4GB1 | pdb_00004gb1

Synthesis and Evaluation of Novel 3-C-alkylated-Neu5Ac2en Derivatives as Probes of Influenza Virus Sialidase 150-loop flexibility

• PDB DOI: https://doi.org/10.2210/pdb4GB1/pdb

• Classification: HYDROLASE
• Organism(s): Influenza A virus (A/duck/Ukraine/1/1963(H3N8))
• Mutation(s): No 


• Deposited: 2012-07-26 Released: 2012-09-26 
• Deposition Author(s): Kerry, P.S., Rudrawar, S., Rameix-Welti, M.-A., Maggioni, A., Dyason, J.C., Rose, F.J., van der Werf, S., Thomson, R.J., Naffakh, N., Russell, R.J.M., von Itzstein, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.280 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Synthesis and evaluation of novel 3-C-alkylated-Neu5Ac2en derivatives as probes of influenza virus sialidase 150-loop flexibility.

Rudrawar, S., Kerry, P.S., Rameix-Welti, M.A., Maggioni, A., Dyason, J.C., Rose, F.J., van der Werf, S., Thomson, R.J., Naffakh, N., Russell, R.J., von Itzstein, M.

(2012) Org Biomol Chem 10: 8628-8639

• PubMed: 22976385 
• DOI: https://doi.org/10.1039/c2ob25627d
• Primary Citation Related Structures: 
  4GB1


• PubMed Abstract: 
  

  Novel 3-C-alkylated-Neu5Ac2en derivatives have been designed to target the expanded active site cavity of influenza virus sialidases with an open 150-loop, currently seen in X-ray crystal structures of influenza A virus group-1 (N1, N4, N5, N8), but not group-2 (N2, N9), sialidases. The compounds show selectivity for inhibition of H5N1 and pdm09 H1N1 sialidases over an N2 sialidase, providing evidence of the relative 150-loop flexibility of these sialidases. In a complex with N8 sialidase, the C3 substituent of 3-phenylally-Neu5Ac2en occupies the 150-cavity while the central ring and the remaining substituents bind the active site as seen for the unsubstituted template. This new class of inhibitors, which can 'trap' the open 150-loop form of the sialidase, should prove useful as probes of 150-loop flexibility.

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Organizational Affiliation: 
• Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland 4222, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (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: 43.66 kDa 
• Atom Count: 3,150 
• Modeled Residue Count: 387 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	390	Influenza A virus (A/duck/Ukraine/1/1963(H3N8))	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for Q07599 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8)) Explore Q07599  Go to UniProtKB:  Q07599

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0LP	B [auth A]	5-acetamido-2,6-anhydro-3,5-dideoxy-3-[(2E)-3-phenylprop-2-en-1-yl]-D-glycero-L-altro-non-2-enonic acid C20 H25 N O8 LRXKGKMIXXSWGY-KXNCHKOWSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.280 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.501	α = 90
b = 90.501	β = 90
c = 108.731	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Kerry, P.S., Rudrawar, S., Rameix-Welti, M.-A., Maggioni, A., Dyason, J.C., Rose, F.J., van der Werf, S., Thomson, R.J., Naffakh, N., Russell, R.J.M., von Itzstein, M.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 2.0: 2020-04-22
  Changes: Atomic model, Data collection, Database references, Structure summary
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 2.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.3: 2024-10-30
  Changes: Structure summary