9U8M | pdb_00009u8m

Drosophila melanogaster Nicotinamidase in Complex with Inhibitor CN2

• PDB DOI: https://doi.org/10.2210/pdb9U8M/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-03-26 Released: 2025-09-03 
• Deposition Author(s): Li, G.-B., Chen, Y.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.229 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

Drosophila melanogaster Nicotinamidase in Complex with Inhibitor CN2

Li, G.-B., Chen, Y.-T.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.47 kDa 
• Atom Count: 2,756 
• Modeled Residue Count: 327 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nicotinamidase	A	357	Drosophila melanogaster	Mutation(s): 0  Gene Names:  Naam, AAM52663, anon-WO0172774.59, anon-WO0172774.60, CG7444, CG7500, D-NAAM, Dmel\CG31216, dNaam, CG31216, Dmel_CG31216 EC: 3.5.1.19
UniProt
Find proteins for Q9VDU7 (Drosophila melanogaster) Explore Q9VDU7  Go to UniProtKB:  Q9VDU7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EOF (Subject of Investigation/LOI)	C [auth A]	[3-(phenylmethyl)imidazol-4-yl]methanimine C11 H11 N3 AMOQDSYRPZELAU-WUXMJOGZSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2	D [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.229 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.863	α = 90
b = 70.41	β = 94.46
c = 76.524	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPX	data processing
autoPX	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Li, G.-B., Chen, Y.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Structure summary