9D3H | pdb_00009d3h

Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with N-carboxy-L-threonine, magnesium and pyrophosphate.

PDB DOI: https://doi.org/10.2210/pdb9D3H/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-08-10 Released: 2025-12-10
Deposition Author(s): Kutshuashvili, A., Swairjo, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.212 (Depositor), 0.186 (DCC)
R-Value Work:
0.187 (Depositor), 0.191 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: in silico
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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 evidence of N-carboxy-L-threonine intermediate in t6A modification of tRNA.

Kutchaushvili, A., Wood, E., Luthra, A., Hung, S.-H., Swinehart, W., Bayooz, S., Scheleen, E., Iwata-Reuyl, D., Swairjo, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 78.77 kDa
Atom Count: 5,670
Modeled Residue Count: 671
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonylcarbamoyl-AMP synthase	A, B	340	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM_0852 EC: 2.7.7.87
UniProt
Find proteins for Q9WZV6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZV6 Go to UniProtKB: Q9WZV6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DPO (Subject of Investigation/LOI) Query on DPO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
U6A (Subject of Investigation/LOI) Query on U6A Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	N-carboxy-L-threonine C₅ H₉ N O₅ OJLPTWSLDBSLEH-GBXIJSLDSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain U [auth B] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	L [auth B] M [auth B] N [auth B] O [auth B] P [auth B] L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], R [auth B], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth B] Focus chain U [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth B] Focus chain U [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain H [auth A]	G [auth A], H [auth A], S [auth B], T [auth B], V [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]