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
  • Alignments of the sequence of 3NYJ with the sequences similar proteins can be viewed for 3NYJ'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 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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