7DP6

Crystal structure of mutant V45T Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate

• PDB DOI: https://doi.org/10.2210/pdb7DP6/pdb

• Classification: TRANSFERASE
• Organism(s): Brugia malayi
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-12-18 Released: 2021-12-22 
• Deposition Author(s): Keyunratsami, K., Nualnoi, T., Wongkamchai, S., Songsiriritthigul, C., Chen, C.-J., Canyuk, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.206 
• R-Value Work: 0.176 

Literature

Crystallographic investigation and inhibition of Brugia malayi thymidylate synthase by a folate analog

Keyunratsami, K., Nualnoi, T., Wongkamchai, S., Songsiriritthigul, C., Chen, C.-J., Canyuk, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.36 kDa 
• Atom Count: 2,479 
• Modelled Residue Count: 285 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	306	Brugia malayi	Mutation(s): 1  Gene Names: Bma-tyms-1.1, BM_BM7277 EC: 2.1.1.45
UniProt
Find proteins for A0A4E9EZW9 (Brugia malayi) Explore A0A4E9EZW9  Go to UniProtKB:  A0A4E9EZW9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP	B [auth A]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	C [auth A], D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.206 
• R-Value Work: 0.176 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.72	α = 90
b = 80.72	β = 90
c = 104.445	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Keyunratsami, K., Nualnoi, T., Wongkamchai, S., Songsiriritthigul, C., Chen, C.-J., Canyuk, B.

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description