3IVG

Crystal structure of pantothenate synthetase in complex with 2-(2-((benzofuran-2-sulfonamido)methyl)-5-methoxy-1H-indol-1-yl)acetic acid

• PDB DOI: https://doi.org/10.2210/pdb3IVG/pdb

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


• Deposited: 2009-09-01 Released: 2009-10-13 
• Deposition Author(s): Silvestre, H.L., Hung, A.W., Wen, S., Ciulli, A., Blundell, T.L., Abell, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.221 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.42 kDa 
• Atom Count: 4,705 
• Modelled Residue Count: 562 
• 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)) Go to UniProtKB:  P9WIL5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FG5	P [auth B]	(2-{[(1-benzofuran-2-ylsulfonyl)amino]methyl}-5-methoxy-1H-indol-1-yl)acetic acid C20 H18 N2 O6 S WZHKFPDZEVEAJG-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], J [auth A], K [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH	E [auth A], F [auth A], G [auth A], M [auth B], N [auth B], O [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FG5	PDBBind:  3IVG	Kd: 5.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.221 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.33	α = 90
b = 70.71	β = 99.6
c = 81.85	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Silvestre, H.L., Hung, A.W., Wen, S., Ciulli, A., 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: 2024-02-21
  Changes: Data collection