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

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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

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT (Subject of Investigation/LOI)	E [auth D]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
OXD (Subject of Investigation/LOI)	F [auth D], G [auth D]	OXALIC ACID C2 H2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-N

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

Entry History & Funding Information

Deposition Data

• Released Date: 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.
• This entry supersedes: 4Q9E

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Funding Organization	Location	Grant Number
Not funded	India	--

Revision History  

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