3DSF Immune System date Jul 12, 2008
title Crystal Structure Of Anti-Osteopontin Antibody 23c3 In Compl W43a Mutated Epitope Peptide
authors J.Du, C.Zhong, H.Yang, J.Ding
compound source
Molecule: Fab Fragment Of Anti-Osteopontin Antibody 23c3, L Chain;
Chain: L
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Tissue: Ascites

Molecule: Fab Fragment Of Anti-Osteopontin Antibody 23c3, H Chain;
Chain: H

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Tissue: Ascites

Molecule: A Peptide From Osteopontin
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Vatalnpdpsqk Is Synthesized At S Hd Bioscience Company
symmetry Space Group: P 21 21 21
R_factor 0.241 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.730 92.058 122.104 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand BMA, MAN, NAG enzyme
Primary referenceMolecular basis of recognition of human osteopontin by 23C3, a potential therapeutic antibody for treatment of rheumatoid arthritis., Du J, Hou S, Zhong C, Lai Z, Yang H, Dai J, Zhang D, Wang H, Guo Y, Ding J, J Mol Biol. 2008 Oct 17;382(4):835-42. Epub 2008 Jul 31. PMID:18694758
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (3dsf.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 3DSF
  • CSU: Contacts of Structural Units for 3DSF
  • Likely Quarternary Molecular Structure file(s) for 3DSF
  • Structure Factors (86 Kb)
  • Retrieve 3DSF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DSF from S2C, [Save to disk]
  • Re-refined 3dsf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DSF 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 3DSF
  • 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 3DSF, from MSDmotif at EBI
  • Fold representative 3dsf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dsf_H] [3dsf_L] [3dsf] [3dsf_P]
  • SWISS-PROT database: [P10451]
  • Domain organization of [OSTP_HUMAN] by SWISSPFAM
  • Domains found in 3DSF: [IG_like] [IGv ] by SMART
  • Other resources with information on 3DSF
  • Community annotation for 3DSF 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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