6FWK

The crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.503 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon.

Parkash, V.Kulkarni, Y.Ter Beek, J.Shcherbakova, P.V.Kamerlin, S.C.L.Johansson, E.

(2019) Nat Commun 10: 373-373


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase epsilon catalytic subunit A
A, B
1191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: POL2 (DUN2)
EC: 2.7.7.7
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21951
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3')P,C11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3')T,D15synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

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Download CCD File 
A, B
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
C, P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.503 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.961α = 90.00
b = 70.342β = 112.82
c = 158.965γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
CancerfondenSweden--
Knut and Alice Wallenberg FoundationSweden--

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references