3TFP

Crystal Structure of Dehydrosqualene Synthase (CrtM) from S. aureus Complexed with BPH-1162

• PDB DOI: https://doi.org/10.2210/pdb3TFP/pdb

• Classification: TRANSFERASE/transferase inhibitor
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-08-16 Released: 2012-04-04 
• Deposition Author(s): Lin, F.-Y., Liu, Y.-L., Zhang, Y., Oldfield, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.241 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Dual dehydrosqualene/squalene synthase inhibitors: leads for innate immune system-based therapeutics.

Lin, F.Y., Zhang, Y., Hensler, M., Liu, Y.L., Chow, O.A., Zhu, W., Wang, K., Pang, R., Thienphrapa, W., Nizet, V., Oldfield, E.

(2012) ChemMedChem 7: 561-564

• PubMed: 22290830 
• DOI: https://doi.org/10.1002/cmdc.201100589
• Primary Citation of Related Structures:  
  3TFN, 3TFP, 3TFV

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Organizational Affiliation: 

Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.3 kDa 
• Atom Count: 2,609 
• Modelled Residue Count: 284 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrosqualene synthase	A	293	Staphylococcus aureus	Mutation(s): 0  Gene Names: crtM EC: 2.5.1
UniProt
Find proteins for A9JQL9 (Staphylococcus aureus) Explore A9JQL9  Go to UniProtKB:  A9JQL9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
03L	D [auth A]	2-({2-chloro-6-[(2,4-dichlorophenyl)sulfanyl]benzyl}carbamoyl)benzoic acid C21 H14 Cl3 N O3 S HLWGMGIORMMWMJ-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
03L	PDBBind:  3TFP	Ki: 340 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.241 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.246	α = 90
b = 80.246	β = 90
c = 92.196	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Lin, F.-Y., Liu, Y.-L., Zhang, Y., Oldfield, E.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description