SMTL ID : 5azb.1

Crystal structure of Escherichia coli Lgt in complex with phosphatidylglycerol and the inhibitor palmitic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 8 residues within 4Å: Chain A: F.103, L.140, Y.236, Y.260, M.263, M.271 Ligands: PLM.2, PGT.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.103, A:L.140 Hydrogen bonds: A:Y.236, A:Y.236 PLM.2: 16 residues within 4Å: Chain A: Y.31, V.110, M.114, S.129, I.136, G.139, L.140, G.143, R.144, S.229, L.233, W.257 Ligands: PLM.1, BOG.3, PGT.4, PGT.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.31, A:V.110, A:I.136, A:L.233 Hydrogen bonds: A:Y.31, A:Y.31 Salt bridges: A:R.144

1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 12 residues within 4Å: Chain A: Y.27, Y.31, V.69, G.99, F.103, G.106, L.107, N.150, E.152, W.257 Ligands: PLM.2, PGT.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.69, A:F.103, A:W.257 Hydrogen bonds: A:G.99, A:E.152

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

PGT.4: 8 residues within 4Å: Chain A: R.123, S.124, F.125, F.126, I.266, L.267 Ligands: PLM.1, PLM.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.266, A:L.267 Hydrogen bonds: A:F.125 Water bridges: A:R.123 PGT.5: 19 residues within 4Å: Chain A: A.23, L.24, H.25, Y.27, G.28, Y.31, L.32, G.34, F.35, A.38, Y.63, F.66, L.67, V.69, M.101, I.132, G.139 Ligands: PLM.2, BOG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.31, A:Y.31, A:Y.31, A:F.35, A:A.38, A:Y.63, A:Y.63, A:Y.63, A:F.66, A:L.67, A:L.67, A:V.69, A:I.132 Hydrogen bonds: A:H.25, A:Y.27 Salt bridges: A:H.25 PGT.6: 11 residues within 4Å: Chain A: M.30, V.33, P.137, F.138, G.141, A.142, L.145, G.208, V.209, F.212 Ligands: PGT.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.30, A:V.33, A:F.138, A:L.145, A:F.212, A:F.212 PGT.7: 7 residues within 4Å: Chain A: I.234, A.238, I.241, V.276, M.279, Y.283 Ligands: PGT.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.234, A:I.234, A:A.238, A:I.241, A:V.276, A:M.279, A:Y.283, A:Y.283 PGT.8: 1 residues within 4Å: Ligands: PGT.7 No protein-ligand interaction detected (PLIP) PGT.9: 8 residues within 4Å: Chain A: N.60, G.72, G.109, V.113, I.116, F.117, R.120, T.121 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.60, A:V.113, A:I.116, A:F.117, A:T.121 PGT.10: 8 residues within 4Å: Chain A: F.37, W.40, L.41, R.44, R.45, F.138, F.212 Ligands: PGT.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.37, A:F.37, A:W.40, A:L.41, A:F.138, A:F.212 PGT.11: 4 residues within 4Å: Chain A: I.269, I.272, V.273, V.276 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.269, A:I.272, A:V.273, A:V.276 PGT.12: 5 residues within 4Å: Chain A: E.11, F.12, D.13, W.26, M.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.12, A:W.26, A:W.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mao, G. et al., Crystal structure of E. coli lipoprotein diacylglyceryl transferase. Nat Commun (2016)

Release Date

2016-01-27

Peptides

Prolipoprotein diacylglyceryl transferase: 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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Prolipoprotein diacylglyceryl transferase

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