4GAF Signaling Protein date Jul 25, 2012
title Crystal Structure Of Ebi-005, A Chimera Of Human Il-1beta An Bound To Human Interleukin-1 Receptor Type 1
authors J.Hou, S.A.Townson, J.T.Kovalchin, A.Masci, O.Kiner, Y.Shu, B.King C.Thomas, K.C.Garcia, E.S.Furfine, T.M.Barnes
compound source
Molecule: Ebi-005
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Interleukin-1 Receptor Type 1
Chain: B
Fragment: Unp Residues 18-336
Synonym: Il-1r-1, Il-1rt-1, Il-1rt1, Cd121 Antigen-Like Fam A, Interleukin-1 Receptor Alpha, Il-1r-Alpha, Interleukin-1 Type I, P80, Interleukin-1 Receptor Type 1, Membrane Form, Mil-1ri, Interleukin-1 Receptor Type 1, Soluble Form, Sil-1 1ri;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il1r1, Il1r, Il1ra, Il1rt1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.216 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.350 149.270 126.170 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand NA, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceDesign of a superior cytokine antagonist for topical ophthalmic use., Hou J, Townson SA, Kovalchin JT, Masci A, Kiner O, Shu Y, King BM, Schirmer E, Golden K, Thomas C, Garcia KC, Zarbis-Papastoitsis G, Furfine ES, Barnes TM, Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3913-8. doi:, 10.1073/pnas.1217996110. Epub 2013 Feb 19. PMID:23431173
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (166 Kb) [Save to disk]
  • Biological Unit Coordinates (4gaf.pdb1.gz) 160 Kb
  • LPC: Ligand-Protein Contacts for 4GAF
  • CSU: Contacts of Structural Units for 4GAF
  • Structure Factors (462 Kb)
  • Retrieve 4GAF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GAF from S2C, [Save to disk]
  • Re-refined 4gaf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GAF 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 4GAF
  • 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 4GAF, from MSDmotif at EBI
  • Fold representative 4gaf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gaf_A] [4gaf_B] [4gaf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4GAF: [IG] [IG_like] [IL1 ] by SMART
  • Other resources with information on 4GAF
  • Community annotation for 4GAF at PDBWiki (http://pdbwiki.org)

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