7JPD

Crystal structure of the trimeric full length mature hemagglutinin from influenza A virus A/Fort Monmouth/1/1947


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of the trimeric full length mature hemagglutinin from influenza A virus A/Fort Monmouth/1/1947

Edwards, T.E.Abendroth, J.Lorimer, D.D.Horanyi, P.S.Seattle Structural Genomics Center for Infectious Disease

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainA, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]329Influenza A virus (A/Fort Monmouth/1/1947(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q20MG8 (Influenza A virus)
Explore Q20MG8 
Go to UniProtKB:  Q20MG8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2 chainB [auth a], D [auth b], F [auth c], H [auth d], J [auth e], L [auth f]170Influenza A virus (A/Fort Monmouth/1/1947(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q20MG8 (Influenza A virus)
Explore Q20MG8 
Go to UniProtKB:  Q20MG8
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth G]3N/AN-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth H], O [auth I], Q [auth K], S [auth M], U [auth O], W [auth Q]2N/AN-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseP [auth J], R [auth L], T [auth N], V [auth P]5N/AN-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth C] , CC [auth E] , DC [auth E] , MA [auth B] , NA [auth B] , OA [auth B] , OB [auth D] , SC [auth F] , 
AB [auth C],  CC [auth E],  DC [auth E],  MA [auth B],  NA [auth B],  OA [auth B],  OB [auth D],  SC [auth F],  TC [auth F],  X [auth A],  ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth A] , AC [auth D] , AD [auth F] , BA [auth A] , BB [auth C] , BC [auth d] , BD [auth F] , CA [auth A] , 
AA [auth A],  AC [auth D],  AD [auth F],  BA [auth A],  BB [auth C],  BC [auth d],  BD [auth F],  CA [auth A],  CB [auth C],  CD [auth F],  DA [auth A],  DB [auth C],  DD [auth F],  EA [auth A],  EB [auth C],  EC [auth E],  ED [auth F],  FA [auth A],  FB [auth C],  FC [auth E],  FD [auth F],  GA [auth A],  GB [auth C],  GC [auth E],  GD [auth F],  HA [auth A],  HB [auth C],  HC [auth E],  IA [auth A],  IB [auth C],  IC [auth E],  JA [auth A],  JB [auth C],  JC [auth E],  KA [auth A],  KB [auth C],  KC [auth E],  LA [auth A],  LB [auth c],  LC [auth E],  MB [auth c],  MC [auth E],  NB [auth c],  NC [auth E],  OC [auth E],  PA [auth B],  PB [auth D],  PC [auth E],  QA [auth B],  QB [auth D],  QC [auth e],  RA [auth B],  RB [auth D],  RC [auth e],  SA [auth B],  SB [auth D],  TA [auth B],  TB [auth D],  UA [auth B],  UB [auth D],  UC [auth F],  VA [auth B],  VB [auth D],  VC [auth F],  WA [auth B],  WB [auth D],  WC [auth F],  XA [auth B],  XB [auth D],  XC [auth F],  YA [auth b],  YB [auth D],  YC [auth F],  Z [auth A],  ZB [auth D],  ZC [auth F]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
Y [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.79α = 90
b = 142.36β = 90
c = 234.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release