SMTL ID : 6nc8.1

Lipid II flippase MurJ, inward occluded conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: D.235, N.374, D.378, V.390, A.393, T.394 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.235, A:N.374, A:T.394, A:T.394

6 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 11 residues within 4Å: Chain A: T.164, I.167, G.168, L.171, Y.175, I.178, S.179, I.182, G.183, I.186 Ligands: OLC.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.167, A:L.171, A:Y.175, A:I.186 OLC.3: 10 residues within 4Å: Chain A: I.19, L.22, F.23, V.26, F.315, F.316, H.319, E.440, F.441 Ligands: 1PE.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.22, A:F.23, A:V.26, A:F.315, A:F.315, A:F.316, A:F.441 Hydrogen bonds: A:E.440 Salt bridges: A:H.319 OLC.4: 5 residues within 4Å: Chain A: I.365, I.369, I.400, Y.404 Ligands: OLC.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.369, A:I.400, A:Y.404 Hydrogen bonds: A:Y.404 OLC.5: 5 residues within 4Å: Chain A: Y.404, F.407, S.408, K.410 Ligands: OLC.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.407, A:K.410 OLC.6: 8 residues within 4Å: Chain A: N.85, S.88, L.89, L.92, Y.204, F.206, T.207, I.208 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.85, A:F.206, A:F.206, A:I.208 Hydrogen bonds: A:T.207, A:I.208 OLC.7: 7 residues within 4Å: Chain A: I.127, I.178, I.182, L.185, I.186, I.189 Ligands: OLC.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.189

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 8 residues within 4Å: Chain A: F.23, V.26, L.27, K.30, Y.31, F.170, H.319 Ligands: OLC.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.30 1PE.9: 7 residues within 4Å: Chain A: F.283, N.284, Y.354, I.357, S.408, V.409, K.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.284 1PE.10: 7 residues within 4Å: Chain A: Y.285, N.288, D.289, K.292, P.413, D.416, Y.462 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.292, A:D.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuk, A.C.Y. et al., Visualizing conformation transitions of the Lipid II flippase MurJ. Nat Commun (2019)

Release Date

2019-04-17

Peptides

Lipid II flippase MurJ: 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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Lipid II flippase MurJ

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