8REO

Crystal structure of reduced ThyX in complex with dUMP

PDB DOI: https://doi.org/10.2210/pdb8REO/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-12 Released: 2025-01-01
Deposition Author(s): Pecqueur, L., Hamdane, D.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.236
R-Value Work: 0.211
R-Value Observed: 0.212

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural Plasticity of Flavin-dependent Thymidylate Synthase controlled by the enzyme redox state

Pecqueur, L., Lombard, M., Hamdane, D.

To be published.

Macromolecule Content

Total Structure Weight: 115.54 kDa
Atom Count: 7,570
Modelled Residue Count: 873
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent thymidylate synthase	A, B, C, D	232	Thermotoga maritima	Mutation(s): 0 Gene Names: thyX, thy1, TM_0449 EC: 2.1.1.148
UniProt
Find proteins for Q9WYT0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYT0 Go to UniProtKB: Q9WYT0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WYT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDA (Subject of Investigation/LOI) Query on FDA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	G [auth A], L [auth B], O [auth C], S [auth D]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D]
UMP (Subject of Investigation/LOI) Query on UMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	E [auth A], I [auth B], M [auth C], Q [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
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]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain R [auth D] MOL2 format, chain H [auth B] MOL2 format, chain R [auth D] mmCIF format, chain H [auth B] mmCIF format, chain R [auth D]	H [auth B], R [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain R [auth D] Interactions & Density Focus chain H [auth B] Focus chain R [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain P [auth C] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth C]	J [auth B], N [auth C], P [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth C] Interactions & Density Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.236
R-Value Work: 0.211
R-Value Observed: 0.212
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.094	α = 90
b = 115.964	β = 90
c = 140.527	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
BUSTER	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-01

Deposition Author(s):

Pecqueur, L.

Hamdane, D.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-15-CE11-0004-01
Agence Nationale de la Recherche (ANR)	France	ANR-11-LABX-0011-01
Agence Nationale de la Recherche (ANR)	France	ANR-11-IDEX-0004-02