2F25

Crystal Structure of the Human Sialidase Neu2 E111Q Mutant in Complex with DANA Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2F25/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-11-15 Released: 2006-11-21 
• Deposition Author(s): Chavas, L.M.G., Kato, R., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.222 
• R-Value Work: 0.192 

Starting Model: experimental

Literature

Crystal Structure of the Human Sialidase Neu2 E111Q Mutant in Complex with DANA Inhibitor

Chavas, L.M.G., Kato, R., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 86.37 kDa 
• Atom Count: 6,410 
• Modelled Residue Count: 743 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase 2	A, B	382	Homo sapiens	Mutation(s): 1  EC: 3.2.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3R4 (Homo sapiens) Explore Q9Y3R4  Go to UniProtKB:  Q9Y3R4
PHAROS:  Q9Y3R4 GTEx:  ENSG00000115488

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAN	C [auth A], F [auth B]	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID C11 H17 N O8 JINJZWSZQKHCIP-UFGQHTETSA-N
EPE	D [auth A], E [auth A], G [auth B], H [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DAN	BindingDB:  2F25	Ki: min: 5000, max: 1.40e+5 (nM) from 3 assay(s)
		IC50: min: 1.80e+4, max: 9.00e+4 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.222 
• R-Value Work: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.37	α = 90
b = 73.64	β = 90.31
c = 78.95	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Chavas, L.M.G., Kato, R., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2021-11-10
  Changes: Database references, Structure summary
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description