SMTL ID : 4j6e.1

Structure of LPXI D225A Mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

2 x UDG: (2R,3R,4R,5S,6R)-2-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)-3-{[(3R)-3-hydroxytetradecanoyl]amino}tetrahydro-2H-pyran-4-yl (3R)-3-hydroxytetradecanoate(Non-covalent)

UDG.1: 30 residues within 4Å: Chain A: G.13, A.15, L.16, I.54, I.60, F.74, G.76, N.77, V.78, S.79, R.80, P.81, D.107, L.110, L.111, V.114, Q.172, E.185, T.190, D.191, K.217, A.228, L.229, P.230, T.231, I.232, G.233, V.234, A.235, T.236 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:I.54, A:I.54, A:I.60, A:F.74, A:F.74, A:F.74, A:V.78, A:P.81, A:D.107, A:L.110, A:L.111, A:L.111, A:V.114 Hydrogen bonds: A:A.15, A:N.77, A:N.77, A:V.78, A:Q.172, A:E.185, A:T.190, A:T.190, A:D.191, A:L.229, A:T.231, A:T.231, A:G.233, A:A.235 Water bridges: A:V.78, A:V.234, A:V.234 Salt bridges: A:K.217, A:K.217 UDG.2: 30 residues within 4Å: Chain B: G.13, A.15, L.16, I.54, I.60, F.74, G.76, N.77, V.78, S.79, R.80, P.81, D.107, L.110, L.111, V.114, Q.172, E.185, T.190, D.191, K.217, A.228, L.229, P.230, T.231, I.232, G.233, V.234, A.235, T.236 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:I.54, B:I.54, B:I.60, B:F.74, B:F.74, B:F.74, B:V.78, B:P.81, B:D.107, B:L.110, B:L.111, B:L.111, B:V.114 Hydrogen bonds: B:A.15, B:N.77, B:N.77, B:V.78, B:D.107, B:Q.172, B:E.185, B:T.190, B:T.190, B:D.191, B:L.229, B:T.231, B:T.231, B:G.233, B:A.235 Water bridges: B:V.78, B:V.234, B:V.234 Salt bridges: B:K.217, B:K.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Metzger IV, L.E. et al., LpxI structures reveal how a lipid A precursor is synthesized. Nat.Struct.Mol.Biol. (2012)

Release Date

2013-05-08

Peptides

UDP-2,3-diacylglucosamine pyrophosphatase LpxI: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-2,3-diacylglucosamine pyrophosphatase LpxI