2F27

Crystal Structure of the Human Sialidase Neu2 E111Q-Q112E Double Mutant in Complex with DANA Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2F27/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: 2.15 Å
• R-Value Free: 0.224 
• R-Value Work: 0.186 

Starting Model: experimental

Literature

Crystal Structure of the Human Sialidase Neu2 E111Q-Q112E Double 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: 6,225 
• 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): 2  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:  2F27	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: 2.15 Å
• R-Value Free: 0.224 
• R-Value Work: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.04	α = 90
b = 74.4	β = 93.39
c = 77.39	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