4H0Z

Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina with N-acetyl muramic acid at 2.0 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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 Ribosome inactivating protein from Momordica balsamina with N-acetyl muramic acid at 2.0 Angstrom resolution

Singh, A.Pandey, S.Kushwaha, G.S.Sinha, M.Bhushan, A.Kaur, P.Sharma, S.Singh, T.P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA N-glycosidase246Momordica balsaminaMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for D9J2T9 (Momordica balsamina)
Explore D9J2T9 
Go to UniProtKB:  D9J2T9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9J2T9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMU
Query on AMU

Download Ideal Coordinates CCD File 
C [auth A]N-acetyl-beta-muramic acid
C11 H19 N O8
MNLRQHMNZILYPY-YVNCZSHWSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.414α = 90
b = 130.414β = 90
c = 40.243γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary