Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 73.14 kDa 
• Atom Count: 5243 
• Modelled Residue Count: 625 
• Deposited 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

• PDB DOI: 10.2210/pdb5HM3/pdb

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


• 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 
• R-Value Observed: 0.188 

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
• Primary Citation of Related Structures:  
  5HM3


• 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Long-chain-fatty-acid--AMP ligase FadD32	A	657	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: fadD32, Rv3801c EC: 6.2.1 (PDB Primary Data), 6.2.1.20 (UniProt)
UniProt
Find proteins for O53580 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53580  Go to UniProtKB:  O53580

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
649	B [auth A]	5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine C27 H38 N6 O8 S VLRIGNDIFPKPGQ-ZCIWVVNKSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	E [auth A], F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Binding Affinity Annotations
ID	Source	Binding Affinity
649	Binding MOAD:  5HM3	IC50: 6800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.239 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 10.18430/m35hm3 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.779	α = 90
b = 74.558	β = 90
c = 127.762	γ = 90

Software Package:

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

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
  Changes: Database references