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 Diffraction	resolution	2.80 Å
ligand	BMA, MAN, NAG	enzyme
Primary reference	Molecular 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] (132 Kb) [Save to disk] Biological Unit Coordinates (3dsf.pdb1.gz) 128 Kb LPC: Ligand-Protein Contacts for 3DSF CSU: Contacts of Structural Units for 3DSF Likely Quarternary Molecular Structure file(s) for 3DSF Structure Factors (87 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_P] SWISS-PROT database: [P10451] Domain organization of [OSTP_HUMAN] by SWISSPFAM Domains found in 3DSF: [IG_like] [IGv ] by SMART Alignments of the sequence of 3DSF with the sequences similar proteins can be viewed for 3DSF's classification [OSTP_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [OSTP_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3DSF

Community annotation for 3DSF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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