SMTL ID : 6p9r.1

E.coli LpxA in complex with UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc and Compound 6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

3 x U20: uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetyl-D-glucosamine(Non-covalent)

U20.1: 30 residues within 4Å: Chain A: Q.73, D.74, L.75, K.76, H.122, A.124, H.125, T.140, L.141, A.142, G.143, H.144, A.158, V.159, H.160, Q.161, F.162, G.176, H.191 Chain B: M.118, N.137, I.152, M.170, N.198, E.200, G.201, R.204, R.205 Ligands: O5M.7, DMS.11 29 PLIP interactions: 19 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:Q.73, A:L.75, A:T.140, A:A.142, A:A.158 Hydrogen bonds: A:Q.73, A:D.74, A:L.75, A:K.76, A:H.122, A:G.143, A:H.144, A:H.144, A:Q.161, A:Q.161, B:N.198, B:N.198, B:G.201, B:R.205 Water bridges: A:K.76, A:H.125, B:R.204, B:R.204, B:R.204, B:R.204, B:R.205 Salt bridges: A:K.76, A:H.125, B:R.204 U20.8: 30 residues within 4Å: Chain B: Q.73, D.74, L.75, K.76, H.122, A.124, H.125, T.140, L.141, A.142, G.143, H.144, A.158, V.159, H.160, Q.161, F.162, G.176, H.191 Chain C: M.118, N.137, I.152, M.170, N.198, E.200, G.201, R.204, R.205 Ligands: O5M.14, DMS.18 28 PLIP interactions: 18 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:Q.73, B:L.75, B:T.140, B:A.142, B:A.158 Hydrogen bonds: B:Q.73, B:L.75, B:K.76, B:H.122, B:G.143, B:H.144, B:H.144, B:Q.161, B:Q.161, C:N.198, C:N.198, C:G.201, C:R.205 Water bridges: B:K.76, B:H.125, C:R.204, C:R.204, C:R.204, C:R.204, C:R.205 Salt bridges: B:K.76, B:H.125, C:R.204 U20.15: 30 residues within 4Å: Chain A: M.118, N.137, I.152, M.170, N.198, E.200, G.201, R.204, R.205 Chain C: Q.73, D.74, L.75, K.76, H.122, A.124, H.125, T.140, L.141, A.142, G.143, H.144, A.158, V.159, H.160, Q.161, F.162, G.176, H.191 Ligands: DMS.4, O5M.21 29 PLIP interactions: 19 interactions with chain C, 10 interactions with chain A Hydrophobic interactions: C:Q.73, C:L.75, C:T.140, C:A.142, C:A.158 Hydrogen bonds: C:Q.73, C:D.74, C:L.75, C:K.76, C:H.122, C:G.143, C:H.144, C:H.144, C:Q.161, C:Q.161, A:N.198, A:N.198, A:G.201, A:R.205 Water bridges: C:K.76, C:H.125, A:R.204, A:R.204, A:R.204, A:R.204, A:R.205 Salt bridges: C:K.76, C:H.125, A:R.204

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

PO4.2: 3 residues within 4Å: Chain A: V.71, R.100 Ligands: PO4.3 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:K.45, A:N.51, A:G.52, A:G.52 Salt bridges: A:R.100 PO4.3: 5 residues within 4Å: Chain A: G.33, P.34, N.51, G.52 Ligands: PO4.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.52 Water bridges: A:H.35, A:N.51, A:N.51, A:N.51, A:N.51, A:G.52 PO4.9: 3 residues within 4Å: Chain B: V.71, R.100 Ligands: PO4.10 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Water bridges: B:N.51, B:G.52, B:G.52, B:Y.77, C:K.45 Salt bridges: B:R.100 PO4.10: 5 residues within 4Å: Chain B: G.33, P.34, N.51, G.52 Ligands: PO4.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.52 Water bridges: B:H.35, B:N.51, B:N.51, B:N.51, B:N.51, B:G.52 PO4.16: 3 residues within 4Å: Chain C: V.71, R.100 Ligands: PO4.17 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Water bridges: C:N.51, C:G.52, C:G.52, A:K.45 Salt bridges: C:R.100 PO4.17: 5 residues within 4Å: Chain C: G.33, P.34, N.51, G.52 Ligands: PO4.16 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.52 Water bridges: C:H.35, C:H.35, C:H.35, C:N.51, C:N.51, C:N.51, C:N.51, C:G.52

9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 8 residues within 4Å: Chain A: D.114, N.115, L.116, R.132, C.133, I.134 Chain C: L.75 Ligands: U20.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.132 DMS.5: 7 residues within 4Å: Chain A: K.55, I.56, G.57, E.85, I.86, G.87, K.110 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.85 DMS.6: 3 residues within 4Å: Chain A: D.148, D.149, A.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.255 Salt bridges: A:D.148, A:D.149 DMS.11: 8 residues within 4Å: Chain A: L.75 Chain B: D.114, N.115, L.116, R.132, C.133, I.134 Ligands: U20.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.132 DMS.12: 7 residues within 4Å: Chain B: K.55, I.56, G.57, E.85, I.86, G.87, K.110 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.85 DMS.13: 3 residues within 4Å: Chain B: D.148, D.149, A.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.255 Salt bridges: B:D.148, B:D.149 DMS.18: 8 residues within 4Å: Chain B: L.75 Chain C: D.114, N.115, L.116, R.132, C.133, I.134 Ligands: U20.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.132 DMS.19: 7 residues within 4Å: Chain C: K.55, I.56, G.57, E.85, I.86, G.87, K.110 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:E.85 DMS.20: 3 residues within 4Å: Chain C: D.148, D.149, A.167 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.255 Salt bridges: C:D.148, C:D.149

3 x O5M: {(3R)-3-[(2-fluorophenyl)methyl]morpholin-4-yl}[3-(4-methylpyridin-2-yl)-1H-pyrazol-5-yl]methanone(Non-covalent)

O5M.7: 17 residues within 4Å: Chain A: H.160, Q.161, A.178, H.191 Chain B: M.118, I.134, A.136, I.152, I.153, G.154, G.155, M.170, V.171, G.172, G.173, Q.188 Ligands: U20.1 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.152 Hydrogen bonds: B:G.155, B:G.173 Water bridges: A:H.160, A:Q.161, A:Q.161 O5M.14: 17 residues within 4Å: Chain B: H.160, Q.161, A.178, H.191 Chain C: M.118, I.134, A.136, I.152, I.153, G.154, G.155, M.170, V.171, G.172, G.173, Q.188 Ligands: U20.8 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.152 Hydrogen bonds: C:G.155, C:G.173 Water bridges: B:H.160, B:Q.161, B:Q.161 O5M.21: 17 residues within 4Å: Chain A: M.118, I.134, A.136, I.152, I.153, G.154, G.155, M.170, V.171, G.172, G.173, Q.188 Chain C: H.160, Q.161, A.178, H.191 Ligands: U20.15 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:I.152 Hydrogen bonds: A:G.155, A:G.173, C:H.160 Water bridges: C:Q.161, C:Q.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, W. et al., Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis. J.Am.Chem.Soc. (2020)

Release Date

2020-03-11

Peptides

Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase

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