2ADF	Blood Clotting Immune System	date	Jul 20, 2005
title	Crystal Structure And Paratope Determination Of 82d6a3, An Antithrombotic Antibody Directed Against The Von Willebrand A3-Domain
authors	S.Staelens, M.A.Hadders, S.Vauterin, C.Platteau, K.Vanhoorelbeke E.G.Huizinga, H.Deckmyn
compound		source
Molecule: Von Willebrand Factor Chain: A Fragment: A3 Domain Synonym: Vwf Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Pet Expression_system_plasmid: Pet15b
Molecule: 82d6a3 Igg Chain: H Fragment: Fab		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Secretion: Ascites
Molecule: 82d6a3 Igg Chain: L Fragment: Fab		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Secretion: Ascites
symmetry	Space Group: P 21 21 21	R_factor 0.191 R_Free 0.220
crystal cell	length a length b length c angle alpha angle beta angle gamma 72.179 89.076 123.511 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	ACY, GOL, SO4	enzyme
Gene Ontology	Chain Function Process Component H antigen binding extracellular region
Primary reference	Paratope determination of the antithrombotic antibody 82D6A3 based on the crystal structure of its complex with the von Willebrand factor A3-domain., Staelens S, Hadders MA, Vauterin S, Platteau C, De Maeyer M, Vanhoorelbeke K, Huizinga EG, Deckmyn H, J Biol Chem. 2006 Jan 27;281(4):2225-31. Epub 2005 Nov 28. PMID:16314412

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk] Biological Unit Coordinates (2adf.pdb1.gz) 105 Kb LPC: Ligand-Protein Contacts for 2ADF CSU: Contacts of Structural Units for 2ADF Likely Quarternary Molecular Structure file(s) for 2ADF Structure Factors (471 Kb) Retrieve 2ADF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2ADF from S2C, [Save to disk] Re-refined 2adf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2ADF 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 2ADF

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 3D motif for 2ADF, from MSDmotif at EBI Fold representative 2adf from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2adf_A] [2adf_H] [2adf_L] SWISS-PROT database: [P84751] [P01837] [P04275] Domain organization of [HVM63_MOUSE] [IGKC_MOUSE] [VWF_HUMAN] by SWISSPFAM Domains found in 2ADF: [IG_like] [IGv] [VWA ] by SMART Alignments of the sequence of 2ADF with the sequences similar proteins can be viewed for 2ADF's classification [HVM63_MOUSE] [IGKC_MOUSE] [VWF_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 [HVM63_MOUSE] [IGKC_MOUSE] [VWF_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2ADF

Community annotation for 2ADF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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