1LB2

Structure of the E. coli alpha C-terminal domain of RNA polymerase in complex with CAP and DNA

Structural Biology Knowledgebase: 1LB2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 1LB2

Classification: GENE REGULATION / DNA

Total Structure Weight: 56099.30


Macromolecule Entities
Molecule Chains Length Organism Details
CATABOLITE GENE ACTIVATOR PROTEIN A 209 Escherichia coli Gene Name(s): crp cap csm b3357 JW5702
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase alpha chain B, E 84 Escherichia coli EC#: 2.7.7.6 IUBMB
Fragment: alpha CTD, alpha Carboxy terminal domain
Gene Name(s): rpoA pez phs sez b3295 JW3257
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3' K 20 synthetic
5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3' J 24 synthetic

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

A 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: 3.1 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.211
  • Space Group: P 62 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 175.97 α = 90.00
b = 175.97 β = 90.00
c = 158.02 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-04-01
  • Released Date: 2002-09-06
  • Deposition author(s): Benoff, B., Yang, H., Lawson, C.L., Parkinson, G., Liu, J., Blatter, E., Ebright, Y.W., Berman, H.M., Ebright, R.H.

Revision History

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