5JO4 | pdb_00005jo4

Antibody Fab Fragment Complex

• PDB DOI: https://doi.org/10.2210/pdb5JO4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-05-01 Released: 2017-11-08 
• Deposition Author(s): Zhang, Z., Prachanronarong, K.P., Marasco, W.A., Schiffer, C.A.S.
• Funding Organization(s): Defense Advanced Research Projects Agency, Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 
  0.248 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Structural Basis of an Influenza Hemagglutinin Stem-Directed Antibody Retaining the G6 Idiotype

Avnir, Y., Zhang, Z., Prachanronarong, K., Schiffer, C.A., Marasco, W.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 94.34 kDa 
• Atom Count: 6,757 
• Modeled Residue Count: 866 
• Deposited Residue Count: 879 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D80 Fab Heavy Chain	A	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D80 Fab Light Chain	B	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
G6 Fab Heavy Chain	C	222	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
G6 Fab Light Chain	D	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.248 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.16	α = 90
b = 50.78	β = 90.9
c = 139.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-08 
Deposition Author(s): Zhang, Z., Prachanronarong, K.P., Marasco, W.A., Schiffer, C.A.S.

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Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency	United States	DARPA-BAA-10-93
Department of Defense (DOD, United States)	United States	HR0011-11-C-0095

Revision History  

• Version 1.0: 2017-11-08
  Type: Initial release
  
• Version 1.1: 2019-04-10
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary