4J3E

The 1.9A crystal structure of humanized Xenopus Mdm2 with nutlin-3a

Structural Biology Knowledgebase: 4J3E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.194

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4J3E

Classification: LIGASE / ANTAGONIST

Total Structure Weight: 10640.25

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase Mdm2 A 86 Xenopus laevis EC#: 6.3.2 IUBMB
Fragment: N-terminal domain (UNP residues 21-105)
Mutation: I50L, P92H, L95I
Gene Name(s): mdm2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4- methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro- 1H-imidazol-1-yl}carbonyl)piperazin-2-one
Nutlin 3a (Synonym)
C30 H30 Cl2 N4 O4
BDUHCSBCVGXTJM-WUFINQPMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NUT N/A in BindingDB
IC50: 88 nM  BindingMOAD
IC50: 88 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.194
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.89 α = 90.00
b = 67.66 β = 90.00
c = 67.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-05
  • Released Date: 2013-04-24
  • Deposition author(s): Graves, B.J., Lukacs, C.M., Kammlott, R.U., Crowther, R.

Revision History

  • 2014-10-08
    Type: Citation | Details: Citation update