3WD5 Immune System date Jun 06, 2013
title Crystal Structure Of Tnfalpha In Complex With Adalimumab Fab
authors S.Hu, S.Y.Liang, Y.J.Guo, Z.Y.Lou
compound source
Molecule: Tumor Necrosis Factor
Chain: A
Fragment: Tumor Necrosis Factor, Soluble Form
Synonym: Tnfalpha
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfa
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Adalimumab Light Chain
Chain: L
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

Molecule: Adalimumab Heavy Chain
Chain: H
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
symmetry Space Group: I 21 3
R_factor 0.187 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
161.849 161.849 161.849 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceComparison of the inhibition mechanisms of adalimumab and infliximab in treating tumor necrosis factor alpha-associated diseases from a molecular view., Hu S, Liang S, Guo H, Zhang D, Li H, Wang X, Yang W, Qian W, Hou S, Wang H, Guo Y, Lou Z, J Biol Chem. 2013 Sep 20;288(38):27059-67. doi: 10.1074/jbc.M113.491530. Epub, 2013 Aug 13. PMID:23943614
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (3wd5.pdb1.gz) 91 Kb
  • CSU: Contacts of Structural Units for 3WD5
  • Structure Factors (185 Kb)
  • Retrieve 3WD5 in mmCIF format [Save to disk]
  • Re-refined 3wd5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WD5 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 3WD5
  • 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
  • 3D motif for 3WD5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wd5_H] [3wd5] [3wd5_A] [3wd5_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3WD5: [IG_like] [IGv] [TNF ] by SMART
  • Other resources with information on 3WD5
  • Community annotation for 3WD5 at PDBWiki (http://pdbwiki.org)

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