2FMA	Metal Binding Protein	date	Jan 08, 2006
title	Structure Of The Alzheimer'S Amyloid Precursor Protein (App) Binding Domain In 'Small Unit Cell' Form, Atomic Resolution
authors	G.K.W.Kong
compound		source
Molecule: Amyloid Beta A4 Protein Precursor Chain: A Fragment: Copper Binding Domain(Residues 133-189) Synonym: Amyloid Precursor Protein, Amyloid Beta A4 Protein App-Alpha, Soluble App-Beta; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Pichia Pastoris Expression_system_taxid: 4922 Expression_system_strain: Gs115 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ppic-9
symmetry	Space Group: P 21 21 21	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 31.289 32.488 50.088 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	0.85 Å
ligand	GOL	enzyme
note	2FMA is a representative structure
Primary reference	Structure of Alzheimer's disease amyloid precursor protein copper-binding domain at atomic resolution., Kong GK, Adams JJ, Cappai R, Parker MW, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Oct 1;63(Pt, 10):819-24. Epub 2007 Sep 19. PMID:17909280

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk] Biological Unit Coordinates (2fma.pdb1.gz) 25 Kb LPC: Ligand-Protein Contacts for 2FMA CSU: Contacts of Structural Units for 2FMA Likely Quarternary Molecular Structure file(s) for 2FMA Structure Factors (301 Kb) Retrieve 2FMA in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2FMA from S2C, [Save to disk] Re-refined 2fma structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2FMA 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 2FMA

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 2FMA, from MSDmotif at EBI Fold representative 2fma from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2fma_A] SWISS-PROT database: [P05067] Belongs to the amyloid -protein peptide (app) family according to TCDB. Domain organization of [A4_HUMAN] by SWISSPFAM Domain found in 2FMA: [A4_EXTRA ] by SMART Alignments of the sequence of 2FMA with the sequences similar proteins can be viewed for 2FMA's classification [A4_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 [A4_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2FMA

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

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