SMTL ID : 4opp.1

Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 11-cyclohexylundecanoic acid and N- acetylglucosamine at 2.30 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

2 x 11Z: 11-cyclohexylundecanoic acid(Non-covalent)

11Z.1: 11 residues within 4Å: Chain A: R.122, Q.125, N.126, A.129 Chain B: P.3, P.4, A.5, C.6, L.134 Chain D: R.31, R.138 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.4, B:A.5, B:L.134, A:Q.125, A:N.126, A:A.129 Hydrogen bonds: B:A.5 11Z.5: 14 residues within 4Å: Chain C: P.96, T.97, Q.150 Chain D: E.24, W.66, C.67, R.85, K.90, G.91, A.92, H.93, G.95, P.96, N.99 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.66, D:A.92, C:P.96 Hydrogen bonds: D:N.99 Salt bridges: D:K.90

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

NAG.2: 11 residues within 4Å: Chain C: W.66, K.90, G.91, A.92, G.95, P.96, N.99 Chain D: P.96, T.97, V.149, Q.150 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:T.97, D:Q.150, C:W.66, C:K.90, C:G.95, C:N.99 Hydrophobic interactions: C:W.66 Water bridges: C:R.85, C:R.85, C:R.85, C:K.90

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 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:T.152, D:L.153, D:S.154, C:T.152, C:L.153, C:S.154 Salt bridges: D:H.37, C:H.37 Water bridges: C:N.110

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain C: P.151, T.152 Chain D: S.36, H.37, T.38, A.39, Y.71, H.146 Ligands: TLA.3 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.36, D:T.38, D:Y.71, D:Y.71, D:H.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamini, S. et al., Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 11-cyclohexylundecanoic acid and N- acetylglucosamine at 2.30 A resolution. To be Published

Release Date

2014-03-05

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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