2RAM

A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER

Structural Biology Knowledgebase: 2RAM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.308
  • R-Value Work: 0.213

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2RAM

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 75046.60


Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (TRANSCRIPTION FACTOR NF-KB P65) A, B 273 Mus musculus Fragment: P65 RESIDUES 19 - 291
Gene Name(s): Rela Nfkb3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU)P*CP*CP*AP*GP*CP*CP*G)-3') C, D 20 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DTV
Query on DTV

A, B (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5IU
Query on 5IU
C, D DNA LINKING C9 H12 I N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.308
  • R-Value Work: 0.213
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.81 α = 90.00
b = 80.62 β = 90.00
c = 167.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-11-23
  • Released Date: 1998-05-27
  • Deposition author(s): Chen, Y.Q., Ghosh, S., Ghosh, G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4