SMTL ID : 7dy5.2 (1 other biounit)

Structure of the ternary complex of peptidoglycan recognition protein-short (PGRP-S) with hexanoic acid and tartaric acid at 2.30A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x 6NA: HEXANOIC ACID(Non-covalent)

6NA.1: 9 residues within 4Å: Chain A: K.90, A.92, H.93, A.94, G.95, P.96, N.99 Chain B: P.96, Q.150 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.92, A:N.99 Hydrogen bonds: A:A.92, A:A.94, A:G.95, A:N.99

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: P.96, Q.150 Chain B: W.66 Ligands: TLA.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:W.66, A:T.97 Hydrogen bonds: A:Q.150 EDO.3: 3 residues within 4Å: Chain A: Y.32, T.97, W.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32 EDO.4: 5 residues within 4Å: Chain A: L.64, W.66 Chain B: T.97, W.98, V.149 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.64 Water bridges: B:T.97

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

TLA.5: 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.7 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.152, A:L.153, B:L.153, B:S.154 Water bridges: A:T.152, A:T.152 Salt bridges: A:H.37, B:H.37 TLA.8: 5 residues within 4Å: Chain B: W.66, C.67, R.85, A.92 Ligands: EDO.2 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.67 Water bridges: B:W.66, A:T.97 Salt bridges: B:R.85

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain B: Y.32, T.97, W.98, I.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.32, B:Y.32 Water bridges: B:W.98 GOL.7: 9 residues within 4Å: Chain A: P.151, T.152, L.153 Chain B: H.37, T.38, A.39, Y.71, H.146 Ligands: TLA.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.71, A:P.151, A:L.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurya, A. et al., Structure of the ternary complex of peptidoglycan recognition protein-short (PGRP-S). To Be Published

Release Date

2021-02-17

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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