M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.192 Ligands: PX4.16 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:M.155, D:F.185 Hydrogen bonds: D:G.182 Water bridges: A:W.213 PX4.4: 11 residues within 4Å: Chain A: G.48, L.49, T.51, S.52, K.53, T.54 Chain B: Y.160, T.180, L.181, G.182 Ligands: PX4.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.49, B:L.181 Hydrogen bonds: A:K.53 PX4.5: 18 residues within 4Å: Chain A: F.158, F.162, M.165, L.169, F.170, R.173, V.208, Y.209, P.210, Y.211, A.212, V.214, F.215, P.218, V.222 Chain D: I.115, L.119, L.122 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.169, A:Y.211, A:V.214, A:F.215, A:P.218, D:I.115, D:I.115 PX4.9: 11 residues within 4Å: Chain A: I.115 Chain B: L.169, F.170, R.173, V.208, Y.209, P.210, Y.211, A.212, V.214, F.215 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.169, B:Y.211, B:F.215 PX4.10: 20 residues within 4Å: Chain A: I.152, M.155, T.156, F.159, T.180, L.181, G.182, E.183, F.185, Y.186, F.189, M.192, M.227 Chain B: M.206, P.210, Y.211, W.213, I.217, F.221 Ligands: PX4.23 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.213, A:M.155, A:F.159, A:F.185, A:F.185, A:F.189 Hydrogen bonds: B:W.213 PX4.11: 12 residues within 4Å: Chain B: I.45, G.48, L.49, T.51, S.52, K.53, T.54 Chain C: Y.160, T.180, L.181, G.182 Ligands: PX4.17 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.160, B:L.49 Hydrogen bonds: C:G.182, B:S.52, B:T.54, B:T.54 PX4.12: 18 residues within 4Å: Chain B: I.152, M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.192 Chain C: M.206, P.210, Y.211, W.213, I.217, F.221 Ligands: PX4.4 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.221, B:M.155, B:F.159, B:F.185 Hydrogen bonds: C:W.213 PX4.16: 12 residues within 4Å: Chain C: I.45, G.48, L.49, T.51, S.52, K.53, T.54 Chain D: Y.160, T.180, L.181, G.182 Ligands: PX4.3 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.49, D:L.181 Hydrogen bonds: C:K.53, C:T.54, C:T.54, D:G.182 PX4.17: 18 residues within 4Å: Chain C: I.152, M.155, T.156, F.159, T.180, G.182, E.183, F.185, Y.186, F.189, M.192 Chain D: M.206, P.210, Y.211, W.213, I.217, F.221 Ligands: PX4.11 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:M.155, C:F.159, C:F.159, C:F.159, C:F.159, C:F.185, C:F.189, D:F.221 Hydrogen bonds: C:G.182, D:W.213 Salt bridges: C:E.183 PX4.18: 15 residues within 4Å: Chain B: I.115, L.119, L.122 Chain C: F.162, M.165, L.169, F.170, V.208, Y.209, P.210, Y.211, A.212, V.214, F.215, P.218 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.162, C:L.169, C:F.215, B:I.115, B:L.119 PX4.23: 11 residues within 4Å: Chain A: Y.160, T.180, L.181, G.182 Chain D: G.48, L.49, T.51, S.52, K.53, T.54 Ligands: PX4.10 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.49, A:L.181 Hydrogen bonds: D:S.52, D:K.53, D:T.54, D:T.54, A:G.182 PX4.24: 11 residues within 4Å: Chain C: I.115 Chain D: L.169, F.170, R.173, V.208, Y.209, P.210, Y.211, A.212, V.214, F.215 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.169, D:V.214, C:I.115 PX4.25: 8 residues within 4Å: Chain D: P.93, W.94, F.97, F.125, T.129, V.138, S.139, I.142 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.94, D:W.94, D:F.97, D:F.97 Hydrogen bonds: D:W.94, D:S.139

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

PO4.6: 3 residues within 4Å: Chain A: P.93, W.94, S.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.94, A:S.139 PO4.13: 4 residues within 4Å: Chain B: P.93, W.94, S.139, I.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.139 PO4.19: 4 residues within 4Å: Chain C: P.93, W.94, S.139, I.142 No protein-ligand interaction detected (PLIP) PO4.26: 4 residues within 4Å: Chain C: Q.133 Chain D: P.146, L.149, S.150 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.133, D:P.146, D:S.150

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 6 residues within 4Å: Chain A: H.257, I.261 Chain B: H.257, I.261 Chain C: H.257 Chain D: H.257 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenaeus, M.J. et al., Structures of closed and open states of a voltage-gated sodium channel. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-04-05

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