8S84

KOD-H4 DNA polymerase mutant in a ternary complex with DNA/DNA and non-hydrolyzable triphosphate

PDB DOI: https://doi.org/10.2210/pdb8S84/pdb
NAKB: 8S84

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

Deposited: 2024-03-05 Released: 2024-11-13
Deposition Author(s): Gutfreund, C., Betz, K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.276
R-Value Work: 0.237
R-Value Observed: 0.238

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

Structural Insights into a DNA Polymerase Reading the Xeno Nucleic Acid HNA

Gutfreund, C., Betz, K.

(2024) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 99.77 kDa
Atom Count: 6,850
Modelled 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(GPAPCPCPAPCPGPGPCPCPAPCPA(XG4))-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(PAPCPTPGPTPGPGPCPCPGPTPGPGPTP*C)-3')	C [auth T]	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XG4 (Subject of Investigation/LOI) Query on XG4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine C₁₀ H₁₇ N₆ O₁₂ P₃ DWGAAFQEGIMTIA-KVQBGUIXSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth P] SDF format, chain M [auth T] MOL2 format, chain L [auth P] MOL2 format, chain M [auth T] mmCIF format, chain L [auth P] mmCIF format, chain M [auth T]	L [auth P], M [auth T]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth P] Focus chain M [auth T] Interactions & Density Focus chain L [auth P] Focus chain M [auth T]
IMD Query on IMD 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]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	D [auth A], E [auth A], F [auth A], H [auth A], I [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 H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A]