3NW3

Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with the PGN Fragment at 2.5 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

Starting Model: experimental
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This is version 4.0 of the entry. See complete history


Literature

Multiligand specificity of pathogen-associated molecular pattern-binding site in peptidoglycan recognition protein

Sharma, P.Dube, D.Sinha, M.Mishra, B.Dey, S.Mal, G.Pathak, K.M.Kaur, P.Sharma, S.Singh, T.P.

(2011) J Biol Chem 286: 31723-31730

  • DOI: https://doi.org/10.1074/jbc.M111.264374
  • Primary Citation of Related Structures:  
    3NG4, 3NW3

  • PubMed Abstract: 

    The peptidoglycan recognition protein PGRP-S is an innate immunity molecule that specifically interacts with microbial peptidoglycans and other pathogen-associated molecular patterns. We report here two structures of the unique tetrameric camel PGRP-S (CPGRP-S) complexed with (i) muramyl dipeptide (MDP) at 2.5 Å resolution and (ii) GlcNAc and β-maltose at 1.7Å resolution. The binding studies carried out using surface plasmon resonance indicated that CPGRP-S binds to MDP with a dissociation constant of 10(-7) M, whereas the binding affinities for GlcNAc and β-maltose separately are in the range of 10(-4) M to 10(-5) M, whereas the dissociation constant for the mixture of GlcNAc and maltose was estimated to be 10(-6) M. The data from bacterial suspension culture experiments showed a significant inhibition of the growth of Staphylococcus aureus cells when CPGRP-S was added to culture medium. The ELISA experiment showed that the amount of MDP-induced production of TNF-α and IL-6 decreased considerably after the introduction of CPGRP-S. The crystal structure determinations of (i) a binary complex with MDP and (ii) a ternary complex with GlcNAc and β-maltose revealed that MDP, GlcNAc, and β-maltose bound to CPGRP-S in the ligand binding cleft, which is situated at the interface of molecules C and D of the homotetramer formed by four protein molecules A, B, C, and D. In the binary complex, the muramyl moiety of MDP is observed at the C-D interface, whereas the peptide chain protrudes into the center of tetramer. In the ternary complex, GlcNAc and β-maltose occupy distinct non-overlapping positions belonging to different subsites.


  • Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India 110029.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan recognition protein 1
A, B, C, D
171Camelus dromedariusMutation(s): 0 
UniProt
Find proteins for Q9GK12 (Camelus dromedarius)
Explore Q9GK12 
Go to UniProtKB:  Q9GK12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GK12
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download Ideal Coordinates CCD File 
E [auth C]2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
TLA
Query on TLA

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F [auth D]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
DGN
Query on DGN

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H [auth D]D-GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-GSVOUGTGSA-N
GOL
Query on GOL

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G [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
LAC
Query on LAC

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J [auth D]LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
ALA
Query on ALA

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I [auth D]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.17α = 90
b = 102β = 90
c = 161.6γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-13
    Changes: Database references
  • Version 2.0: 2020-07-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 4.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations