9UGE | pdb_00009uge

Crystal structure of the complex of camel peptidoglycan recognition protein, PGRP-S with malic acid and oxalic acid at 2.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb9UGE/pdb
Entry: 9UGE supersedes: 4Q9E

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

Deposited: 2025-04-11 Released: 2025-05-14
Deposition Author(s): Barik, D., Ahmad, N., Maurya, A., Yamini, S., Sharma, P., Yadav, S.P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.283 (Depositor), 0.281 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the complex of camel peptidoglycan recognition protein, PGRP-S with malic acid and oxalic acid at 2.3 A resolution

Barik, D., Ahmad, N., Maurya, A., Yamini, S., Sharma, P., Yadav, S.P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 76.36 kDa
Atom Count: 5,740
Modeled Residue Count: 684
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

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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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLT (Subject of Investigation/LOI) Query on MLT Download:Ideal Coordinates CCD File SDF format, chain E [auth D] MOL2 format, chain E [auth D] mmCIF format, chain E [auth D]	E [auth D]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]
OXD (Subject of Investigation/LOI) Query on OXD Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth D] MOL2 format, chain G [auth D] MOL2 format, chain F [auth D] mmCIF format, chain G [auth D] mmCIF format, chain F [auth D]	F [auth D], G [auth D]	OXALIC ACID C₂ H₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain G [auth D] Interactions & Density Focus chain F [auth D] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.283 (Depositor), 0.281 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.308	α = 90
b = 101.623	β = 90
c = 162.683	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
AMoRE	phasing
DENZO	data reduction
SCALEPACK	data scaling
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

This entry supersedes: 4Q9E

Funding Organization	Location	Grant Number
Not funded	India	--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.