5KAQ

Crystal structure of broadly neutralizing Influenza A antibody 31.a.83 in complex with Hemagglutinin Hong Kong 1968.

• PDB DOI: https://doi.org/10.2210/pdb5KAQ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/Hong Kong/1-4-MA21-1/1968(H3N2)), Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-06-01 Released: 2017-02-22 
• Deposition Author(s): Joyce, M.G., Thomas, P.V., Wheatley, A.K., McDermott, A.B., Mascola, J.R., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.51 Å
• R-Value Free: 0.313 
• R-Value Work: 0.270 
• R-Value Observed: 0.272 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A5B3C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 321.84 kDa 
• Atom Count: 21,766 
• Modelled Residue Count: 2,780 
• Deposited Residue Count: 2,886 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B [auth C], E [auth B]	512	Influenza A virus (A/Hong Kong/1-4-MA21-1/1968(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for E1AFM4 (Influenza A virus) Explore E1AFM4  Go to UniProtKB:  E1AFM4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY 31.A.83 FAB HEAVY CHAIN	C [auth F], F [auth H], H [auth Q]	236	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY 31.A.83 FAB LIGHT CHAIN	D [auth G], G [auth L], I [auth R]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.51 Å
• R-Value Free: 0.313 
• R-Value Work: 0.270 
• R-Value Observed: 0.272 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 279.435	α = 90
b = 154.283	β = 116.86
c = 157.937	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Joyce, M.G., Thomas, P.V., Wheatley, A.K., McDermott, A.B., Mascola, J.R., Kwong, P.D.

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Structure summary
• Version 1.2: 2017-03-22
  Changes: Source and taxonomy
• Version 1.3: 2017-04-19
  Changes: Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary