SMTL ID : 5kn7.1

Lipid A secondary acyltransferase LpxM from Acinetobacter baumannii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: N.209, G.212, Y.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.209, A:G.212 SO4.2: 3 residues within 4Å: Chain A: K.223, T.260, A.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.261 Water bridges: A:Q.226, A:D.262 Salt bridges: A:K.223 SO4.3: 4 residues within 4Å: Chain A: K.98, R.102 Chain B: P.27, I.28 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.98, A:R.102 Hydrogen bonds: B:I.28 Water bridges: B:Q.29 SO4.17: 3 residues within 4Å: Chain B: N.209, G.212, Y.266 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.209, B:G.212, B:Y.266 SO4.18: 3 residues within 4Å: Chain B: K.223, T.260, A.261 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.261 Water bridges: B:Q.226, B:D.262 Salt bridges: B:K.223 SO4.19: 4 residues within 4Å: Chain A: P.27, I.28 Chain B: K.98, R.102 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.98, B:R.102 Hydrogen bonds: A:I.28 Water bridges: A:Q.29

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

NA.4: 3 residues within 4Å: Chain A: A.61, F.211, Y.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.277, A:Y.277 NA.5: 2 residues within 4Å: Chain A: T.260, D.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.262, A:D.262 NA.6: 5 residues within 4Å: Chain A: W.92, E.133, N.136, R.165, E.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.133, A:R.165, A:R.165 NA.20: 3 residues within 4Å: Chain B: A.61, F.211, Y.277 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.61 NA.21: 2 residues within 4Å: Chain B: T.260, D.262 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.260, B:D.262 NA.22: 5 residues within 4Å: Chain B: W.92, E.133, N.136, R.165, E.168 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.133, B:E.133, B:R.165, B:R.165

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: Y.236, E.250, L.275, Q.278 Ligand excluded by PLIP GOL.8: 1 residues within 4Å: Chain A: S.144 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: W.132, E.133, N.136, I.147, R.165, V.194, L.196 Ligands: LMT.15 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: S.94, S.95, S.97, K.98 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: S.95, N.96, S.97, R.167 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: T.321, S.322, E.326, P.327, I.328, Q.329, T.330 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: I.103, H.104, R.105, I.106, E.109 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: K.150, H.199, Y.287 Ligands: LMT.15 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain B: Y.236, E.250, L.275, Q.278 Ligand excluded by PLIP GOL.24: 1 residues within 4Å: Chain B: S.144 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain B: W.132, E.133, N.136, I.147, R.165, V.194, L.196 Ligands: LMT.31 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: S.94, S.95, S.97, K.98 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: S.95, N.96, S.97, R.167 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain B: T.321, S.322, E.326, P.327, I.328, Q.329, T.330 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain B: I.103, H.104, R.105, I.106, E.109 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: K.150, H.199, Y.287 Ligands: LMT.31 Ligand excluded by PLIP

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.15: 11 residues within 4Å: Chain A: Y.85, L.89, W.92, W.132, E.133, Y.149, K.150, R.165 Chain B: L.20 Ligands: GOL.9, GOL.14 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.85, A:Y.85, A:L.89, B:L.20 Hydrogen bonds: A:K.150, A:R.165, A:R.165 Water bridges: A:L.148 LMT.31: 11 residues within 4Å: Chain A: L.20 Chain B: Y.85, L.89, W.92, W.132, E.133, Y.149, K.150, R.165 Ligands: GOL.25, GOL.30 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.85, B:Y.85, B:L.89, A:L.20 Hydrogen bonds: B:Y.85, B:K.150, B:R.165, B:R.165 Water bridges: B:L.148

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.16: 4 residues within 4Å: Chain A: K.288, K.291, Y.300, N.301 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.301 Water bridges: A:N.301, A:N.301 Salt bridges: A:K.288, A:K.291 PO4.32: 4 residues within 4Å: Chain B: K.288, K.291, Y.300, N.301 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.301 Water bridges: B:N.301, B:N.301 Salt bridges: B:K.288, B:K.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dovala, D. et al., Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-09-28

Peptides

Lipid A biosynthesis lauroyl acyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Lipid A biosynthesis lauroyl acyltransferase