3DI2 Cytokine Cytokine Receptor date Jun 19, 2008
title Crystal Structure Of The Complex Of Human Interleukin-7 With Unglycosylated Human Interleukin-7 Receptor Alpha Ectodomain
authors C.A.Mcelroy, J.A.Dohm, S.T.R.Walsh
compound source
Molecule: Interleukin-7
Chain: A, C
Fragment: Unp Residues 26 To 177
Synonym: Il-7
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il7
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3) Codon Plus Rp
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b

Molecule: Interleukin-7 Receptor Subunit Alpha
Chain: B, D
Fragment: Unp Residues 21 To 239 (Ligand Binding Ectodomain);
Synonym: Il-7r-Alpha, Cd127 Antigen, Cdw127
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il7r
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3) Codon Plus Rp
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b
symmetry Space Group: P 1 21 1
R_factor 0.212 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.202 113.021 87.534 90.00 105.10 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 1PE enzyme
note 3DI2 is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceStructural and Biophysical Studies of the Human IL-7/IL-7Ralpha Complex., McElroy CA, Dohm JA, Walsh ST, Structure. 2009 Jan;17(1):54-65. PMID:19141282
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (3di2.pdb1.gz) 52 Kb
  • Biological Unit Coordinates (3di2.pdb2.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 3DI2
  • CSU: Contacts of Structural Units for 3DI2
  • Likely Quarternary Molecular Structure file(s) for 3DI2
  • Structure Factors (139 Kb)
  • Retrieve 3DI2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DI2 from S2C, [Save to disk]
  • Re-refined 3di2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DI2 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 3DI2
  • 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 3DI2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m3di2, region I:115-226 [Jmol] [rasmolscript] [script source]
  • Fold representative 3di2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3di2] [3di2_A] [3di2_B] [3di2_C] [3di2_D]
  • SWISS-PROT database: [P16871] [P13232]
  • Domain organization of [IL7RA_HUMAN] [IL7_HUMAN] by SWISSPFAM
  • Domain found in 3DI2: [IL7 ] by SMART
  • Other resources with information on 3DI2
  • Community annotation for 3DI2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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