SMTL ID : 8v24.1

LapB cytoplasmic domain in complex with LpxC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: C.357, K.359, C.360, F.362, C.371, S.373, C.374, T.379 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.357, A:C.360, A:C.371, A:C.374 ZN.4: 7 residues within 4Å: Chain B: E.78, H.79, T.191, H.238, D.242, H.265 Ligands: ACT.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.79, B:H.238, B:D.242, B:D.242 ZN.5: 6 residues within 4Å: Chain C: C.357, C.360, F.362, C.371, S.373, C.374 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.357, C:C.360, C:C.371, C:C.374 ZN.8: 6 residues within 4Å: Chain D: E.78, H.79, T.191, H.238, D.242 Ligands: ACT.7 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.78, D:H.79, D:H.238, D:D.242, D:D.242

2 x 24G: uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine(Non-covalent)

24G.2: 32 residues within 4Å: Chain A: F.362, P.372, S.373 Chain B: L.18, H.19, M.61, L.62, K.143, F.157, I.159, D.160, F.161, T.191, F.192, G.193, F.194, M.195, I.198, L.201, Q.202, C.207, G.210, S.211, F.212, A.215, V.217, K.239, K.262, S.263, G.264, H.265 Ligands: ACT.3 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.18, B:L.18, B:I.198, B:I.198, B:I.198, B:A.215, B:V.217, A:P.372 Hydrogen bonds: B:D.160, B:K.239, B:K.262, B:H.265, B:H.265 Salt bridges: B:K.143, B:K.239, B:K.239 24G.6: 32 residues within 4Å: Chain C: F.362, P.372, S.373 Chain D: L.18, H.19, M.61, L.62, K.143, F.157, I.159, D.160, F.161, T.191, F.192, G.193, F.194, M.195, I.198, L.201, C.207, G.210, S.211, F.212, C.214, A.215, V.217, K.239, K.262, S.263, G.264, H.265 Ligands: ACT.7 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.18, D:L.18, D:F.161, D:T.191, D:I.198, D:I.198, D:I.198, D:A.215, D:V.217, C:F.362, C:P.372 Hydrogen bonds: D:K.239, D:H.265 Salt bridges: D:K.143, D:K.239, D:K.239, D:H.265

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

ACT.3: 14 residues within 4Å: Chain B: L.18, H.19, L.62, C.63, T.76, E.78, H.79, I.103, T.191, H.238, D.242, H.265 Ligands: 24G.2, ZN.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.78, B:T.191 Salt bridges: B:H.79, B:H.238, B:H.265 ACT.7: 13 residues within 4Å: Chain D: L.18, H.19, L.62, C.63, T.76, E.78, H.79, I.103, T.191, H.238, D.242 Ligands: 24G.6, ZN.8 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.18, D:T.191 Salt bridges: D:H.79, D:H.238, D:H.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shu, S. et al., Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-04-24

Peptides

Lipopolysaccharide assembly protein B: AC
UDP-3-O-acyl-N-acetylglucosamine deacetylase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Lipopolysaccharide assembly protein B

UDP-3-O-acyl-N-acetylglucosamine deacetylase

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