4PHE

Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The spontaneous base substitution mechanisms of human DNA polymerase beta

Koag, M.C.Lee, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
329Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens)
Go to Gene View: POLB
Go to UniProtKB:  P06746
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')T16synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')P10synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*CP*GP*G)-3')D5synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
XG4
Query on XG4

Download SDF File 
Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
C10 H17 N6 O12 P3
DWGAAFQEGIMTIA-KVQBGUIXSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.535α = 90.00
b = 79.093β = 105.78
c = 54.796γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-05-06 
  • Released Date: 2015-05-06 
  • Deposition Author(s): Koag, M.C., Lee, S.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES23101

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence