5UGP

DNA polymerase beta complex with a 1nt gap and dCMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 5UGP

Classification: Transferase / DNA

Total Structure Weight: 48222.65


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(P*GP*TP*CP*GP*G)-3') D 5 Synthetic construct
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') P 10 Synthetic construct
DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T 16 Synthetic construct

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
8CP
Query on 8CP

A 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine
C9 H17 N4 O12 P3
ICHPBSCTWPZUQK-SHYZEUOFSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.183
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.78 α = 90.00
b = 79.97 β = 107.68
c = 55.45 γ = 90.00

Structure Validation

View Full Validation Report



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

  • 2017-08-02
    Type: Author supporting evidence
  • 2017-08-16
    Type: Database references