2IPU Immune System date Oct 12, 2006
title Pfa1 Fab Fragment Complexed With Abeta 1-8 Peptide
authors A.S.Gardberg, C.Dealwis
compound source
Molecule: Igg2a Fab Fragment Heavy Chain
Chain: L, K
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: Balbc
Other_details: Hybridoma

Molecule: Igg2a Fab Fragment Light Chain Kappa
Chain: H, G

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: Balbc
Other_details: Hybridoma

Molecule: Abeta 1-8 Peptide
Chain: P, Q
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Homo Sapie (Humans)
symmetry Space Group: P 1
R_factor 0.182 R_Free 0.225
length a length b length c angle alpha angle beta angle gamma
43.070 70.335 74.197 72.32 86.08 86.02
method X-Ray Diffractionresolution 1.65 Å
ligand ACM, GOL enzyme
K, L

Primary referenceMolecular basis for passive immunotherapy of Alzheimer's disease., Gardberg AS, Dice LT, Ou S, Rich RL, Helmbrecht E, Ko J, Wetzel R, Myszka DG, Patterson PH, Dealwis C, Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15659-64. Epub 2007 Sep 25. PMID:17895381
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (2ipu.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (2ipu.pdb2.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 2IPU
  • CSU: Contacts of Structural Units for 2IPU
  • Likely Quarternary Molecular Structure file(s) for 2IPU
  • Structure Factors (698 Kb)
  • Retrieve 2IPU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IPU from S2C, [Save to disk]
  • Re-refined 2ipu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IPU 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 2IPU
  • 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 2IPU, from MSDmotif at EBI
  • Fold representative 2ipu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ipu_G] [2ipu_P] [2ipu_L] [2ipu_K] [2ipu] [2ipu_Q] [2ipu_H]
  • SWISS-PROT database: [P05067] [P01863]
  • Belongs to the amyloid β-protein peptide (aβpp) family according to TCDB.
  • Domain organization of [A4_HUMAN] [GCAA_MOUSE] by SWISSPFAM
  • Domains found in 2IPU: [IG_like] [IGv ] by SMART
  • Other resources with information on 2IPU
  • Community annotation for 2IPU 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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