2F10 | pdb_00002f10

Crystal Structure of the Human Sialidase Neu2 in Complex with Peramivir inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2F10/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-11-14 Released: 2006-11-21 
• Deposition Author(s): Chavas, L.M.G., Kato, R., McKimm-Breschkin, J., Colman, P.M., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.292 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of the Human Sialidase Neu2 in Complex with Peramivir inhibitor

Chavas, L.M.G., Kato, R., McKimm-Breschkin, J., Colman, P.M., 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.

Macromolecule Content

• Total Structure Weight: 42.84 kDa 
• Atom Count: 2,801 
• Modelled Residue Count: 349 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase 2	A	382	Homo sapiens	Mutation(s): 0  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
BCZ	C [auth A]	3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID C15 H28 N4 O4 XRQDFNLINLXZLB-CKIKVBCHSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
BCZ	BindingDB:  2F10	Ki: 5.60e+4 (nM) from 1 assay(s)
		IC50: 7.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.292 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.34	α = 90
b = 92.25	β = 90
c = 92.69	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., McKimm-Breschkin, J., Colman, P.M., 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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description