7XFX | pdb_00007xfx

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.28 A resolution.

PDB DOI: https://doi.org/10.2210/pdb7XFX/pdb
Entry: 7XFX supersedes: 6JVE

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: 2.28 ?
R-Value Free:
0.255 (Depositor), 0.260 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.28 A resolution.

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

To be published.

Macromolecule Content

Total Structure Weight: 77.23 kDa
Atom Count: 5,694
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 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 J [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain Q [auth D]	E [auth A], J [auth C], Q [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth C] Focus chain Q [auth D]
6NA (Subject of Investigation/LOI) Query on 6NA Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A] G [auth A] H [auth B] K [auth C] N [auth C] F [auth A], G [auth A], H [auth B], K [auth C], N [auth C], R [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth C] Focus chain R [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	M [auth C], O [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain M [auth C] Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 ?
R-Value Free: 0.255 (Depositor), 0.260 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 88.661	α = 90
b = 101.653	β = 90
c = 163.328	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-11

Deposition Author(s):

This entry supersedes: 6JVE

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-05-11
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary