6M7U

Human DNA polymerase eta in a non-productive ternary complex with Mg2+ and dTMPNPP oppositing cdA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution

Weng, P.Gao, Y.Gregory, M.T.Wang, P.Wang, Y.Yang, W.

(2018) Proc.Natl.Acad.Sci.Usa --: --


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(*AP*GP*TP*GP*TP*GP*AP*G)-3')P8Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*(02I)P*CP*TP*CP*AP*CP*AP*CP*T)-3')T11Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
1FZ
Query on 1FZ

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Download CCD File 
A
5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
C10 H18 N3 O13 P3
YRKUYVYMPXAOAT-XLPZGREQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
02I
Query on 02I
T
DNA LINKINGC10 H12 N5 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.310α = 90.00
b = 80.470β = 90.00
c = 142.070γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK036146

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release