7XU8 | pdb_00007xu8

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

PDB DOI: https://doi.org/10.2210/pdb7XU8/pdb
Entry: 7XU8 supersedes: 3UML

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

Deposited: 2022-05-18 Released: 2022-06-15
Deposition Author(s): Maurya, A., Ahmad, N., Viswanathan, V., Singh, P.K., Yamini, S., Sharma, P., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.282 (Depositor), 0.285 (DCC)
R-Value Work:
0.220 (Depositor), 0.225 (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

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.

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

(2022) Int J Biochem Mol Biol 13: 28-39

PubMed: 36188729 Search on PubMed Search on PubMed Central
Primary Citation Related Structures:
7XU8

PubMed Abstract:
Peptidoglycan recognition proteins (PGRPs) are important components of the innate immune system which provide the first line of defense against invading microbes. There are four members in the family of PGRPs in animals of which PGRP-S is a common domain. It is responsible for the binding to microbial cell wall molecules. In order to understand the mode of binding of PGRP-S to the components of the bacterial cell wall, the structure of the complex of camel PGRP-S (CPGRP-S) with heptanoic acid has been determined at 2.15 Å resolution. The structure determination showed the presence of four crystallographically independent protein molecules which are designated as A, B, C, and D. These four protein molecules associate in the form of two homodimers which are represented as A-B and C-D dimers. The association between molecules A and B gives rise to a shallow cleft on the surface at one end of the dimeric interface. One molecule of heptanoic acid is observed at this binding site in the A-B dimer. The association of C and D molecules results in the formation of a long zig-zag tunnel along with the C-D interface. In the cleft at the C-D interface, three molecules of hydrogen peroxide along with other non-water solvent molecules have been observed. The analysis of the several complexes of CPGRP-S with fatty acids and non-fatty acids such as peptidoglycan, lipopolysaccharide, and lipoteichoic acid shows that the fatty acids bind at the A-B site while non-fatty acids interact through C-D interface.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 76.93 kDa
Atom Count: 5,886
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
SHV (Subject of Investigation/LOI) Query on SHV 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]	HEPTANOIC ACID C₇ H₁₄ O₂ MNWFXJYAOYHMED-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
MPD (Subject of Investigation/LOI) Query on MPD Download:Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain E [auth A] MOL2 format, chain R [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain E [auth A] mmCIF format, chain R [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain E [auth A]	E [auth A], M [auth C], N [auth C], R [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth C]
CO3 (Subject of Investigation/LOI) Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEO (Subject of Investigation/LOI) Query on PEO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	F [auth A] I [auth B] J [auth B] L [auth B] O [auth C] F [auth A], I [auth B], J [auth B], L [auth B], O [auth C], P [auth C], Q [auth C], S [auth D], T [auth D]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]