3QMK Cell Adhesion date Feb 04, 2011
title Crystal Structure Of The E2 Domain Of Aplp1 In Complex With Hexasaccharide
authors Y.Xue, Y.Ha
compound source
Molecule: Amyloid-Like Protein 1
Chain: A, B
Fragment: Aplp1 E2 Domain
Synonym: Aplp, Aplp-1, C30
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aplp1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 21 21 21
R_factor 0.218 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.183 81.899 90.790 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.21 Å
ligand IDS, SGN, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of amyloid precursor-like protein 1 and heparin complex suggests a dual role of heparin in E2 dimerization., Xue Y, Lee S, Ha Y, Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16229-34. Epub 2011 Sep 19. PMID:21930949
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (3qmk.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 3QMK
  • CSU: Contacts of Structural Units for 3QMK
  • Structure Factors (402 Kb)
  • Retrieve 3QMK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QMK from S2C, [Save to disk]
  • Re-refined 3qmk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QMK 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 3QMK
  • 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
  • 3D motif for 3QMK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qmk] [3qmk_B] [3qmk_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3QMK
  • Community annotation for 3QMK at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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