6D0Z

Polymerase Eta cytarabine (AraC) extension ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for polymerase eta-promoted resistance to the anticancer nucleoside analog cytarabine.

Rechkoblit, O.Choudhury, J.R.Buku, A.Prakash, L.Prakash, S.Aggarwal, A.K.

(2018) Sci Rep 8: 12702-12702


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase eta
A
435Homo sapiensMutation(s): 1 
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*TP*GP*CP*AP*GP*TP*GP*CP*T)-3')T12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA/RNA (5'-D(*AP*GP*CP*AP*CP*TP*G)-R(P*(CAR))-3')P8synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DZ4
Query on DZ4

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Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
C10 H17 N6 O11 P3
WKIPJDSLGCBQCU-RRKCRQDMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAR
Query on CAR
P
RNA LINKINGC9 H14 N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 98.789α = 90.00
b = 98.789β = 90.00
c = 81.772γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA200575

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release