8QYA

J22.9-FNY, fully humanized, CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA; with VH CDR2 glycosylation

• PDB DOI: https://doi.org/10.2210/pdb8QYA/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-25 Released: 2024-01-17 
• Deposition Author(s): Marino, S.F., Daumke, O.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.297 
• R-Value Work: 0.244 
• R-Value Observed: 0.247 

Literature

Structure-based humanization of a therapeutic antibody for Multiple Myeloma

Marino, S.F., Daumke, O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 50.63 kDa 
• Atom Count: 3,597 
• Modelled Residue Count: 464 
• Deposited Residue Count: 464 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: L	A [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: H	B [auth H]	216	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: A	C [auth A]	34	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	E [auth L], F [auth H]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.297 
• R-Value Work: 0.244 
• R-Value Observed: 0.247 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.266	α = 90
b = 55.371	β = 108.009
c = 69.486	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Marino, S.F., Daumke, O.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release