7XFW | pdb_00007xfw

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.07 A resolution.

PDB DOI: https://doi.org/10.2210/pdb7XFW/pdb
Entry: 7XFW supersedes: 6J3W

Classification: IMMUNE SYSTEM
Organism(s): Camelus dromedarius
Mutation(s): No

Deposited: 2022-04-02 Released: 2022-05-11
Deposition Author(s): Maurya, A., Singh, P.K., Viswanathan, V., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.258 (Depositor), 0.263 (DCC)
R-Value Work:
0.200 (Depositor), 0.208 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of the complex of camel peptidoglycan recognition protein-S with hexanoic acid reveals novel features of the versatile ligand-binding site at the dimeric interface.

Maurya, A., Sharma, P., Singh, P.K., Viswanathan, V., Kaur, P., Sharma, S., Singh, T.P.

(2022) Biochim Biophys Acta Proteins Proteom 1871: 140887-140887

PubMed: 36596432 Search on PubMed
DOI: https://doi.org/10.1016/j.bbapap.2022.140887
Primary Citation Related Structures:
7XFW

PubMed Abstract:
The short peptidoglycan recognition protein (PGRP-S) of the innate immune system recognizes the invading microbes through binding to their cell wall molecules. In order to understand the mode of binding of PGRP-S to bacterial cell wall molecules, the structure of the complex of camel PGRP-S (CPGRP-S) with hexanoic acid has been determined at 2.07 Å resolution. Previously, we had reported the structures of CPGRP-S in the native unbound state as well as in the complexed forms with the components of various bacterial cell wall molecules such as peptidoglycan (PGN), lipopolysaccharide (LPS), lipoteichoic acid (LTA), mycolic acid (MA) and other fatty acids. These structures revealed that CPGRP-S formed two homodimers which were designated as A-B and CD dimers. It also showed that the fatty acids bind to CPGRP-S in the binding site at the A-B dimer while the non-fatty acids were shown to bind at the interfaces of both A-B and CD dimers. The present structure of the complex of CPGRP-S with hexanoic acid (HA) showed that HA binds to CPGRP-S at the interface of CD dimer. HA was located in the same groove at the CD interface which was occupied by non-fatty acids such as PGN, LPS and LTA and interacts with residues from both C and D molecules. HA is firmly held in the groove with several hydrogen bonds and a number of van der Waals contacts. This is the first structure which reports the binding of a fatty acid in the cleft at the interface of CD dimer.

Organizational Affiliation

Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.

Macromolecule Content

Total Structure Weight: 77.29 kDa
Atom Count: 5,757
Modeled Residue Count: 664
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan recognition protein 1	A, B, C, D	171	Camelus dromedarius	Mutation(s): 0
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12 Go to UniProtKB: Q9GK12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GK12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA (Subject of Investigation/LOI) Query on TLA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain R [auth D]	E [auth A], L [auth C], R [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth A] Focus chain L [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth C] Focus chain R [auth D]
6NA (Subject of Investigation/LOI) Query on 6NA Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	F [auth A] G [auth B] J [auth B] M [auth C] P [auth C] F [auth A], G [auth B], J [auth B], M [auth C], P [auth C], Q [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth C] Focus chain Q [auth C]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain O [auth C] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C]	H [auth B], I [auth B], O [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain O [auth C] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain O [auth C]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]