6A89

Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution

• PDB DOI: https://doi.org/10.2210/pdb6A89/pdb

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


• Deposited: 2018-07-06 Released: 2018-07-25 
• Deposition Author(s): Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.249 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution

Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., 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.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.94 kDa 
• Atom Count: 5,559 
• Modelled Residue Count: 668 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan recognition protein 1	A, B, C, D	167	Camelus dromedarius	Mutation(s): 0
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12  Go to UniProtKB:  Q9GK12

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
API	F [auth B]	2,6-DIAMINOPIMELIC ACID C7 H14 N2 O4 GMKMEZVLHJARHF-SYDPRGILSA-N
RIB	I [auth D]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N
TLA	H [auth D]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL	G [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.249 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.5	α = 90
b = 101.37	β = 90
c = 163.04	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Structure summary
• Version 3.1: 2023-11-22
  Changes: Refinement description