SMTL ID : 8qr0.1

Cryo-EM structure of the light-driven sodium pump ErNaR in the pentameric form at pH 4.3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

Oligo State

homo-pentamer

Ligands

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

LMT.1: 15 residues within 4Å: Chain A: A.31, G.32, Y.35, L.247, V.251, Q.255, A.272 Chain B: P.45, L.49, V.56, M.108, G.121, L.124, W.128 Ligands: LFA.3 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.56, B:V.56, B:W.128, A:Y.35, A:Y.35, A:L.247 Hydrogen bonds: B:P.45, B:L.49, B:G.121, B:G.121, A:Y.35, A:Q.255 Water bridges: B:R.48, A:T.39, A:S.254 LMT.14: 13 residues within 4Å: Chain B: G.32, Y.35, L.247, V.251, Q.255, A.272 Chain C: P.45, L.49, V.56, G.121, L.124, W.128 Ligands: LFA.10 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.56, C:W.128, B:L.247 Hydrogen bonds: C:P.45, C:L.49, C:G.121, C:G.121, B:Y.35, B:Q.255 Water bridges: C:R.48, B:T.39, B:S.254 LMT.17: 14 residues within 4Å: Chain C: G.32, Y.35, L.247, V.251, Q.255, A.272 Chain D: P.45, L.49, V.56, M.108, G.121, L.124, W.128 Ligands: LFA.19 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:Y.35, C:L.247, D:V.56, D:W.128 Hydrogen bonds: C:Y.35, C:Q.255, D:P.45, D:L.49, D:G.121 Water bridges: C:T.39, C:S.254, D:R.48 LMT.27: 13 residues within 4Å: Chain D: G.32, Y.35, V.251, Q.255, A.272 Chain E: P.45, L.49, V.56, G.121, L.124, R.125, W.128 Ligands: LFA.28 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:V.56, E:V.56, E:W.128, D:Y.35 Hydrogen bonds: E:P.45, E:L.49, E:G.121, D:Y.35, D:Q.255 Water bridges: E:R.48 LMT.37: 15 residues within 4Å: Chain A: P.45, L.49, V.56, G.121, L.124, W.128 Chain E: V.28, A.31, G.32, Y.35, L.247, V.251, Q.255, A.272 Ligands: LFA.38 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:V.56, A:W.128, E:A.31, E:Y.35, E:L.247, E:L.247 Hydrogen bonds: A:P.45, A:L.49, A:G.121, E:Y.35, E:Q.255 Water bridges: A:R.48

36 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.2: 4 residues within 4Å: Chain A: R.125, T.132, I.133 Ligands: LFA.40 Ligand excluded by PLIP LFA.3: 8 residues within 4Å: Chain A: L.247, V.251, I.252, Q.255 Chain B: R.125, W.128 Ligands: LMT.1, LFA.5 Ligand excluded by PLIP LFA.4: 6 residues within 4Å: Chain A: F.203, W.206, F.207, A.210, T.211, S.244 Ligand excluded by PLIP LFA.5: 5 residues within 4Å: Chain A: V.240, V.243, S.244 Ligands: LFA.3, LFA.9 Ligand excluded by PLIP LFA.6: 5 residues within 4Å: Chain A: W.13 Chain B: M.1, Y.143, Y.147, F.148 Ligand excluded by PLIP LFA.7: 2 residues within 4Å: Chain B: L.70 Ligands: LFA.13 Ligand excluded by PLIP LFA.8: 8 residues within 4Å: Chain A: A.37, M.38 Chain B: L.33, V.34, A.37 Chain C: L.30, L.63 Ligands: LFA.15 Ligand excluded by PLIP LFA.9: 3 residues within 4Å: Chain B: T.132, I.133 Ligands: LFA.5 Ligand excluded by PLIP LFA.10: 7 residues within 4Å: Chain B: L.247, V.251, Q.255 Chain C: R.125, W.128 Ligands: LFA.12, LMT.14 Ligand excluded by PLIP LFA.11: 6 residues within 4Å: Chain B: F.203, W.206, F.207, A.210, T.211, S.244 Ligand excluded by PLIP LFA.12: 6 residues within 4Å: Chain B: F.24, V.240, V.243, S.244 Ligands: LFA.10, LFA.21 Ligand excluded by PLIP LFA.13: 2 residues within 4Å: Chain C: L.70 Ligands: LFA.7 Ligand excluded by PLIP LFA.15: 3 residues within 4Å: Ligands: LFA.8, LFA.24, LFA.35 Ligand excluded by PLIP LFA.16: 6 residues within 4Å: Chain B: W.13, V.17 Chain C: M.1, Y.143, Y.147, F.148 Ligand excluded by PLIP LFA.18: 6 residues within 4Å: Chain C: F.203, W.206, F.207, A.210, T.211, S.244 Ligand excluded by PLIP LFA.19: 7 residues within 4Å: Chain C: L.247, V.251, Q.255 Chain D: R.125, W.128 Ligands: LMT.17, LFA.20 Ligand excluded by PLIP LFA.20: 7 residues within 4Å: Chain C: F.203, V.240, V.243, S.244, V.248 Ligands: LFA.19, LFA.31 Ligand excluded by PLIP LFA.21: 3 residues within 4Å: Chain C: T.132, I.133 Ligands: LFA.12 Ligand excluded by PLIP LFA.22: 1 residues within 4Å: Chain D: L.70 Ligand excluded by PLIP LFA.23: 6 residues within 4Å: Chain A: L.30 Chain D: A.37 Chain E: L.33, V.34, A.37 Ligands: LFA.24 Ligand excluded by PLIP LFA.24: 9 residues within 4Å: Chain C: A.37, M.38 Chain D: L.33, V.34 Chain E: L.33, V.59 Ligands: LFA.15, LFA.23, LFA.25 Ligand excluded by PLIP LFA.25: 8 residues within 4Å: Chain B: A.37 Chain C: L.33, V.34, A.37 Chain D: L.30, A.62, L.63 Ligands: LFA.24 Ligand excluded by PLIP LFA.26: 7 residues within 4Å: Chain C: W.13, V.17, V.236 Chain D: M.1, Y.143, Y.147, F.148 Ligand excluded by PLIP LFA.28: 6 residues within 4Å: Chain D: L.247, I.252 Chain E: R.125, W.128 Ligands: LMT.27, LFA.29 Ligand excluded by PLIP LFA.29: 5 residues within 4Å: Chain D: V.240, V.243, S.244 Ligands: LFA.28, LFA.41 Ligand excluded by PLIP LFA.30: 6 residues within 4Å: Chain D: F.203, W.206, F.207, A.210, T.211, S.244 Ligand excluded by PLIP LFA.31: 6 residues within 4Å: Chain D: R.125, W.128, A.129, T.132, I.133 Ligands: LFA.20 Ligand excluded by PLIP LFA.32: 1 residues within 4Å: Chain E: L.70 Ligand excluded by PLIP LFA.33: 7 residues within 4Å: Chain A: M.1, Y.143, Y.147, F.148 Chain E: D.11, W.13, V.17 Ligand excluded by PLIP LFA.34: 1 residues within 4Å: Chain A: L.70 Ligand excluded by PLIP LFA.35: 5 residues within 4Å: Chain A: L.33, V.34 Chain E: A.37, M.38 Ligands: LFA.15 Ligand excluded by PLIP LFA.36: 5 residues within 4Å: Chain D: W.13 Chain E: M.1, Y.143, Y.147, F.148 Ligand excluded by PLIP LFA.38: 6 residues within 4Å: Chain A: W.128 Chain E: L.247, V.248, Q.255 Ligands: LMT.37, LFA.40 Ligand excluded by PLIP LFA.39: 6 residues within 4Å: Chain E: F.203, W.206, F.207, A.210, T.211, S.244 Ligand excluded by PLIP LFA.40: 5 residues within 4Å: Chain E: V.240, V.243, S.244 Ligands: LFA.2, LFA.38 Ligand excluded by PLIP LFA.41: 3 residues within 4Å: Chain E: T.132, I.133 Ligands: LFA.29 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Podoliak, E. et al., A subgroup of light-driven sodium pumps with an additional Schiff base counterion. Nat Commun (2024)

Release Date

2024-04-24

Peptides

Bacteriorhodopsin-like protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin-like protein

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