6HGB

Influenza A virus N6 neuraminidase native structure (Duck/England/56).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (In preparation)

Salinger, M.T.Hobbs, J.R.Murray, J.W.Laver, W.G.Kuhn, P.Garman, E.F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeuraminidaseA, B, C, D389Influenza A virus (A/duck/England/1/1956(H11N6))Mutation(s): 0 
Gene Names: NA
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
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, H, J, K, N2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL, M6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G94106MV
GlyCosmos:  G94106MV
GlyGen:  G94106MV
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
CB [auth D], Y [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth C] , BB [auth C] , HA [auth B] , IA [auth B] , JA [auth B] , JB [auth D] , KA [auth B] , KB [auth D] , 
AB [auth C],  BB [auth C],  HA [auth B],  IA [auth B],  JA [auth B],  JB [auth D],  KA [auth B],  KB [auth D],  LA [auth B],  LB [auth D],  MA [auth B],  MB [auth D],  NA [auth B],  NB [auth D],  OA [auth B],  OB [auth D],  X [auth A],  YA [auth C],  ZA [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
GA [auth B], V [auth A], W [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , DA [auth B] , DB [auth D] , EA [auth B] , EB [auth D] , FB [auth D] , 
AA [auth B],  BA [auth B],  CA [auth B],  DA [auth B],  DB [auth D],  EA [auth B],  EB [auth D],  FB [auth D],  GB [auth D],  HB [auth D],  O [auth A],  P [auth A],  PA [auth C],  Q [auth A],  QA [auth C],  R [auth A],  RA [auth C],  S [auth A],  SA [auth C],  T [auth A],  TA [auth C],  UA [auth C],  VA [auth C],  WA [auth C],  Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
FA [auth B], IB [auth D], U [auth A], XA [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.2α = 90
b = 73.9β = 90.3
c = 106.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary