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 Diffractionresolution 2.80 Å
note 3NYL supersedes 1RW6
Gene HCG
Primary referenceThe 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.
  • Visual 3D analysis of 3NYL
  • 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 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] [3nyl]
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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