4CNI Immune System date Jan 22, 2014
title Crystal Structure Of The Fab Portion Of Olokizumab In Complex With Il-6
authors S.Shaw, T.Bourne, C.Meier, B.Carrington, R.Gelinas, A.Henry, A.Pop R.Adams, T.Baker, S.Rapecki, D.Marshall, H.Neale, A.Lawson
compound source
Molecule: Olokizumab Light Chain, Fab Portion
Chain: L, B
Fragment: Fab Portion
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho Cells
Expression_system_tissue: Ovary

Molecule: Olokizumab Heavy Chain, Fab Portion
Chain: H, A
Fragment: Fab Portion
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho Cells
Expression_system_tissue: Ovary

Molecule: Interleukin-6
Chain: C, D
Fragment: Residues 41-212
Synonym: Il-6, B-Cell Stimulatory Factor 2, Bsf-2, Ctl Differentiation Factor, Cdf, Hybridoma Growth Factor, Inte Beta-2, Ifn-Beta-2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 6
R_factor 0.17608 R_Free 0.21549
crystal
cell
length a length b length c angle alpha angle beta angle gamma
241.988 241.988 76.591 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand SO4, TAM enzyme
Gene
Ontology
ChainFunctionProcessComponent
D, C
  • cytokine activity
  • growth factor activity
  • regulation of vascular endot...
  • positive regulation of chemo...
  • positive regulation of trans...
  • positive regulation of immun...

  • Primary referenceDiscovery 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, MAbs. 2014 May 1;6(3):773-81. doi: 10.4161/mabs.28612. Epub 2014 Apr 2. PMID:24670876
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (228 Kb) [Save to disk]
  • Biological Unit Coordinates (4cni.pdb1.gz) 115 Kb
  • Biological Unit Coordinates (4cni.pdb2.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 4CNI
  • CSU: Contacts of Structural Units for 4CNI
  • Structure Factors (2444 Kb)
  • Retrieve 4CNI in mmCIF format [Save to disk]
  • Re-refined 4cni structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4CNI in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4CNI
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4CNI, from MSDmotif at EBI
  • Fold representative 4cni from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4cni_D] [4cni_C] [4cni_B] [4cni_A] [4cni_L] [4cni_H] [4cni]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4CNI: [IG_like] [IGv] [IL6 ] by SMART
  • Other resources with information on 4CNI
  • Community annotation for 4CNI at PDBWiki (http://pdbwiki.org)

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