5VKK Immune System date Apr 21, 2017
title Crystal Structure Of Fab Fragment Of Anti-Cd22 Epratuzumab
authors T.Sicard, J.Ereno-Orbea, J.P.Julien
compound source
Molecule: Epratuzumab Fab Heavy Chain
Chain: H, A
Engineered: Yes
Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090, 9606
Gene: Dkfzp686p15220
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606

Molecule: Epratuzumab Fab Light Chain
Chain: L, B
Engineered: Yes

Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090, 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
symmetry Space Group: P 1
R_factor 0.212 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.712 61.564 65.285 71.81 81.07 75.95
method X-Ray Diffractionresolution 2.01 Å
Primary referenceMolecular basis of human CD22 function and therapeutic targeting., Ereno-Orbea J, Sicard T, Cui H, Mazhab-Jafari MT, Benlekbir S, Guarne A, Rubinstein JL, Julien JP, Nat Commun. 2017 Oct 2;8(1):764. doi: 10.1038/s41467-017-00836-6. PMID:28970495
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (288 Kb) [Save to disk]
  • Biological Unit Coordinates (5vkk.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (5vkk.pdb2.gz) 142 Kb
  • CSU: Contacts of Structural Units for 5VKK
  • Structure Factors (1357 Kb)
  • Retrieve 5VKK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VKK from S2C, [Save to disk]
  • View 5VKK 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 5VKK
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vkk_B] [5vkk_A] [5vkk_H] [5vkk_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VKK
  • Community annotation for 5VKK at PDBWiki (http://pdbwiki.org)

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