3K39 | pdb_00003k39

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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3K39

Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1021/jm100621s
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 711.21 kDa 
  • Atom Count: 49,796 
  • Modeled Residue Count: 6,224 
  • Deposited Residue Count: 6,352 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuraminidase
A, B, C, D, E
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 
EC: 3.2.1.18
UniProt
Find proteins for Q3S340 (Influenza B virus)
Explore Q3S340 
Go to UniProtKB:  Q3S340
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3S340
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCZ

Query on BCZ



Download:Ideal Coordinates CCD File
CA [auth D]
CB [auth L]
GA [auth E]
GB [auth M]
JA [auth F]
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
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth D]
AB [auth L]
EA [auth E]
EB [auth M]
HA [auth F]
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
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
CA

Query on CA



Download:Ideal Coordinates CCD File
BA [auth D]
BB [auth L]
FA [auth E]
FB [auth M]
IA [auth F]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
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



Ligand Structure Quality Assessment 


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
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary