2LLM Protein Fibril date Nov 15, 2011
title Structure Of Amyloid Precursor Protein'S Transmembrane Domai
authors K.D.Nadezhdin, O.V.Bocharova, E.V.Bocharov, A.S.Arseniev
compound source
Molecule: Amyloid Beta A4 Protein
Chain: A
Fragment: Unp Residues 686-726
Synonym: Abpp, Appi, App, Alzheimer Disease Amyloid Protein Vascular Amyloid Peptide, Cvap, Prea4, Protease Nexin-II, P 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;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: App, A4, Ad1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Pgemex-1
methodSolution NMR
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side
Primary referenceStructural and dynamic study of the transmembrane domain of the amyloid precursor protein., Nadezhdin KD, Bocharova OV, Bocharov EV, Arseniev AS, Acta Naturae. 2011 Jan;3(1):69-76. PMID:22649674
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (2llm.pdb1.gz) 13 Kb
  • CSU: Contacts of Structural Units for 2LLM
  • Original NMR restraints for 2LLM from PDB
  • Retrieve 2LLM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2LLM from S2C, [Save to disk]
    • View 2LLM 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 2LLM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2LLM, from MSDmotif at EBI
  • Fold representative 2llm from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2llm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 2LLM with the sequences similar proteins can be viewed for 2LLM'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 2LLM
  • Community annotation for 2LLM at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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