4KPV

Crystal structure of the complex of ribosome inactivating protein from Momordica balsamina with Pyrimidine-2,4(1H,3H)-dione at 2.57 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the complex of ribosome inactivating protein from Momordica balsamina with Pyrimidine-2,4(1H,3H)-dione at 2.57 A resolution

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA N-glycosidase A246Momordica balsaminaMutation(s): 0 
Gene Names: RIP
EC: 3.2.2.22
Find proteins for D9J2T9 (Momordica balsamina)
Explore D9J2T9 
Go to UniProtKB:  D9J2T9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
URA
Query on URA

Download Ideal Coordinates CCD File 
A
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.95α = 90
b = 129.95β = 90
c = 39.434γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary