5JQD | pdb_00005jqd

Antibody Fab Fragment

• PDB DOI: https://doi.org/10.2210/pdb5JQD/pdb

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


• Deposited: 2016-05-04 Released: 2017-11-08 
• Deposition Author(s): Zhang, Z., Prachanronarong, K., Gellatly, K., Marasco, W.A., Schiffer, C.A.
• 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: 2.59 Å
• R-Value Free: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.9 kDa 
• Atom Count: 6,431 
• Modeled Residue Count: 851 
• Deposited Residue Count: 886 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D80 Fab Fragment Light Chain	A, B	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D80 Fab Fragment Heavy Chain	C, D	228	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.055	α = 90
b = 91.577	β = 90
c = 106.759	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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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