5UGO

DNA polymerase beta nick complex with imidodiphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 5UGO

Classification: Transferase / DNA

Total Structure Weight: 48254.20


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase beta A 335 Homo sapiens EC#: 2.7.7.7 IUBMB 4.2.99 IUBMB
Gene Name(s): POLB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T 16 Synthetic construct
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') P 11 Synthetic construct
DNA (5'-D(P*GP*TP*CP*GP*G)-3') D 5 Synthetic construct

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

A IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.179
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.60 α = 90.00
b = 79.31 β = 107.55
c = 55.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-01-09
  • Released Date: 2017-07-26
  • Deposition author(s): Freudenthal, B.D., Wilson, S.H., Beard, W.A.

Revision History

  • Version 1_0: 2017-07-26

    Type: Initial release

  • Version 1_1: 2017-08-02

    Type: Author supporting evidence

  • Version 1_2: 2017-08-16

    Type: Database references

  • Version 1_3: 2017-10-04

    Type: Database references