9DB6 | pdb_00009db6

Sialidase682 co-crystallized with inhibitor DANA

• PDB DOI: https://doi.org/10.2210/pdb9DB6/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides finegoldii DSM 17565
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-08-23 Released: 2025-07-02 
• Deposition Author(s): Young, M.A., Rees, S.D., Chang, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Models: experimental

Literature

Sialidase682 co-crystallized with inhibitor DANA

Young, M.A., Rees, S.D., Chang, G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 243.36 kDa 
• Atom Count: 17,460 
• Modeled Residue Count: 2,084 
• Deposited Residue Count: 2,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BNR/Asp-box repeat protein	A, B, C, D	540	Bacteroides finegoldii DSM 17565	Mutation(s): 0  Gene Names: BACFIN_07125 EC: 3.2.1.18
UniProt
Find proteins for K5BUM2 (Bacteroides finegoldii CL09T03C10) Explore K5BUM2  Go to UniProtKB:  K5BUM2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAN (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID C11 H17 N O8 JINJZWSZQKHCIP-UFGQHTETSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.248	α = 90
b = 149.52	β = 113.299
c = 100.437	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Young, M.A., Rees, S.D., Chang, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release