3NFP Immune System Cytokine date Jun 10, 2010
title Crystal Structure Of The Fab Fragment Of Therapeutic Antibod Daclizumab In Complex With Il-2ra (Cd25) Ectodomain
authors H.Yang, J.Wang, J.Du, C.Zhong, Y.Guo, J.Ding
compound source
Molecule: Heavy Chain Of Fab Fragment Of Daclizumab
Chain: A, H
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Purchased From Roche, Expressed In A Mammal Expression System;

Molecule: Light Chain Of Fab Fragment Of Daclizumab
Chain: B, L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Purchased From Roche, Expressed In A Mammal Expression System;

Molecule: Interleukin-2 Receptor Subunit Alpha
Chain: I, K
Fragment: Unp Residues 22-238
Synonym: Il-2 Receptor Subunit Alpha, Il-2r Subunit Alpha, Il2-Ra, P55, Tac Antigen, Cd_antigen=Cd25;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il2ra
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Hi-5
Expression_system_vector_type: Baculovirus
symmetry Space Group: C 2 2 21
R_factor 0.253 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.167 114.973 247.555 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.86 Å
note 3NFP is a representative structure
Primary referenceStructural basis of immunosuppression by the therapeutic antibody daclizumab., Yang H, Wang J, Du J, Zhong C, Zhang D, Guo H, Guo Y, Ding J, Cell Res. 2010 Sep 7. PMID:20820193
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (329 Kb) [Save to disk]
  • Biological Unit Coordinates (3nfp.pdb1.gz) 161 Kb
  • Biological Unit Coordinates (3nfp.pdb2.gz) 165 Kb
  • CSU: Contacts of Structural Units for 3NFP
  • Structure Factors (250 Kb)
  • Retrieve 3NFP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NFP from S2C, [Save to disk]
  • Re-refined 3nfp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NFP 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 3NFP
  • 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 3NFP, from MSDmotif at EBI
  • Fold representative 3nfp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nfp] [3nfp_L] [3nfp_H] [3nfp_A] [3nfp_I] [3nfp_B] [3nfp_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3NFP: [CCP] [IGc1] [IGv ] by SMART
  • Alignments of the sequence of 3NFP with the sequences similar proteins can be viewed for 3NFP's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3NFP
  • Community annotation for 3NFP 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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