SMTL ID : 6t1z.1

LmrP from L. lactis, in an outward-open conformation, bound to Hoechst 33342

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x HT1: 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE(Non-covalent)

HT1.1: 16 residues within 4Å: Chain A: A.53, V.54, N.147, I.227, M.228, F.230, D.231, A.265, C.266, E.323, M.354, P.355, S.358 Ligands: XP4.2, LMU.4, LMU.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.53, A:V.54, A:I.227, A:F.230, A:M.354, A:P.355 Hydrogen bonds: A:D.231, A:D.231, A:S.358 Salt bridges: A:E.323

2 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

XP4.2: 15 residues within 4Å: Chain A: G.21, S.24, Y.25, F.29, S.52, T.56, Q.83, S.112, Y.115, N.116, I.119, L.172, M.354 Ligands: HT1.1, LMU.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.25, A:F.29, A:F.29, A:Y.115, A:Y.115, A:L.172 XP4.3: 6 residues within 4Å: Chain A: A.92, S.93, H.98, N.100, W.102, S.103 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.102 Hydrogen bonds: A:H.98, A:N.100

2 x LMU: DODECYL-ALPHA-D-MALTOSIDE(Non-covalent)

LMU.4: 12 residues within 4Å: Chain A: S.30, I.151, A.154, A.155, F.230, D.231, L.258, T.259, L.262, I.263 Ligands: HT1.1, LMU.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.151, A:A.154, A:I.263, A:I.263 Hydrogen bonds: A:F.230, A:T.259 LMU.5: 9 residues within 4Å: Chain A: Y.25, T.33, L.49, D.231, C.266, S.358 Ligands: HT1.1, XP4.2, LMU.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.358

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: S.284, Q.286 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Debruycker, V. et al., An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-29

Peptides

LmrP integral membrane 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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LmrP integral membrane protein