4CNI

Crystal structure of the Fab portion of Olokizumab in complex with IL- 6

PDB DOI: https://doi.org/10.2210/pdb4CNI/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Escherichia coli
Mutation(s): No

Deposited: 2014-01-22 Released: 2014-04-30
Deposition Author(s): Shaw, S., Bourne, T., Meier, C., Carrington, B., Gelinas, R., Henry, A., Popplewell, A., Adams, R., Baker, T., Rapecki, S., Marshall, D., Neale, H., Lawson, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.215 (Depositor), 0.219 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Discovery and Characterization of Olokizumab: A Humanized Antibody Targeting Interleukin-6 and Neutralizing Gp130-Signaling.

Shaw, S., Bourne, T., Meier, C., Carrington, B., Gelinas, R., Henry, A., Popplewell, A., Adams, R., Baker, T., Rapecki, S., Marshall, D., Moore, A., Neale, H., Lawson, A.

(2014) MAbs 6: 773

PubMed: 24670876 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.4161/mabs.28612
Primary Citation of Related Structures:
4CNI

PubMed Abstract:
Interleukin-6 (IL-6) is a critical regulator of the immune system and has been widely implicated in autoimmune disease. Here, we describe the discovery and characterization of olokizumab, a humanized antibody to IL-6. Data from structural biology, cell biology and primate pharmacology demonstrate the therapeutic potential of targeting IL-6 at "Site 3", blocking the interaction with the signaling co-receptor gp130.

Organizational Affiliation

UCB Pharma; Berkshire, UK.

Macromolecule Content

Total Structure Weight: 134.59 kDa
Atom Count: 10,999
Modelled Residue Count: 1,209
Deposited Residue Count: 1,210
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OLOKIZUMAB HEAVY CHAIN, FAB PORTION	A, E [auth H]	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
OLOKIZUMAB LIGHT CHAIN, FAB PORTION	B, F [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERLEUKIN-6	C, D	171	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05231
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAM Query on TAM Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth H] MOL2 format, chain G [auth A] MOL2 format, chain L [auth H] mmCIF format, chain G [auth A] mmCIF format, chain L [auth H]	G [auth A], L [auth H]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth H] Interactions & Density Focus chain G [auth A] Focus chain L [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain M [auth H] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain M [auth H] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain M [auth H]	H [auth C], I [auth C], J [auth D], K [auth D], M [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth H] Interactions & Density Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.215 (Depositor), 0.219 (DCC)
R-Value Work: 0.176 (Depositor), 0.178 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 241.988	α = 90
b = 241.988	β = 90
c = 76.591	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2019-04-03
Changes: Data collection, Other, Source and taxonomy
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Other, Structure summary