SMTL ID : 3ogx.1

Crystal structure of the complex of Peptidoglycan Recognition protein (PGRP-s) with Heparin-Dissacharide at 2.8 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

1 x SGN- UAP: 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose(Non-covalent)

SGN-UAP.1: 21 residues within 4Å: Chain A: R.31, N.140, Y.141, E.142, R.170 Chain C: E.24, L.64, G.65, W.66, K.90, A.92, H.93, A.94, G.95, N.99 Chain D: G.95, P.96, T.97, W.98, V.149, Q.150 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:G.95, C:N.99, A:E.142, A:E.142, D:Q.150, A:R.31, A:N.140, D:T.97, C:W.66 Salt bridges: C:K.90, C:K.90, A:K.144, A:R.170 Hydrophobic interactions: A:N.140

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: G.65, W.66, C.67, R.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.65, A:R.85 GOL.4: 9 residues within 4Å: Chain C: P.151, T.152, L.153 Chain D: H.37, T.38, A.39, Y.71, H.146 Ligands: TLA.3 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:P.151, C:L.153, D:S.36, D:S.36, D:Y.71

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

TLA.3: 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.4 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:T.152, C:L.153, C:S.154, D:T.152, D:L.153, D:S.154 Salt bridges: C:H.37, D:H.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, P. et al., Structural basis of heparin binding to camel peptidoglycan recognition protein-S. Int J Biochem Mol Biol (2012)

Release Date

2010-09-01

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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