Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 73140.36 
• Atom Count: 5107 
• Residue Count: 657 
• Unique protein chains: 1

5HM3

2.25 Angstrom Resolution Crystal Structure of Long-chain-fatty-acid-AMP Ligase FadD32 from Mycobacterium tuberculosis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine

• DOI: 10.2210/pdb5HM3/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2016-01-15 Released: 2016-08-03 
• Deposition Author(s): Minasov, G., Warwrzak, Z., Kuhn, M.L., Shuvalova, L., Flores, K.J., Wilson, D.J., Grimes, K.D., Aldrich, C.C., Anderson, W.A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.239 
• R-Value Work: 0.185 

Literature

Structure of the Essential Mtb FadD32 Enzyme: A Promising Drug Target for Treating Tuberculosis.

Kuhn, M.L., Alexander, E., Minasov, G., Page, H.J., Warwrzak, Z., Shuvalova, L., Flores, K.J., Wilson, D.J., Shi, C., Aldrich, C.C., Anderson, W.F.

(2016) Acs Infect Dis. 2: 579-591

• PubMed: 27547819 
• DOI: 10.1021/acsinfecdis.6b00082


• PubMed Abstract: 
  

Mycolic acids are indispensible lipids of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and contribute to the distinctive architecture and impermeability of the mycobacterial cell envelope. FadD32 plays a pivotal role in mycolic acid biosynthesis by functionally linking fatty acid synthase (FAS) and polyketide synthase (PKS) biosynthetic pathways. FadD32, a fatty acyl-AMP ligase (FAAL), represents one of the best genetically and chemically validated new TB drug targets. We have determined the three-dimensional crystal structure of Mtb FadD32 in complex with a ligand specifically designed to stabilize the catalytically active adenylate-conformation, which provides a foundation for structure-based drug design efforts against this essential protein. The structure also captures the unique interactions of a FAAL-specific insertion sequence and provides insight into the specificity and mechanism of fatty acid transfer.

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Organizational Affiliation: 

Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States; Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Long-chain-fatty-acid--AMP ligase FadD32	A	657	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mutation(s): 0  Gene Names: fadD32 EC: 6.2.1.-
Find proteins for O53580 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  O53580

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
649	A	5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine C27 H38 N6 O8 S VLRIGNDIFPKPGQ-ZCIWVVNKSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
649	IC50: 6800 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.239 
• R-Value Work: 0.185 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 
  10.18430/m35hm3 Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 62.779	α = 90.00
b = 74.558	β = 90.00
c = 127.762	γ = 90.00

Software Package:

Software Name	Purpose
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-01-15 
• Released Date: 2016-08-03 
• Deposition Author(s): Minasov, G., Warwrzak, Z., Kuhn, M.L., Shuvalova, L., Flores, K.J., Wilson, D.J., Grimes, K.D., Aldrich, C.C., Anderson, W.A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History 

• Version 1.0: 2016-08-03
  Type: Initial release
• Version 1.1: 2016-09-07
  Type: Database references