5V2A Viral Protein Immune System date Mar 03, 2017
title Crystal Structure Of Fab H7.167 In Complex With Influenza Vi Hemagglutinin From Ashanghai022013 (H7n9)
authors H.Zhang, X.Zhu, I.A.Wilson
compound source
Molecule: Hemagglutinin
Chain: A
Engineered: Yes
Other_details: Ha1
 Organism_scientific: Influenza A Virus (Achickenhenan1092013(H7n9));
Organism_taxid: 1574512
Strain: Achickenhenan1092013(H7n9)
Gene: Ha
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Hemagglutinin
Chain: B
Engineered: Yes
Other_details: Ha2
Organism_scientific: Influenza A Virus (Apigeonwuxi0405007g2013(H7n9));
Organism_taxid: 1560294
Strain: Apigeonwuxi0405007g2013(H7n9)
Gene: Ha
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Light Chain (Kappa) Of H7.167 Antibody
Chain: L
Engineered: Yes
Other_details: Fab
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Heavy Chain Of H7.167 Antibody
Chain: H
Engineered: Yes
Other_details: Fab
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
symmetry Space Group: I 21 3
R_factor 0.258 R_Free 0.334
crystal
cell
length a length b length c angle alpha angle beta angle gamma
207.276 207.276 207.276 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.66 Å
ligand BMA, NAG enzyme
note 5V2A supersedes 5F45
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceH7N9 influenza virus neutralizing antibodies that possess few somatic mutations., Thornburg NJ, Zhang H, Bangaru S, Sapparapu G, Kose N, Lampley RM, Bombardi RG, Yu Y, Graham S, Branchizio A, Yoder SM, Rock MT, Creech CB, Edwards KM, Lee D, Li S, Wilson IA, Garcia-Sastre A, Albrecht RA, Crowe JE Jr, J Clin Invest. 2016 Apr 1;126(4):1482-94. doi: 10.1172/JCI85317. Epub 2016 Mar 7. PMID:26950424
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (5v2a.pdb1.gz) 397 Kb
  • LPC: Ligand-Protein Contacts for 5V2A
  • CSU: Contacts of Structural Units for 5V2A
  • Structure Factors (217 Kb)
  • Retrieve 5V2A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V2A from S2C, [Save to disk]
  • Re-refined 5v2a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5V2A in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5V2A
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v2a] [5v2a_A] [5v2a_B] [5v2a_L] [5v2a_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5V2A
  • Community annotation for 5V2A at PDBWiki (http://pdbwiki.org)

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