3COR

Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with N-acetylgalactosamine at 3.1 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.208 

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 complex of peptidoglycan recognition protein (PGRP-S) with N-acetylgalactosamine at 3.1 A resolution

Sharma, P.Vikram, G.Singh, N.Sinha, M.Sharma, S.Kaur, P.Singh, T.P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidoglycan recognition proteinA, B, C, D171Camelus dromedariusMutation(s): 0 
Gene Names: PGLYRP1PGLYRPPGRP
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGA
Query on NGA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
G [auth C]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.208 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.21α = 90
b = 102.44β = 90
c = 163.44γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
CNSrefinement
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: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary