2CFM

ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS

Structural Biology Knowledgebase: 2CFM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 2CFM

Classification: LIGASE

Total Structure Weight: 64991.80

Macromolecule Entities
Molecule Chains Length Organism Details
THERMOSTABLE DNA LIGASE A 561 Pyrococcus furiosus EC#: 6.5.1.1 IUBMB
Details: AMP IS BOUND IN THE POCKET NON-COVALENTLY
Gene Name(s): lig PF1635
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.204
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.87 α = 90.00
b = 87.40 β = 109.22
c = 62.65 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-02-22
  • Released Date: 2006-07-12
  • Deposition author(s): Nishida, H., Ishino, Y., Morikawa, K.

Revision History

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