9EN0 | pdb_00009en0

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

PDB DOI: https://doi.org/10.2210/pdb9EN0/pdb
NAKB: 9EN0

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

Deposited: 2024-03-12 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: 2.51 Å
R-Value Free:
0.285 (Depositor), 0.272 (DCC)
R-Value Work:
0.226 (Depositor)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Gutfreund, C., Betz, K.

To be published.

Macromolecule Content

Total Structure Weight: 99.39 kDa
Atom Count: 6,808
Modeled Residue Count: 782
Deposited Residue Count: 803
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWU9
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(PAPCP(6HT)P(6HG)P(6HT)P(6HG)P(6HG)P(6HC)PCPGPTPGPGPTP*C)-3')	B [auth T]	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(GPAPCPCPAPCPGPGPCPCPAPCP*A)-3')	C [auth P]	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth T] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth T] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth T] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], K [auth T]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth T] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth T]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]