3IME

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.40 Ang resolution in complex with fragment compound 1-Benzofuran-2-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb3IME/pdb

• Classification: LIGASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-08-10 Released: 2009-10-13 
• Deposition Author(s): Ciulli, A., Hung, A.W., Silvestre, H.L., Wen, S., Blundell, T.L., Abell, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.261 
• R-Value Work: 0.156 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase.

Hung, A.W., Silvestre, H.L., Wen, S., Ciulli, A., Blundell, T.L., Abell, C.

(2009) Angew Chem Int Ed Engl 48: 8452-8456

• PubMed: 19780086 
• DOI: https://doi.org/10.1002/anie.200903821
• Primary Citation of Related Structures:  
  3IMC, 3IME, 3IMG, 3ISJ, 3IUB, 3IUE, 3IVC, 3IVG, 3IVX

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Organizational Affiliation: 

Department of Chemistry, University of Cambridge, UK.

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: 63.74 kDa 
• Atom Count: 4,374 
• Modelled Residue Count: 555 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate synthetase	A, B	301	Mycobacterium tuberculosis	Mutation(s): 2  Gene Names: MT3707, MTCY07H7B.20, panC, Rv3602c EC: 6.3.2.1
UniProt
Find proteins for P9WIL5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIL5  Go to UniProtKB:  P9WIL5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BZ2	C [auth A], H [auth B]	1-benzofuran-2-carboxylic acid C9 H6 O3 OFFSPAZVIVZPHU-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EOH	F [auth A], G [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BZ2	PDBBind:  3IME	Kd: 1.00e+6 (nM) from 1 assay(s)
	BindingDB:  3IME	Kd: 1.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.261 
• R-Value Work: 0.156 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.632	α = 90
b = 71.338	β = 99.51
c = 82.06	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Ciulli, A., Hung, A.W., Silvestre, H.L., Wen, S., Blundell, T.L., Abell, C.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description