8CT4

Cryo-EM structure of Mtb Lpd bound to inhibitor complex with 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide

• PDB DOI: https://doi.org/10.2210/pdb8CT4/pdb
• EM Map EMD-26981: EMDB EMDataResource

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


• Deposited: 2022-05-13 Released: 2022-05-25 
• Deposition Author(s): Kochanczyk, T., Arango, N., Lima, C.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of Mtb Lpd bound to the inhibitor 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide at 2.17 Angstrom resolution

Kochanczyk, T., Arango, N., Michino, M., Sun, S., Ginn, J., Bryk, R., Nathan, C., Lima, C.D.

Not Published 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 101.44 kDa 
• Atom Count: 7,983 
• Modelled Residue Count: 928 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B	466	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: lpdC, lpd, Rv0462, MTV038.06 EC: 1.8.1.4
UniProt
Find proteins for P9WHH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHH9  Go to UniProtKB:  P9WHH9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
OU6 (Subject of Investigation/LOI)	D [auth A], E [auth B]	N~2~-(2-cyano-5-methyl-1H-indole-7-sulfonyl)-N~2~-methyl-N-[4-(oxetan-3-yl)-3,4-dihydro-2H-1,4-benzoxazin-7-yl]glycinamide C24 H25 N5 O5 S LICCSNABLLQTEJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.9
MODEL REFINEMENT	PHENIX	1.20.1-44487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Kochanczyk, T., Arango, N., Lima, C.D.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118080
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA008748

Revision History  

• Version 1.0: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2023-06-07
  Changes: Database references, Refinement description
• Version 1.2: 2024-06-12
  Changes: Data collection, Refinement description