4F9N

Crystal structure of the complex of type I Ribosome inactivating protein from Momordica balsamina with N7-methylated guanine at 2.65 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome inactivating protein246Momordica 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
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MY6
Query on MY6
Download Ideal Coordinates CCD File 
C [auth A]2-amino-7-methyl-1,7-dihydro-6H-purin-6-one
C6 H7 N5 O
FZWGECJQACGGTI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.428α = 90
b = 131.428β = 90
c = 39.808γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary