1U8B

Crystal structure of the methylated N-ADA/DNA complex

Structural Biology Knowledgebase: 1U8B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.235

Literature

Macromolecules
Sequence Display for 1U8B

Classification: METAL BINDING PROTEIN / DNA

Total Structure Weight: 26433.12


Macromolecule Entities
Molecule Chains Length Organism Details
Ada polyprotein A 133 Escherichia coli Mutation: E75D, A79P, Q80R
Gene Name(s): ada b2213 JW2201
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*TP*AP*AP*AP*TP*T)-3' B 6 synthetic
5'-D(P*AP*AP*TP*TP*T)-3' C 5 synthetic
5'-D(P*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*AP*T)-3' D 12 synthetic
5'-D(*AP*AP*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*T)-3' E 13 synthetic

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

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET
SMC
Query on SMC
A L-PEPTIDE LINKING C4 H9 N O2 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.235
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 28.84 α = 90.00
b = 84.59 β = 90.00
c = 108.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-08-05
  • Released Date: 2005-10-11
  • Deposition author(s): He, C., Hus, J.-C., Sun, L.J., Zhou, P., Norman, D.P.G., Dotsch, V., Gross, J.D., Lane, W.S., Wagner, G., Verdine, G.L.

Revision History

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