3NYL	Cell Adhesion	date	Jul 15, 2010
title	The X-Ray Structure Of An Antiparallel Dimer Of The Human Am Precursor Protein E2 Domain
authors	Y.Ha, J.Hu, S.Lee, X.Liu, Y.Wang
compound		source
Molecule: Amyloid Beta (A4) Protein (Peptidase Nexin-II, Al Disease), Isoform Cra_b; Chain: A Fragment: Unp Residues 346-551 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: App, Hcg_1810805 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28
symmetry	Space Group: I 4 2 2	R_factor 0.258 R_Free 0.322
crystal cell	length a length b length c angle alpha angle beta angle gamma 83.589 83.589 147.341 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
note	3NYL supersedes 1RW6
Gene	HCG
Primary reference	The X-ray structure of an antiparallel dimer of the human amyloid precursor protein E2 domain., Wang Y, Ha Y, Mol Cell. 2004 Aug 13;15(3):343-53. PMID:15304215

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk] Biological Unit Coordinates (3nyl.pdb1.gz) 61 Kb CSU: Contacts of Structural Units for 3NYL Structure Factors (50 Kb) Retrieve 3NYL in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3NYL from S2C, [Save to disk] Re-refined 3nyl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3NYL 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 3NYL

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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 3NYL, from MSDmotif at EBI Fold representative 3nyl from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3nyl_A] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3NYL with the sequences similar proteins can be viewed for 3NYL's classification 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 at ProtoMap. Click on the Cluster number.

Other resources with information on 3NYL

Community annotation for 3NYL at PDBWiki (http://pdbwiki.org)

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