3I2C

Crystal structure of anti-IL-23 antibody CNTO4088

• PDB DOI: https://doi.org/10.2210/pdb3I2C/pdb

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


• Deposited: 2009-06-29 Released: 2009-07-07 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Noncanonical conformation of CDR L1 in the anti-IL-23 antibody CNTO4088.

Teplyakov, A., Obmolova, G., Rogers, A., Gilliland, G.L.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 229-232

• PubMed: 20208149 
• DOI: https://doi.org/10.1107/S1744309109054141
• Primary Citation of Related Structures:  
  3I2C


• PubMed Abstract: 
  

  CNTO4088 is a monoclonal antibody to human IL-23. The X-ray structure of the Fab fragment revealed an unusual noncanonical conformation of CDR L1. Most antibodies with the kappa light chain exhibit a canonical structure for CDR L1 in which residue 29 anchors the CDR loop to the framework. Analysis of the residues believed to define the conformation of CDR L1 did not explain why it should not adopt a canonical conformation in this antibody. This makes CNTO4088 a benchmark case for developing prediction methods and structure-modeling tools.

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Organizational Affiliation: 

Centocor R&D Inc., 145 King of Prussia Road, Radnor, PA 19087, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 47.95 kDa 
• Atom Count: 3,359 
• Modelled Residue Count: 440 
• Deposited Residue Count: 440 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CNTO4088 LIGHT CHAIN	A [auth L]	218	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CNTO4088 HEAVY CHAIN	B [auth H]	222	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.43	α = 90
b = 99.43	β = 90
c = 115.04	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Teplyakov, A., Obmolova, G., Gilliland, G.L.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary