4O9H

Structure of Interleukin-6 in complex with a Camelid Fab fragment

• PDB DOI: https://doi.org/10.2210/pdb4O9H/pdb

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


• Deposited: 2014-01-02 Released: 2015-04-15 
• Deposition Author(s): Klarenbeek, A., Blanchetot, C., Schragel, G., Sadi, A.S., Ongenae, N., Hemrika, W., Wijdenes, J., Spinelli, S., Desmyter, A., Cambillau, C., Hultberg, A., Kretz-rommel, A., Dreier, T., De haard, H.J.W., Roovers, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.244 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 

Literature

Combining residues of naturally-occurring Camelid somatic affinity variants yields ultra-potent human therapeutic IL-6 antibodies

Klarenbeek, A., Blanchetot, C., Schragel, G., Sadi, A.S., Ongenae, N., Hemrika, W., Wijdenes, J., Spinelli, S., Desmyter, A., Cambillau, C., Hultberg, A., Kretz-Rommel, A., Dreier, T., De haard, H.J.W., Roovers, R.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 67.17 kDa 
• Atom Count: 4,489 
• Modelled Residue Count: 563 
• Deposited Residue Count: 624 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-6	A	186	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 Camelid Fab fragment 61H7	B [auth H]	223	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of the Camelid Fab fragment 61H7	C [auth L]	215	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.244 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.21	α = 90
b = 47.47	β = 97
c = 148.32	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Klarenbeek, A., Blanchetot, C., Schragel, G., Sadi, A.S., Ongenae, N., Hemrika, W., Wijdenes, J., Spinelli, S., Desmyter, A., Cambillau, C., Hultberg, A., Kretz-rommel, A., Dreier, T., De haard, H.J.W., Roovers, R.C.

Revision History  

• Version 1.0: 2015-04-15
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Other
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary