4FQS | pdb_00004fqs

Crystal Structure of Mycobacterium tuberculosis ThyA in complex with UMP and Pemetrexed

• PDB DOI: https://doi.org/10.2210/pdb4FQS/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-25 Released: 2013-08-07 
• Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Harshbarger, W., Sacchettini, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.199 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal structure of binary and ternary complexes of thymidylate synthase (ThyA) from Mycobacterium tuberculosis: insights into the selectivity and mode of inhibition

Reddy, M.C.M., Bruning, J.B., Harshbarger, W., Sacchettini, J.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 61.24 kDa 
• Atom Count: 5,399 
• Modeled Residue Count: 526 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	263	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: MT2834, MTV002.29c, Rv2764c, thyA EC: 2.1.1.45
UniProt
Find proteins for P9WFR9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFR9  Go to UniProtKB:  P9WFR9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYA	D [auth A], F [auth B]	2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID C20 H21 N5 O6 WBXPDJSOTKVWSJ-ZDUSSCGKSA-N
UMP	C [auth A], E [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.199 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.099	α = 90
b = 57.045	β = 107.95
c = 113.694	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Harshbarger, W., Sacchettini, J.C.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations