4KWN

A new stabilizing water structure at the substrate binding site in ribosome inactivating protein from Momordica balsamina at 1.80 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A new stabilizing water structure at the substrate binding site in ribosome inactivating protein from Momordica balsamina at 1.80 A resolution

Yamini, S.Pandey, S.Singh, A.Bhushan, A.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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.212α = 90
b = 130.212β = 90
c = 39.847γ = 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  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Structure summary
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary