9DDR | pdb_00009ddr

Ternary substrate complex of DNA polymerase iota with DNA (template A), Ca2+, and dTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Visualizing DNA polymerase iota catalyze Hoogsteen-directed DNA synthesis

Frevert, Z.Reusch, D.T.Gildenberg, M.S.Jordan, S.M.Ryan, B.J.Freudenthal, B.D.Washington, M.T.

(2025) Nat Commun 16: 5979


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase iota420Homo sapiensMutation(s): 0 
Gene Names: POLIRAD30B
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNA4 (Homo sapiens)
Explore Q9UNA4 
Go to UniProtKB:  Q9UNA4
PHAROS:  Q9UNA4
GTEx:  ENSG00000101751 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNA4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')18Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.556α = 90
b = 97.556β = 90
c = 202.148γ = 120
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM081433

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release