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

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.28 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

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

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

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

EDO.2: 3 residues within 4Å: Chain A: E.14, P.46, A.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.14 Water bridges: A:E.14 EDO.5: 5 residues within 4Å: Chain A: P.96, T.97, Q.150 Chain B: W.66 Ligands: TLA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.97, A:Q.150 EDO.9: 5 residues within 4Å: Chain A: L.64, W.66 Chain B: T.97, W.98, V.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.149

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

6NA.3: 10 residues within 4Å: Chain A: W.66, K.90, A.92, H.93, A.94, G.95, P.96, N.99 Chain B: P.96, Q.150 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.96, A:N.99, B:P.96 Hydrogen bonds: A:A.94, A:G.95, A:N.99, B:Q.150 Water bridges: A:Q.150, A:Q.150

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: Y.32, W.98 No protein-ligand interaction detected (PLIP) ACT.6: 3 residues within 4Å: Chain B: T.97, W.98, I.101 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.101

1 x GOL: GLYCEROL(Non-functional Binders)

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.1 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:P.151, A:L.153, B:T.38, B:Y.71, B:T.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurya, A. et al., Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.28 A resolution. To Be Published

Release Date

2022-05-11

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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