9KE8 | pdb_00009ke8

Crystal Structure of HdNadV and its complex with NMN

• PDB DOI: https://doi.org/10.2210/pdb9KE8/pdb

• Classification: TRANSFERASE
• Organism(s): [Haemophilus] ducreyi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-04 Released: 2025-11-12 
• Deposition Author(s): Lin, T., Zhengjuan, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.235 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: in silico

Literature

The Structural Basis of NMN Synthesis Catalyzed by NadV from Haemophilus ducreyi

Lin, T., Zhengjuan, W., Jia, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 112.06 kDa 
• Atom Count: 7,832 
• Modeled Residue Count: 958 
• Deposited Residue Count: 990 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	495	[Haemophilus] ducreyi	Mutation(s): 0  Gene Names: nadV, PNAD10009, RZ57_05785 EC: 2.4.2.12
UniProt
Find proteins for G1U9V7 (Haemophilus ducreyi) Explore G1U9V7  Go to UniProtKB:  G1U9V7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMN (Subject of Investigation/LOI)	C [auth A], D [auth B]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.235 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.52	α = 90
b = 158.52	β = 90
c = 130.4	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Lin, T., Zhengjuan, W.

---

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

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release