7DY5 | pdb_00007dy5

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 (Depositor), 0.250 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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
Modeled 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] mmCIF format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF 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] mmCIF 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] mmCIF format, chain M [auth D] mmCIF 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] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF 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] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.252 (Depositor), 0.250 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.085	α = 90
b = 101.355	β = 90
c = 163.022	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

This entry supersedes: 6JTE

Revision History (Full details and data files)

Version 1.0: 2021-02-17
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary