SMTL ID : 4q8s.2 (1 other biounit)

Crystal structure of mammalian Peptidoglycan recognition protein PGRP-S with paranitrophenyl palmitate and N-acetyl glucosamine at 2.09 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 11 residues within 4Å: Chain A: W.66, A.92, G.95, P.96, N.99 Chain B: P.96, T.97, W.98, V.149, Q.150 Ligands: PNR.4 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.95, A:N.99, B:T.97, B:T.97, B:Q.150, B:Q.150, B:Q.150 Water bridges: A:G.91, B:T.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: P.151, T.152 Chain B: H.37, T.38, A.39, Y.71, H.146 Ligands: TLA.3, PNR.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.38, B:Y.71 Water bridges: B:H.146

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

TLA.3: 11 residues within 4Å: Chain A: H.37, A.39, T.152, L.153, S.154 Chain B: H.37, A.39, T.152, L.153, S.154 Ligands: GOL.2 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.152, B:L.153, B:S.154, A:L.153, A:S.154 Salt bridges: B:H.37, A:H.37 Water bridges: A:N.110

1 x PNR: 4-nitrophenyl hexadecanoate(Non-covalent)

PNR.4: 22 residues within 4Å: Chain A: W.66, A.92, H.93, A.94, G.95, P.96, T.97, V.149, Q.150, P.151 Chain B: W.66, C.67, R.85, A.92, H.93, A.94, G.95, N.99, Q.150, P.151 Ligands: NAG.1, GOL.2 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.66, B:A.92, B:P.151, A:W.66, A:P.151 pi-Stacking: B:W.66 Hydrogen bonds: A:T.97 Water bridges: A:T.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamini, S. et al., Crystal structure of mammalian Peptidoglycan recognition protein PGRP-S with paranitrophenyl palmitate and N-acetyl glucosamine at 2.09 A resolution. To be Published

Release Date

2014-05-21

Peptides

Peptidoglycan recognition protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Peptidoglycan recognition protein 1

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