9EMF | pdb_00009emf

KOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA containing one HNA nucleotide

PDB DOI: https://doi.org/10.2210/pdb9EMF/pdb
NAKB: 9EMF

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: 3.00 Å
R-Value Free:
0.270 (Depositor), 0.271 (DCC)
R-Value Work:
0.234 (Depositor), 0.234 (DCC)
R-Value Observed:
0.236 (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

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

Gutfreund, C., Betz, K.

To be published.

Macromolecule Content

Total Structure Weight: 99.41 kDa
Atom Count: 6,811
Modeled Residue Count: 784
Deposited Residue Count: 803
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWU9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPAPCPCPAPCPGPGPCPCPAPCP*A)-3')	B [auth P]	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PAPCP(6HT)PGPTPGPGPCPCPGPTPGPGPTP*C)-3')	C [auth T]	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6BX Query on 6BX Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	(2S)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid C₇ H₁₅ N O₅ S NUFBIAUZAMHTSP-ZETCQYMHSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth P] MOL2 format, chain J [auth A] MOL2 format, chain L [auth P] mmCIF format, chain J [auth A] mmCIF format, chain L [auth P]	J [auth A], L [auth P]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth P] Interactions & Density Focus chain J [auth A] Focus chain L [auth P]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [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] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]