1W20

Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 3 hours at 291 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.195 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SIAClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view detailsBest fitted MANClick on this verticalbar to view detailsBest fitted BMAClick on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

The Crystal Structure of Type a Influenza Virus Neuraminidase of the N6 Subtype Reveals the Existence of Two Separate Neu5Ac Binding Sites

Rudino-Pinera, E.Tunnah, P.Crennell, S.J.Webster, R.G.Laver, W.G.Garman, E.F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEURAMINIDASE SUBTYPE N6
A, B, C, D
389Influenza A virusMutation(s): 0 
EC: 3.2.1.18
UniProt
Find proteins for Q6XV27 (Influenza A virus (strain A/Duck/England/1/1956 H11N6))
Explore Q6XV27 
Go to UniProtKB:  Q6XV27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XV27
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, H
2N/A
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
3N/A
Glycosylation Resources
GlyTouCan:  G41734DZ
GlyCosmos:  G41734DZ
GlyGen:  G41734DZ
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA
Query on SIA

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
I [auth A]
J [auth A]
LA [auth D]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth C],
L [auth A],
M [auth A],
OA [auth D],
V [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
FA [auth C]
GA [auth C]
HA [auth C]
IA [auth C]
O [auth A]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA
Query on BMA

Download Ideal Coordinates CCD File 
JA [auth C],
N [auth A],
W [auth B]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth C],
K [auth A],
NA [auth D],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth B],
KA [auth C],
PA [auth D],
R [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.195 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.478α = 90
b = 73.995β = 90.5
c = 106.465γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SIAClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view detailsBest fitted MANClick on this verticalbar to view detailsBest fitted BMAClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary