5VKM Immune System date Apr 21, 2017
title Crystal Structure Of Human Cd22 Ig Domains 1-3 In Complex Wi 2-6 Sialyllactose
authors J.P.Julien, J.Ereno-Orbea, T.Sicard
compound source
Molecule: B-Cell Receptor Cd22
Chain: A
Fragment: Extracellular Domain Residues 20-330
Synonym: B-Lymphocyte Cell Adhesion Molecule,Bl-Cam,Sialic Binding Ig-Like Lectin 2,Siglec-2,T-Cell Surface Antigen Le
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd22, Siglec2
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
symmetry Space Group: C 1 2 1
R_factor 0.210 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.283 57.912 48.081 90.00 106.99 90.00
method X-Ray Diffractionresolution 2.20 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] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (5vkm.pdb1.gz) 54 Kb
  • CSU: Contacts of Structural Units for 5VKM
  • Structure Factors (425 Kb)
  • Retrieve 5VKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VKM from S2C, [Save to disk]
  • View 5VKM 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 5VKM
  • 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
  • Fold representative 5vkm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vkm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VKM
  • Community annotation for 5VKM at PDBWiki (http://pdbwiki.org)

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