4NIG

Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 4NIG

Classification: OXIDOREDUCTASE / DNA

Total Structure Weight: 31062.62


Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-ketoglutarate-dependent dioxygenase AlkB A 205 Escherichia coli EC#: 1.14.11.33 IUBMB
Fragment: UNP residues 13-216
Mutation: S129C, D135I, E136H
Gene Name(s): alkB aidD b2212 JW2200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3' B 13 synthetic
5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3' C 13 synthetic

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

A 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
6MA
Query on 6MA
B DNA LINKING C11 H16 N5 O6 P A
2YR
Query on 2YR
B NON-POLYMER C11 H18 N3 O7 P S --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.180
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 41.49 α = 90.00
b = 76.08 β = 108.46
c = 52.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-11-06
  • Released Date: 2014-04-16
  • Deposition author(s): Yi, C.Q., Zhu, C.X.

Revision History

  • 2014-05-28
    Type: Non-polymer description, Structure summary