4I47

Crystal structure of the Ribosome inactivating protein complexed with methylated guanine

Structural Biology Knowledgebase: 4I47 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.165

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I47

Classification: HYDROLASE

Total Structure Weight: 27683.52

Macromolecule Entities
Molecule Chains Length Organism Details
rRNA N-glycosidase A 246 Momordica balsamina EC#: 3.2.2.22 IUBMB
Gene Name(s): RIP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MY6
Query on MY6

A 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one
C6 H7 N5 O
FZWGECJQACGGTI-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MY6 N/A in BindingDB
N/A in BindingMoad
Kd: 120 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.165
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 131.43 α = 90.00
b = 131.43 β = 90.00
c = 39.81 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-27
  • Released Date: 2012-12-12
  • Deposition author(s): Yamini, S., Kushwaha, G.S., Bhushan, A., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History

  • 2013-05-15
    Type: Citation | Details: Citation update