8BSO

crystal structure of antibody Fab with SiaLac-amidine-Lys

• PDB DOI: https://doi.org/10.2210/pdb8BSO/pdb

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


• Deposited: 2022-11-25 Released: 2023-09-27 
• Deposition Author(s): Moynie, L., Naismith, J.H.
• Funding Organization(s): UK Research and Innovation (UKRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.220 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

crystal structure of antibody Fab with SiaLac-amidine-Lys

Moynie, L., Naismith, J.H., Sattentau, Q., Deimel, L., Khan, A., Davis, B., Baldwin, A., Buchanan, C.

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)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 98.22 kDa 
• Atom Count: 7,135 
• Modelled Residue Count: 861 
• Deposited Residue Count: 892 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BAR-1 Fab heavy chain	A [auth H], C	227	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BAR-1 Fab light chain	B [auth L], D	219	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	E [auth G], F [auth I]	3		N/A
Glycosylation Resources
GlyTouCan:  G91237TK GlyCosmos:  G91237TK GlyGen:  G91237TK

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SL9 (Subject of Investigation/LOI)	J [auth L], L [auth D]	(2~{S})-2-acetamido-6-(2-sulfanylethanimidoylamino)hexanamide C10 H20 N4 O2 S VZQPDVWZAWZPHB-QMMMGPOBSA-N
GOL	G [auth H], H, I [auth L], K [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002443	E [auth G], F [auth I]	SiaLac-amidine-Lys	Oligosaccharide /

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.220 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.688	α = 90
b = 130.251	β = 123.77
c = 77.693	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Moynie, L., Naismith, J.H.

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Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	--

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release