3D85 Immune System Cytokine date May 22, 2008
title Crystal Structure Of Il-23 In Complex With Neutralizing Fab
authors B.M.Beyer, R.Ingram, L.Ramanathan, P.Reichert, H.Le, V.Madison
compound source
Molecule: Fab Of Antibody 7g10, Light Chain
Chain: A
Fragment: Light Chain
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fab Of Antibody 7g10, Heavy Chain
Chain: B
Fragment: Heavy Chain

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Interleukin-23 Subunit P19
Chain: C
Fragment: Subunit P19
Synonym: Interleukin-23 Subunit Alpha; Il-23 Subunit Alpha; Il-23p19;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il23a, Sgrf, Unq2498pro5798
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: Hi-Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Dual

Molecule: Interleukin-12 Subunit P40
Chain: D
Fragment: Subunit P40
Synonym: Il-12b; Il-12 Subunit P40; Cytotoxic Lymphocyte Maturation Factor 40 Kda Subunit; Clmf P40; Nk Cell Stimulatory Factor Chain 2; Nksf2;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il12b, Nksf2
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: Hi-Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Dual
symmetry Space Group: P 1 21 1
R_factor 0.171 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.386 62.091 107.261 90.00 97.44 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand IMD, MPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
C
  • positive regulation of inter...
  • positive regulation of inter...

  • D
  • positive regulation of inter...
  • positive regulation of inter...

  • Primary referenceCrystal Structures of the Pro-Inflammatory Cytokine Interleukin-23 and Its Complex with a High-Affinity Neutralizing Antibody., Beyer BM, Ingram R, Ramanathan L, Reichert P, Le HV, Madison V, Orth P, J Mol Biol. 2008 Aug 7. PMID:18708069
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (3d85.pdb1.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 3D85
  • CSU: Contacts of Structural Units for 3D85
  • Likely Quarternary Molecular Structure file(s) for 3D85
  • Structure Factors (1275 Kb)
  • Retrieve 3D85 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D85 from S2C, [Save to disk]
  • Re-refined 3d85 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D85 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 3D85
  • 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 3D85, from MSDmotif at EBI
  • Fold representative 3d85 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d85_A] [3d85_C] [3d85_D] [3d85_B] [3d85]
  • SWISS-PROT database: [P01857] [P01834] [P29460] [Q9NPF7]
  • Domain organization of [IGHG1_HUMAN] [IGKC_HUMAN] [IL12B_HUMAN] [IL23A_HUMAN] by SWISSPFAM
  • Domains found in 3D85: [IGc1] [IGc2] [IGv ] by SMART
  • Alignments of the sequence of 3D85 with the sequences similar proteins can be viewed for 3D85's classification [IGHG1_HUMAN] [IGKC_HUMAN] [IL12B_HUMAN] [IL23A_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [IGHG1_HUMAN] [IGKC_HUMAN] [IL12B_HUMAN] [IL23A_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3D85
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