4GLX

DNA ligase A in complex with inhibitor

Structural Biology Knowledgebase: 4GLX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GLX

Classification: LIGASE / LIGASE INHIBITOR / DNA

Total Structure Weight: 81353.51


Macromolecule Entities
Molecule Chains Length Organism Details
DNA ligase A 586 Escherichia coli EC#: 6.5.1.2 IUBMB
Gene Name(s): ligA dnaL lig lop pdeC b2411 JW2403
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (26-MER) B 26 Synthetic construct
DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3') C 13 Synthetic construct
DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3') D 13 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0XS
Query on 0XS

A 2-amino-6-bromo-7-(trifluoromethyl)-1,8-naphthyridine- 3-carboxamide
C10 H6 Br F3 N4 O
CENBBVPSOFGGNG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0XS N/A in BindingDB
N/A in BindingMoad
Kd: 16 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.201
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.99 α = 90.00
b = 100.14 β = 105.50
c = 86.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-15
  • Released Date: 2012-10-10
  • Deposition author(s): Prade, L., Lange, R., Tidten-Luksch, N., Chambovey, A.

Revision History

  • 2012-10-31
    Type: Citation | Details: Citation update