7ARN

Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody

• PDB DOI: https://doi.org/10.2210/pdb7ARN/pdb

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


• Deposited: 2020-10-25 Released: 2021-11-03 
• Deposition Author(s): Pryce, R., Allen, J.D., Watanabe, Y., Crispin, M., Bowden, T.A.
• Funding Organization(s): Bloodwise, Cancer Research UK, Medical Research Council (MRC, United Kingdom), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.232 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody

Allen, J.D., Pryce, R., Watanabe, Y., Crispin, M., Bowden, T.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 56.18 kDa 
• Atom Count: 3,823 
• Modelled Residue Count: 438 
• Deposited Residue Count: 509 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab Fragment Heavy Chain	A [auth H]	262	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab Fragment Light Chain	B [auth L]	247	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G94626GC GlyCosmos:  G94626GC GlyGen:  G94626GC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth H], F [auth H], G [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.232 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.55	α = 90
b = 60.58	β = 111.91
c = 82.45	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Pryce, R., Allen, J.D., Watanabe, Y., Crispin, M., Bowden, T.A.

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Funding Organization	Location	Grant Number
Bloodwise	United Kingdom	18009
Cancer Research UK	United Kingdom	C42023/A29370
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L009528/1 and MR/S007555/1
Wellcome Trust	United Kingdom	203141/Z/16/Z

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description