9OAU | pdb_00009oau

TNA polymerase, 7-47, binary complex

PDB DOI: https://doi.org/10.2210/pdb9OAU/pdb

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

Deposited: 2025-04-21 Released: 2025-12-10
Deposition Author(s): Lee, J.J., Maola, V.A., Chim, N., Chaput, J.C.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.188 (Depositor), 0.189 (DCC)
R-Value Observed:
0.190 (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

Directed Evolution of a TNA Polymerase Identifies Independent Paths to Fidelity and Catalysis

Hajjar, M., Maola, V.A., Lee, J.J., Holguin, M.J., Quijano, R.N., Nguyen, K.K., Ho, K.L., Medina, J.V., Botello-Cornejo, E., Barpuzary, B., Chim, N., Chaput, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 100.13 kDa
Atom Count: 7,358
Modeled Residue Count: 791
Deposited Residue Count: 806
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
7-47, TNA polymerase	A	775	Thermococcus kodakarensis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
Template	B [auth T]	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
Primer	C [auth P]	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5CY Query on 5CY Download Ideal Coordinates CCD File SDF format, chain G [auth T] MOL2 format, chain G [auth T] mmCIF format, chain G [auth T]	G [auth T]	1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium C₃₁ H₃₉ N₂ O₂ VFBDPICHYNKCQJ-UHFFFAOYSA-N		Interactions Focus chain G [auth T] Interactions & Density Focus chain G [auth T]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth T] MOL2 format, chain I [auth T] mmCIF format, chain I [auth T]	I [auth T]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth T] Interactions & Density Focus chain I [auth T]
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 H [auth T] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth T] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth T]	D [auth A], E [auth A], F [auth A], H [auth T]	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 T] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth T]