2OH2 | pdb_00002oh2

Ternary Complex of Human DNA Polymerase

• PDB DOI: https://doi.org/10.2210/pdb2OH2/pdb
• NAKB: 2OH2

• Classification: Transferase/DNA
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2007-01-09 Released: 2007-02-27 
• Deposition Author(s): Lone, S., Townson, S.A., Uljon, S.N., Prakash, S., Prakash, L., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.294 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.224 (DCC) 

Literature

Ternary complex of the catalytic core of human DNA polymerase Kappa with DNA and dTT

Lone, S., Townson, S.A., Uljon, S.N., Johnson, R.E., Brahma, A., Nair, D.T., Prakash, S., Prakash, L., Aggarwal, A.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 135.98 kDa 
• Atom Count: 7,583 
• Modeled Residue Count: 918 
• Deposited Residue Count: 1,078 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase kappa	E [auth A], F [auth B]	508	Homo sapiens	Mutation(s): 0  Gene Names: POLK, DINB1 EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT6 (Homo sapiens) Explore Q9UBT6  Go to UniProtKB:  Q9UBT6
PHAROS:  Q9UBT6 GTEx:  ENSG00000122008

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3'	A [auth S], C [auth P]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'	B [auth Q], D [auth T]	18	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	H [auth A], J [auth B]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
MG	G [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.294 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.224 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.15	α = 90
b = 152.472	β = 90
c = 217.389	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Lone, S., Townson, S.A., Uljon, S.N., Prakash, S., Prakash, L., Aggarwal, A.K.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations