5FUC

Biophysical and cellular characterisation of a junctional epitope antibody that locks IL-6 and gp80 together in a stable complex: implications for new therapeutic strategies

• PDB DOI: https://doi.org/10.2210/pdb5FUC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Camelus dromedarius
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-01-25 Released: 2017-01-25 
• Deposition Author(s): Adams, R., Griffin, R., Doyle, C., Ettorre, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.287 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 120.15 kDa 
• Atom Count: 7,672 
• Modelled Residue Count: 943 
• Deposited Residue Count: 1,058 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERLEUKIN-6	A, B	166	Homo sapiens	Mutation(s): 0
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
INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR	C, D	231	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P08887 (Homo sapiens) Explore P08887  Go to UniProtKB:  P08887
PHAROS:  P08887 GTEx:  ENSG00000160712

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH6	E, F [auth V]	132	Camelus dromedarius	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth C], H [auth C], I [auth D], J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.287 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 249.03	α = 90
b = 67.8	β = 104.53
c = 78.16	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Adams, R., Griffin, R., Doyle, C., Ettorre, A.

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Database references
• Version 1.2: 2019-04-03
  Changes: Advisory, Data collection, Derived calculations, Source and taxonomy
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2024-01-10
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary