3UMI Metal Binding Protein date Nov 13, 2011
title X-Ray Structure Of The E2 Domain Of The Human Amyloid Precur Protein (App) In Complex With Zinc
authors S.O.Dahms, I.Konnig, D.Roeser, K.H.Guhrs, M.E.Than
compound source
Molecule: Amyloid Beta A4 Protein
Chain: A
Fragment: Human Amyloid Precursor Protein E2 Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 43
R_factor 0.204 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.757 39.757 126.425 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ACT, CD, ZN enzyme
Primary referenceMetal Binding Dictates Conformation and Function of the Amyloid Precursor Protein (APP) E2 Domain., Dahms SO, Konnig I, Roeser D, Guhrs KH, Mayer MC, Kaden D, Multhaup G, Than ME, J Mol Biol. 2012 Jan 4. PMID:22245578
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (3umi.pdb1.gz) 34 Kb
  • LPC: Ligand-Protein Contacts for 3UMI
  • CSU: Contacts of Structural Units for 3UMI
  • Structure Factors (52 Kb)
  • Retrieve 3UMI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UMI from S2C, [Save to disk]
  • Re-refined 3umi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UMI 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 3UMI
  • 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 3UMI, from MSDmotif at EBI
  • Fold representative 3umi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3umi] [3umi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3UMI with the sequences similar proteins can be viewed for 3UMI'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 3UMI
  • Community annotation for 3UMI at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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