4ORV

Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 7- phenylheptanoic acid and N- acetylglucosamine at 2.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb4ORV/pdb

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

Deposited: 2014-02-12 Released: 2014-03-05
Deposition Author(s): Yamini, S., Sharma, P., Yadav, S.P., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.231
R-Value Work: 0.210
R-Value Observed: 0.210

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

Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 7- phenylheptanoic acid and N- acetylglucosamine at 2.50 A resolution

Yamini, S., Sharma, P., Yadav, S.P., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 76.92 kDa
Atom Count: 5,798
Modelled Residue Count: 684
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
XXC Query on XXC Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain E [auth B] MOL2 format, chain I [auth D] MOL2 format, chain E [auth B] mmCIF format, chain I [auth D] mmCIF format, chain E [auth B]	E [auth B], I [auth D]	7-phenylheptanoic acid C₁₃ H₁₈ O₂ ZVSXKFNTWOIGJI-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain I [auth D] Interactions & Density Focus chain E [auth B] Focus chain I [auth D]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.231
R-Value Work: 0.210
R-Value Observed: 0.210
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.535	α = 90
b = 101.56	β = 90
c = 163.457	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-05
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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4ORV

Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 7- phenylheptanoic acid and N- acetylglucosamine at 2.50 A resolution

Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 7- phenylheptanoic acid and N- acetylglucosamine at 2.50 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)