SMTL ID : 8qle.1

Crystal structure of the light-driven sodium pump ErNaR in the monomeric form at pH 4.6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

LFA.1: 1 residues within 4Å: Chain A: V.240 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.240 LFA.2: 4 residues within 4Å: Chain A: A.31, Y.35, V.251, Q.255 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.31, A:Y.35, A:Y.35, A:Y.35, A:Q.255 LFA.4: 6 residues within 4Å: Chain A: L.63, G.66, Q.67, L.70, L.71 Ligands: LFA.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.67, A:L.70, A:L.71 LFA.5: 3 residues within 4Å: Chain A: A.31, V.34, M.38 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.34 LFA.6: 2 residues within 4Å: Chain A: V.236, I.237 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.236, A:I.237 LFA.7: 12 residues within 4Å: Chain A: T.172, F.175, V.176, L.179, L.180, A.183, R.187, F.205, W.206, S.213, P.216 Ligands: OLA.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.172, A:V.176, A:L.179, A:L.180, A:A.183, A:F.205, A:W.206, A:P.216 LFA.8: 4 residues within 4Å: Chain A: I.169, T.172, A.173, V.176 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.172, A:A.173, A:V.176 LFA.9: 2 residues within 4Å: Chain A: L.33, A.37 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.33, A:L.33, A:A.37 LFA.10: 4 residues within 4Å: Chain A: T.132, I.133, V.136, L.137 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.132, A:I.133, A:V.136, A:L.137 LFA.12: 3 residues within 4Å: Chain A: V.243, L.247, V.251 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.243, A:L.247, A:V.251 LFA.13: 3 residues within 4Å: Chain A: L.63, N.101 Ligands: LFA.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.63 LFA.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x OLA: OLEIC ACID(Non-covalent)

OLA.3: 5 residues within 4Å: Chain A: F.148, G.160, E.162, Q.163, W.167 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.148, A:Q.163, A:W.167 Hydrogen bonds: A:Q.163 OLA.11: 4 residues within 4Å: Chain A: R.187, K.202, W.206 Ligands: LFA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.206 Salt bridges: A:K.202

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

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

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