SMTL ID : 6lvf.1

Cryo-EM structure of the multiple peptide resistance factor (MprF) loaded with one lysyl-phosphatidylglycerol molecule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x EV9: [(2~{R})-3-[[(2~{S})-3-[(2~{S})-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] hexadecanoate(Non-covalent)

EV9.1: 22 residues within 4Å: Chain A: L.23, L.24, G.116, N.117, A.126, T.152, F.155, G.156, L.167, I.188, D.234, S.238, Y.260, A.261, I.262, V.264, G.265, V.268, L.269, H.271, A.274, Y.307 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.155, A:I.188, A:I.262, A:I.262, A:V.264, A:V.264, A:L.269, A:L.269, A:Y.307 Hydrogen bonds: A:D.234, A:A.274 Salt bridges: A:H.271 EV9.4: 22 residues within 4Å: Chain B: L.23, L.24, G.116, N.117, A.126, T.152, F.155, G.156, L.167, I.188, D.234, S.238, Y.260, A.261, I.262, V.264, G.265, V.268, L.269, H.271, A.274, Y.307 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.155, B:I.188, B:I.262, B:I.262, B:V.264, B:V.264, B:L.269, B:L.269, B:Y.307 Hydrogen bonds: B:D.234, B:A.274 Salt bridges: B:H.271

2 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.2: 18 residues within 4Å: Chain A: F.150, L.157, S.161, M.165, V.200, R.204, N.205, P.219, S.221, W.224, F.228 Chain B: R.226, L.229, V.230, A.232, F.233 Ligands: LHG.5, PGT.6 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.150, A:V.200, A:P.219, A:W.224, A:W.224, A:W.224, B:L.229, B:V.230, B:A.232, B:F.233 Hydrogen bonds: A:S.221, A:S.221 Salt bridges: B:R.226 LHG.5: 18 residues within 4Å: Chain A: R.226, L.229, V.230, A.232, F.233 Chain B: F.150, L.157, S.161, M.165, V.200, R.204, N.205, P.219, S.221, W.224, F.228 Ligands: LHG.2, PGT.3 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.229, A:V.230, A:A.232, A:F.233, B:F.150, B:V.200, B:P.219, B:W.224, B:W.224, B:W.224 Salt bridges: A:R.226 Hydrogen bonds: B:S.221, B:S.221

2 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.3: 16 residues within 4Å: Chain A: L.73, F.77, A.166, F.233, A.236, S.240, Y.243, V.244, L.246, E.248 Chain B: M.165, L.168, R.186, L.193 Ligands: LHG.5, PGT.6 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.193, A:F.77, A:F.233, A:F.233, A:A.236 Salt bridges: B:R.186, B:R.186 Hydrogen bonds: A:Y.243, A:V.244 PGT.6: 17 residues within 4Å: Chain A: M.165, L.168, R.186, I.190, L.193 Chain B: L.73, F.77, A.166, F.233, A.236, S.240, Y.243, V.244, L.246, E.248 Ligands: LHG.2, PGT.3 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.77, B:F.233, B:F.233, B:A.236, A:I.190, A:L.193 Hydrogen bonds: B:Y.243, B:V.244 Salt bridges: A:R.186, A:R.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, D. et al., Phospholipid translocation captured in a bifunctional membrane protein MprF. Nat Commun (2021)

Release Date

2021-02-03

Peptides

Low pH-inducible protein LpiA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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Low pH-inducible protein LpiA

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