SMTL ID : 3nw3.1

Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with the PGN Fragment at 2.5 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.1: 12 residues within 4Å: Chain C: W.66, A.92, H.93, A.94, G.95, N.99, Q.150 Chain D: P.96, Q.150, P.151 Ligands: ALA.5, LAC.6 8 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C, 2 interactions with chain D Water bridges: A:R.170, C:R.85, C:R.85, D:T.97 Hydrogen bonds: C:G.95, C:N.99, C:Q.150, D:Q.150

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 11 residues within 4Å: Chain C: H.37, A.39, T.152, L.153, S.154 Chain D: H.37, A.39, T.152, L.153, S.154 Ligands: GOL.3 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.152, D:L.153, D:S.154, C:L.153, C:S.154 Water bridges: D:H.37, D:N.110 Salt bridges: D:H.37, C:H.37

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain C: P.151, T.152, L.153 Chain D: H.37, T.38, A.39, Y.71, H.146, T.152 Ligands: TLA.2 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:L.153, D:T.38, D:Y.71, D:H.146, D:T.152 Water bridges: C:T.152, D:T.152

1 x DGN: D-GLUTAMINE(Non-covalent)

DGN.4: 8 residues within 4Å: Chain A: S.139 Chain C: L.64 Chain D: W.98, K.144, D.148, V.149, A.171 Ligands: ALA.5 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:W.98 Hydrogen bonds: D:W.98, A:S.139, A:S.139 Water bridges: D:K.144, D:K.144

1 x ALA: ALANINE(Non-covalent)

ALA.5: 9 residues within 4Å: Chain A: N.140 Chain C: L.64, W.66 Chain D: T.97, W.98, V.149 Ligands: NDG.1, DGN.4, LAC.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:N.140 Hydrogen bonds: D:T.97, D:T.97

1 x LAC: LACTIC ACID(Non-covalent)

LAC.6: 10 residues within 4Å: Chain C: W.66 Chain D: A.94, G.95, P.96, T.97, W.98, V.149, Q.150 Ligands: NDG.1, ALA.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, P. et al., Multiligand specificity of pathogen-associated molecular pattern-binding site in peptidoglycan recognition protein. J.Biol.Chem. (2011)

Release Date

2010-08-04

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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