5VL3 Immune System date Apr 24, 2017
title Cd22 D1-D3 In Complex With Therapeutic Fab Epratuzumab
authors T.Sicard, J.Ereno-Orbea, J.P.Julien
compound source
Molecule: B-Cell Receptor Cd22
Chain: Q, R, S, T
Synonym: B-Lymphocyte Cell Adhesion Molecule,Bl-Cam,Sialic Binding Ig-Like Lectin 2,Siglec-2,T-Cell Surface Antigen Le
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd22, Siglec2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606

Molecule: Epratuzumab Fab Heavy Chain
Chain: A, C, E, H
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

Molecule: Epratuzumab Fab Light Chain
Chain: B, D, F, L
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 0.280 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.110 90.220 136.632 70.83 80.81 80.99
method X-Ray Diffractionresolution 3.10 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] (972 Kb) [Save to disk]
  • Biological Unit Coordinates (5vl3.pdb1.gz) 248 Kb
  • Biological Unit Coordinates (5vl3.pdb2.gz) 246 Kb
  • Biological Unit Coordinates (5vl3.pdb3.gz) 249 Kb
  • Biological Unit Coordinates (5vl3.pdb4.gz) 246 Kb
  • CSU: Contacts of Structural Units for 5VL3
  • Structure Factors (1904 Kb)
  • Retrieve 5VL3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VL3 from S2C, [Save to disk]
  • View 5VL3 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 5VL3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5vl3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vl3_H] [5vl3_Q] [5vl3_S] [5vl3_C] [5vl3_A] [5vl3_D] [5vl3_B] [5vl3_T] [5vl3_E] [5vl3_F] [5vl3_L] [5vl3_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VL3
  • Community annotation for 5VL3 at PDBWiki (http://pdbwiki.org)

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