3U7G

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTAp)

Structural Biology Knowledgebase: 3U7G SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 3U7G

Classification: HYDROLASE TRANSFERASE / DNA

Total Structure Weight: 44134.50


Macromolecule Entities
Molecule Chains Length Organism Details
Bifunctional polynucleotide phosphatase/kinase A 379 Mus musculus EC#: 2.7.1.78 IUBMB 3.1.3.32 IUBMB
Mutation: D170A
Gene Name(s): Pnkp
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA X 5 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A, X PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.207
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 77.16 α = 90.00
b = 43.03 β = 107.12
c = 127.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-10-13
  • Released Date: 2011-12-14
  • Deposition author(s): Coquelle, N., Havali, Z., Bernstein, N., Green, R., Glover, J.N.M.

Revision History

  • 2012-08-29
    Type: Citation | Details: Citation update