1O3T

PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES

Structural Biology Knowledgebase: 1O3T SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.303
  • R-Value Work: 0.230

Literature

Macromolecules
Sequence Display for 1O3T

Classification: GENE REGULATION / DNA

Total Structure Weight: 64787.46


Macromolecule Entities
Molecule Chains Length Organism Details
CATABOLITE GENE ACTIVATOR PROTEIN A, B 200 Escherichia coli Gene Name(s): crp cap csm b3357 JW5702
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3' C, F 14 synthetic
5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*TP*CP*G)-3' D, E 17 synthetic

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

A, B ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
CYCLIC AMP; CAMP (Synonym)
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CMP IC50: 129690 nM (95) BindingDB
ΔG: -32.2 - -25.5 kJ/mol (100) BindingDB
ΔH: -19.2 - 51.5 kJ/mol (100) BindingDB
-TΔS: -83.2 - -9.5 kJ/mol (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.303
  • R-Value Work: 0.230
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 136.99 α = 90.00
b = 152.80 β = 90.00
c = 76.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-03-18
  • Released Date: 2003-04-08
  • Deposition author(s): Chen, S., Vojtechovsky, J., Parkinson, G.N., Ebright, R.H., Berman, H.M.
  • Previous versions: 1DBC

Revision History

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