SMTL ID : 4gf9.1

Structural insights into the dual strategy of recognition of peptidoglycan recognition protein, PGRP-S: ternary complex of PGRP-S with LPS and fatty acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

1 x STE: STEARIC ACID(Non-covalent)

STE.1: 7 residues within 4Å: Chain A: N.126, A.129 Chain B: P.4, A.5, C.6 Chain D: R.31, R.138 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.31 Salt bridges: D:R.138 Hydrophobic interactions: A:A.129, B:A.5, B:A.5

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)

LP5.2: 27 residues within 4Å: Chain A: S.139, N.140 Chain C: L.64, W.66, K.90, A.92, H.93, A.94, G.95, P.96, N.99, P.100, Q.150, P.151 Chain D: A.92, H.93, A.94, G.95, P.96, T.97, W.98, N.99, K.144, V.149, Q.150, P.151 Ligands: GOL.3 14 PLIP interactions: 7 interactions with chain D, 6 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:A.92, D:K.144, D:P.151, C:P.151, A:N.140 Hydrogen bonds: D:T.97, D:T.97, D:T.97, D:W.98, C:A.94, C:G.95, C:N.99 Water bridges: C:R.85 Salt bridges: C:K.90

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain C: P.151, T.152 Chain D: H.37, T.38, A.39, Y.71, H.146 Ligands: LP5.2 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.71, C:P.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, P. et al., Structural insights into the dual strategy of recognition by peptidoglycan recognition protein, PGRP-S: structure of the ternary complex of PGRP-S with lipopolysaccharide and stearic acid. Plos One (2013)

Release Date

2012-09-26

Peptides

Peptidoglycan recognition protein 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Peptidoglycan recognition protein 1

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