4IBU

Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R in sequence-specific complex with DNA

Structural Biology Knowledgebase: 4IBU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.163

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IBU

Classification: DNA BINDING PROTEIN / DNA

Total Structure Weight: 106061.32


Macromolecule Entities
Molecule Chains Length Organism Details
Cellular tumor antigen p53 A, B, C, D 200 Homo sapiens Fragment: DNA binding domain
Mutation: R273C, T284R
Gene Name(s): TP53 Gene View P53
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') E, F, G, H 12 synthetic

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

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, C, D 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

B, H ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.163
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.54 α = 82.96
b = 58.16 β = 87.78
c = 77.97 γ = 73.57

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-09
  • Released Date: 2013-08-14
  • Deposition author(s): Eldar, A., Rozenberg, H., Diskin-Posner, Y., Shakked, Z.

Revision History

  • 2013-10-23
    Type: Citation | Details: Citation update
  • 2013-08-28
    Type: Biological assembly | Details: Updated biological assembly information