3VD6

Both Zn Fingers of GATA1 Bound to Palindromic DNA Recognition Site, P21 Crystal Form

Structural Biology Knowledgebase: 3VD6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.218

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VD6

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 26029.09


Macromolecule Entities
Molecule Chains Length Organism Details
Erythroid transcription factor C 119 Mus musculus Fragment: N and C Fingers, residues 200-318
Gene Name(s): Gata1 Gf-1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3') A 20 synthetic
DNA (5'-D(*AP*AP*GP*AP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*C)-3') B 20 synthetic

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

C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A 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: 1.98 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.218
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.33 α = 90.00
b = 37.40 β = 98.51
c = 65.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-04
  • Released Date: 2013-01-16
  • Deposition author(s): Jacques, D.A., Ripin, N., Wilkinson-White, L.E., Guss, J.M., Matthews, J.M.

Revision History

No revisions since initial release