8ACF | pdb_00008acf

Structure of the argX-117 in complex with a complement C2 fragment at low pH

• PDB DOI: https://doi.org/10.2210/pdb8ACF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-05 Released: 2024-01-17 
• Deposition Author(s): Olesen, H.G., Andersen, G.R.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Structure-function analysis of ARGX-117, a calcium- and pH-dependent clinical phase complement C2 blocking antibody

Olesen, H.G., Andersen, G.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.94 kDa 
• Atom Count: 5,722 
• Modeled Residue Count: 697 
• Deposited Residue Count: 762 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C2b fragment	A	197	Homo sapiens	Mutation(s): 0  Gene Names: C2
UniProt & NIH Common Fund Data Resources
Find proteins for P06681 (Homo sapiens) Explore P06681  Go to UniProtKB:  P06681
PHAROS:  P06681 GTEx:  ENSG00000166278
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P06681-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of mAb ARGX-117 Fab	B [auth H]	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody specific for the kappa-light chain	C [auth K]	128	Lama glama	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of mAb ARGX-117 Fab	D [auth L]	218	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	E [auth X]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A], I [auth L]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CA	G [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth K], J [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.83	α = 90
b = 89.14	β = 90
c = 146.49	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Olesen, H.G., Andersen, G.R.

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Funding Organization	Location	Grant Number
Other private	Belgium	Not applicable

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary