8YWR

Crystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a domain-swapped IL-6 dimer

• PDB DOI: https://doi.org/10.2210/pdb8YWR/pdb

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


• Deposited: 2024-03-31 Released: 2024-11-06 
• Deposition Author(s): Bukhdruker, S., Yudenko, A., Borshchevskiy, V.
• Funding Organization(s): Ministry of Education and Science of the Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 0.256 
• R-Value Work: 0.214 
• R-Value Observed: 0.218 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4ZS7

Literature

Structural basis of signaling complex inhibition by IL-6 domain-swapped dimers

Yudenko, A., Bukhdruker, S., Shishkin, P., Rodin, S., Burtseva, A., Petrov, A., Pigareva, N., Sokolov, A., Zinovev, E., Eliseev, I., Remeeva, A., Marin, E., Mishin, A., Godeliy, V., Gushchin, I., Ischenko, A., Borshchevskiy, V.

(2025) Structure 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.63 kDa 
• Atom Count: 4,283 
• Modelled Residue Count: 564 
• Deposited Residue Count: 609 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-6	A	171	Homo sapiens	Mutation(s): 0  Gene Names: IL6, IFNB2
UniProt & NIH Common Fund Data Resources
Find proteins for P05231 (Homo sapiens) Explore P05231  Go to UniProtKB:  P05231
PHAROS:  P05231 GTEx:  ENSG00000136244

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2	B [auth H]	222	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of the Fab fragment of anti-IL-6 antibody 68F2	C [auth L]	216	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth L], E [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 0.256 
• R-Value Work: 0.214 
• R-Value Observed: 0.218 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.55	α = 90
b = 92.86	β = 103.93
c = 84.63	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
BUSTER	refinement
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Bukhdruker, S., Yudenko, A., Borshchevskiy, V.

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Funding Organization	Location	Grant Number
Ministry of Education and Science of the Russian Federation	Russian Federation	075-15-2021-1354

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release