5F9N

CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dCMPNPP ACROSS A DNA TEMPLATE CONTAINING 1,N2-ETHENODEOXYGUANOSINE LESION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Bypass of the 1, N2-Ethenodeoxyguanosine Lesion by Human DNA Polymerase Eta

Patra, A.Egli, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase eta
A
435Homo sapiensMutation(s): 0 
Gene Names: POLH (RAD30, RAD30A, XPV)
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Go to Gene View: POLH
Go to UniProtKB:  Q9Y253
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*TP*(GNE)P*AP*TP*GP*AP*CP*GP*CP*T)-3')T12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')P8synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0KX
Query on 0KX

Download SDF File 
Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
C9 H17 N4 O12 P3
STYMTWKSQLVXJN-SHYZEUOFSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GNE
Query on GNE
T
DNA LINKINGC12 H14 N5 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.158 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 99.080α = 90.00
b = 99.080β = 90.00
c = 81.890γ = 120.00
Software Package:
Software NamePurpose
xia2data scaling
xia2data reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-12-09 
  • Released Date: 2016-12-21 
  • Deposition Author(s): Patra, A., Egli, M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence
  • Version 1.2: 2019-01-16
    Type: Data collection, Source and taxonomy
  • Version 1.3: 2019-12-25
    Type: Author supporting evidence