SMTL ID : 7xu8.1 (1 other biounit)

Structure of the complex of camel peptidoglycan recognition protein-short (PGRP-S) with heptanoic acid at 2.15 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: W.66, C.67, R.85 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.67, A:R.85, A:R.85 Water bridges: A:E.24, A:W.66, A:K.90

4 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.2: 4 residues within 4Å: Chain A: W.166, S.167, Y.169, R.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.169 PEO.5: 4 residues within 4Å: Chain B: W.66, C.67, R.85 Ligands: PEO.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.67, B:R.85, B:R.85 PEO.6: 3 residues within 4Å: Chain B: T.38, H.60, Y.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.71 PEO.8: 2 residues within 4Å: Chain B: W.66 Ligands: PEO.5 3 PLIP interactions: 3 interactions with chain B Water bridges: B:C.67, B:N.99, B:N.99

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.3: 1 residues within 4Å: Chain A: S.139 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.168

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: R.170, A.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.171, A:A.171 Water bridges: A:A.171, A:A.171

1 x SHV: HEPTANOIC ACID(Non-covalent)

SHV.7: 4 residues within 4Å: Chain A: C.6, N.126, A.129 Chain B: C.6 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.6, A:N.126 Hydrophobic interactions: A:A.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurya, A. et al., Ligand recognition by peptidoglycan recognition protein-S (PGRP-S): structure of the complex of camel PGRP-S with heptanoic acid at 2.15 angstrom resolution. Int J Biochem Mol Biol (2022)

Release Date

2022-06-15

Peptides

Peptidoglycan recognition protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptidoglycan recognition protein 1

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