3GIZ Immune System date Mar 07, 2009
title Crystal Structure Of The Fab Fragment Of Anti-Cd20 Antibody Ofatumumab
authors J.Du, H.Yang, J.Ding
compound source
Molecule: Fab Fragment Of Anti-Cd20 Antibody Ofatumumab, 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
Expression_system_strain: K1
Expression_system_cell_line: Ovary (Cho) Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna3.1

Molecule: Fab Fragment Of Anti-Cd20 Antibody Ofatumumab, 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
Expression_system_strain: K1
Expression_system_cell_line: Ovary (Cho) Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna3.1
symmetry Space Group: C 1 2 1
R_factor 0.195 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
136.330 55.944 79.780 90.00 122.17 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand ZN enzyme
Primary referenceStructure of the Fab fragment of therapeutic antibody Ofatumumab provides insights into the recognition mechanism with CD20., Du J, Yang H, Guo Y, Ding J, Mol Immunol. 2009 May 6. PMID:19427037
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (3giz.pdb1.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 3GIZ
  • CSU: Contacts of Structural Units for 3GIZ
  • Likely Quarternary Molecular Structure file(s) for 3GIZ
  • Structure Factors (191 Kb)
  • Retrieve 3GIZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GIZ from S2C, [Save to disk]
  • Re-refined 3giz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GIZ 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 3GIZ
  • 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 3GIZ, from MSDmotif at EBI
  • Fold representative 3giz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3giz_L] [3giz] [3giz_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3GIZ: [IG_like] [IGv ] by SMART
  • Other resources with information on 3GIZ
  • Community annotation for 3GIZ 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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