8S87

KOD-H4 DNA polymerase mutant - apo structure

PDB DOI: https://doi.org/10.2210/pdb8S87/pdb

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

Deposited: 2024-03-06 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: 1.82 Å
R-Value Free: 0.271
R-Value Work: 0.230
R-Value Observed: 0.231

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

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: 90.81 kDa
Atom Count: 6,412
Modelled Residue Count: 753
Deposited Residue Count: 774
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain R [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth A]	F [auth A], G [auth A], K [auth A], N [auth A], R [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain N [auth A] Focus chain R [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain N [auth A] Focus chain R [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] L [auth A] B [auth A], C [auth A], D [auth A], E [auth A], L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A]	H [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain J [auth A]