5CHP

T. maritima ThyX in complex with TyC5-03

• PDB DOI: https://doi.org/10.2210/pdb5CHP/pdb

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


• Deposited: 2015-07-10 Released: 2016-10-19 
• Deposition Author(s): Surade, S., Luciani, R., Saxena, P., Santucci, M., Ferrari, S., Venturelli, A., Marverti, G., Ponterini, G., Abell, C.A., Blundell, T.L., Costi, M.P.
• Funding Organization(s): EU FP6

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Identification of inhibitors targeting substrate-binding site in Mycobacterium tuberculosis FAD-dependent Thymidylate synthase (ThyX) through Virtual Screening: A New study de-fining the binding mechanism of Inhibitors

Surade, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.78 kDa 
• Atom Count: 2,109 
• Modelled Residue Count: 217 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase ThyX	A	234	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
51Q	C [auth A]	(2S)-2-[(3-hydroxy-5-oxo-4,5-dihydro-1,2,4-triazin-6-yl)sulfanyl]propanoic acid C6 H7 N3 O4 S RHHZZMNGKMZLIA-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.58	α = 90
b = 110.58	β = 90
c = 122.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Surade, S., Luciani, R., Saxena, P., Santucci, M., Ferrari, S., Venturelli, A., Marverti, G., Ponterini, G., Abell, C.A., Blundell, T.L., Costi, M.P.

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Funding Organization	Location	Grant Number
EU FP6	United Kingdom	--

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description