7DY5

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

PDB DOI: https://doi.org/10.2210/pdb7DY5/pdb
Entry: 7DY5 supersedes: 6JTE

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

Deposited: 2021-01-20 Released: 2021-02-17
Deposition Author(s): Maurya, A., Viswanathan, V., Sharma, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.252
R-Value Work: 0.188
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of the ternary complex of peptidoglycan recognition protein-short (PGRP-S)

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

To be published.

Macromolecule Content

Total Structure Weight: 77.08 kDa
Atom Count: 5,698
Modelled Residue Count: 664
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GK12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 D] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain O [auth D]	E [auth A], L [auth D], O [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth A] Focus chain L [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth D] Focus chain O [auth D]
6NA (Subject of Investigation/LOI) Query on 6NA Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C]	H [auth C]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D]	M [auth D], N [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain M [auth D] Focus chain N [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C]	F [auth A], I [auth C], J [auth C], K [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]