9EMH | pdb_00009emh

KOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA containing two HNA nucleotides

• PDB DOI: https://doi.org/10.2210/pdb9EMH/pdb
• NAKB: 9EMH

• Classification: TRANSFERASE
• Organism(s): Thermococcus kodakarensis KOD1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-08 Released: 2025-09-24 
• Deposition Author(s): Gutfreund, C., Betz, K.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystallographic Insights into a Mutant Archaeal B-Family Polymerase processing HNA

Gutfreund, C., Betz, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 99.28 kDa 
• Atom Count: 6,861 
• Modeled Residue Count: 785 
• Deposited Residue Count: 803 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	774	Thermococcus kodakarensis KOD1	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for D0VWU9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore D0VWU9  Go to UniProtKB:  D0VWU9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*CP*A)-3')	B [auth P]	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*CP*(6HT)P*(6HG)P*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')	C [auth T]	16	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	D [auth A], G [auth A], H [auth A], J [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.481	α = 90
b = 151.624	β = 90
c = 67.584	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Gutfreund, C., Betz, K.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release