3K39

Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Peramivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses.

Oakley, A.J.Barrett, S.Peat, T.S.Newman, J.Streltsov, V.A.Waddington, L.Saito, T.Tashiro, M.McKimm-Breschkin, J.L.

(2010) J Med Chem 

  • DOI: 10.1021/jm100621s
  • Primary Citation of Related Structures:  
    3K36, 3K37, 3K38, 3K39, 3K3A

  • PubMed Abstract: 
  • We have identified a virus, B/Perth/211/2001, with a spontaneous mutation, D197E in the neuraminidase (NA), which confers cross-resistance to all NA inhibitors. We analyzed enzyme properties of the D197 and E197 NAs and compared these to a D197N NA, known to arise after oseltamivir treatment ...

    We have identified a virus, B/Perth/211/2001, with a spontaneous mutation, D197E in the neuraminidase (NA), which confers cross-resistance to all NA inhibitors. We analyzed enzyme properties of the D197 and E197 NAs and compared these to a D197N NA, known to arise after oseltamivir treatment. Zanamivir and peramivir bound slowly to the wild type NA, but binding of oseltamivir was more rapid. The D197E/N mutations resulted in faster binding of all three inhibitors. Analysis of the crystal structures of D197 and E197 NAs with and without inhibitors showed that the D197E mutation compromised the interaction of neighboring R150 with the N-acetyl group, common to the substrate sialic acid and all NA inhibitors. Although rotation of the E275 in the NA active site occurs upon binding peramivir in both the D197 and E197 NAs, this does not occur upon binding oseltamivir in the E197 NA. Lack of the E275 rotation would also account for the loss of slow binding and the partial resistance of influenza B wild type NAs to oseltamivir.


    Organizational Affiliation

    CSIRO Materials Science and Engineering, Parkville, 343 Royal Parade, Parkville, Victoria, 3052, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neuraminidase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
397Influenza B virus (B/Perth/211/2001)Mutation(s): 1 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for Q3S340 (Influenza B virus)
Explore Q3S340 
Go to UniProtKB:  Q3S340
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCZ (Subject of Investigation/LOI)
Query on BCZ

Download Ideal Coordinates CCD File 
CA [auth D] , CB [auth L] , GA [auth E] , GB [auth M] , JA [auth F] , JB [auth N] , MA [auth G] , MB [auth O] , 
CA [auth D], CB [auth L], GA [auth E], GB [auth M], JA [auth F], JB [auth N], MA [auth G], MB [auth O], PA [auth H], PB [auth P], S [auth A], TA [auth I], W [auth B], WA [auth J], Z [auth C], ZA [auth K]
3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID
C15 H28 N4 O4
XRQDFNLINLXZLB-CKIKVBCHSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D] , AB [auth L] , EA [auth E] , EB [auth M] , HA [auth F] , HB [auth N] , KA [auth G] , KB [auth O] , 
AA [auth D], AB [auth L], EA [auth E], EB [auth M], HA [auth F], HB [auth N], KA [auth G], KB [auth O], NA [auth H], NB [auth P], Q [auth A], RA [auth I], U [auth B], UA [auth J], X [auth C], XA [auth K]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
YT3
Query on YT3

Download Ideal Coordinates CCD File 
DA [auth E], DB [auth M], QA [auth I], T [auth A]YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth D] , BB [auth L] , FA [auth E] , FB [auth M] , IA [auth F] , IB [auth N] , LA [auth G] , LB [auth O] , 
BA [auth D], BB [auth L], FA [auth E], FB [auth M], IA [auth F], IB [auth N], LA [auth G], LB [auth O], OA [auth H], OB [auth P], R [auth A], SA [auth I], V [auth B], VA [auth J], Y [auth C], YA [auth K]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BCZ PDBBind:  3K39 Ki: 8.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.964α = 90.03
b = 124.874β = 92.11
c = 125.245γ = 91.27
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2021-11-10
    Changes: Database references, Structure summary