SMTL ID : 5k8k.1

Structure of the Haemophilus influenzae LpxH-lipid X complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.9, D.42, N.80, H.115, H.196 Ligands: MN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.42, A:H.115, A:H.196 MN.2: 6 residues within 4Å: Chain A: D.9, H.11, D.42, H.198 Ligands: MN.1, LP5.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.9, A:H.11, A:D.42

1 x LP5: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE(Non-covalent)

LP5.3: 22 residues within 4Å: Chain A: N.80, R.81, F.83, D.123, Y.126, F.129, V.133, L.138, Q.139, F.142, A.154, I.157, R.158, K.160, S.161, D.164, K.165, K.168, M.173, H.196, H.198 Ligands: MN.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.83, A:F.129, A:F.129, A:F.129, A:V.133, A:L.138, A:L.138, A:Q.139, A:F.142, A:F.142, A:A.154, A:I.157, A:K.160 Hydrogen bonds: A:N.80, A:N.80, A:D.123, A:S.161, A:S.161, A:K.168, A:K.168, A:K.168 Salt bridges: A:R.81, A:K.165, A:K.165, A:K.168, A:H.196, A:H.196, A:H.198

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 7 residues within 4Å: Chain A: L.12, S.13, E.14, F.44, D.45, F.46, E.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.45, A:F.46 ACT.5: 4 residues within 4Å: Chain A: Q.73, C.74, Y.75, Q.96 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: Y.38, Y.75, Q.96, L.98, Q.102, I.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.38, A:Y.38, A:Q.96 Water bridges: A:R.36 GOL.7: 2 residues within 4Å: Chain A: Q.135, W.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.135, A:W.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, J. et al., Structure of the essential Haemophilus influenzae UDP-diacylglucosamine pyrophosphohydrolase LpxH in lipid A biosynthesis. Nat Microbiol (2016)

Release Date

2016-08-10

Peptides

UDP-2,3-diacylglucosamine hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-2,3-diacylglucosamine hydrolase