1W1X

Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 3 hours at 277 K.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 2.0 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
MoleculeChainsSequence LengthOrganismDetailsImage
NEURAMINIDASEA, B, C, D389Influenza 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranoseE 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G91725EU
GlyCosmos:  G91725EU
GlyGen:  G91725EU
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF, J 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranoseH 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G77384RA
GlyCosmos:  G77384RA
GlyGen:  G77384RA
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G41734DZ
GlyCosmos:  G41734DZ
GlyGen:  G41734DZ
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIA
Query on SIA

Download Ideal Coordinates CCD File 
GA [auth D],
HA [auth D],
K [auth A],
L [auth A],
R [auth B],
GA [auth D],
HA [auth D],
K [auth A],
L [auth A],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
NAG
Query on NAG

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EA [auth C],
KA [auth D],
O [auth A],
P [auth A],
V [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download Ideal Coordinates CCD File 
JA [auth D]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download Ideal Coordinates CCD File 
BA [auth C],
CA [auth C],
DA [auth C],
N [auth A],
U [auth B]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
X [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
FA [auth C],
LA [auth D],
Q [auth A],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C],
IA [auth D],
M [auth A],
T [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900118
Query on PRD_900118
H6alpha-alpha-mannobioseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.993α = 90
b = 73.464β = 90.38
c = 107.413γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



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