3NYJ Protein Fibril date Jul 15, 2010
title Crystal Structure Analysis Of App E2 Domain
authors Y.Ha, J.Hu, S.Lee, X.Liu
compound source
Molecule: Amyloid Beta A4 Protein
Chain: A
Synonym: Alzheimer Disease Amyloid Protein, Abpp, Appi, App Cerebral Vascular Amyloid Peptide, Cvap, Protease Nexin-II, App, Soluble App-Alpha, S-App-Alpha, Soluble App-Beta, S-Ap C99, Beta-Amyloid Protein 42, Beta-App42, Beta-Amyloid Prot Beta-App40, C83, P3(42), P3(40), C80, Gamma-Secretase C-Ter Fragment 59, Gamma-Ctf(59), Amyloid Intracellular Domain 59 Aid(59), Gamma-Secretase C-Terminal Fragment 57, Gamma-Ctf( Amyloid Intracellular Domain 57, Aicd-57, Aid(57), Gamma-Se Terminal Fragment 50, Gamma-Ctf(50), Amyloid Intracellular Aicd-50, Aid(50), C31;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: A4, Ad1, App
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: P 21 21 2
R_factor 0.297 R_Free 0.380
length a length b length c angle alpha angle beta angle gamma
114.979 40.149 58.376 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand MSE, OS enzyme

Primary referenceThe E2 Domains of APP and APLP1 Share a Conserved Mode of Dimerization., Lee S, Xue Y, Hu J, Wang Y, Liu X, Demeler B, Ha Y, Biochemistry. 2011 May 26. PMID:21574595
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (3nyj.pdb1.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 3NYJ
  • CSU: Contacts of Structural Units for 3NYJ
  • Structure Factors (35 Kb)
  • Retrieve 3NYJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NYJ from S2C, [Save to disk]
  • Re-refined 3nyj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NYJ 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 3NYJ
  • 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 3NYJ, from MSDmotif at EBI
  • Fold representative 3nyj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nyj] [3nyj_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3NYJ
  • Community annotation for 3NYJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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