2B2X	Immune System	date	Sep 19, 2005
title	Vla1 Rdeltah I-Domain Complexed With A Quadruple Mutant Of T Fab
authors	L.A.Clark, P.A.Boriack-Sjodin, J.Eldredge, C.Fitch, B.Friedman, K M.Jarpe, S.F.Liparoto, Y.Li, A.Lugovskoy
compound		source
Molecule: Integrin Alpha-1 Chain: A, B Fragment: I Domain R Delta H Synonym: Laminin And Collagen Receptor, Vla-1, Cd49a Engineered: Yes Mutation: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Gene: Itga1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Dh5alpha Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgrti
Molecule: Antibody Aqc2 Fab Chain: H, I Fragment: Aqc2 Fab Heavy Chain Engineered: Yes Mutation: Yes		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Top10 Expression_system_vector_type: Plasmid Expression_system_plasmid: Yl037
Molecule: Antibody Aqc2 Fab Chain: L, M Fragment: Aqc2 Fab Light Chain Engineered: Yes Mutation: Yes		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Top10 Expression_system_vector_type: Plasmid Expression_system_plasmid: Yl037
symmetry	Space Group: P 1 2 1	R_factor 0.238 R_Free 0.272
crystal cell	length a length b length c angle alpha angle beta angle gamma 106.120 43.680 153.880 90.00 104.10 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	MG	enzyme
Primary reference	Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design., Clark LA, Boriack-Sjodin PA, Eldredge J, Fitch C, Friedman B, Hanf KJ, Jarpe M, Liparoto SF, Li Y, Lugovskoy A, Miller S, Rushe M, Sherman W, Simon K, van Vlijmen H, Protein Sci. 2006 Apr 5;. PMID:16597831

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (196 Kb) [Save to disk] Biological Unit Coordinates (2b2x.pdb1.gz) 98 Kb Biological Unit Coordinates (2b2x.pdb2.gz) 97 Kb LPC: Ligand-Protein Contacts for 2B2X CSU: Contacts of Structural Units for 2B2X Likely Quarternary Molecular Structure file(s) for 2B2X Structure Factors (1164 Kb) Retrieve 2B2X in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2B2X from S2C, [Save to disk] Re-refined 2b2x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2B2X 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 2B2X

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 3D motif for 2B2X, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2b2x_B] [2b2x_I] [2b2x_M] [2b2x_L] [2b2x] [2b2x_A] [2b2x_H] SWISS-PROT database: [P01868] [P18614] Domain organization of [IGHG1_MOUSE] [ITA1_RAT] by SWISSPFAM Domains found in 2B2X: [IG_like] [IGv] [VWA ] by SMART

Other resources with information on 2B2X

Community annotation for 2B2X at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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