4YXK Immune System date Mar 23, 2015
title Crystal Structure Of Elk Prion Protein Complexed With Pom1 F
authors P.K.Baral, M.Swayampakula, M.N.G.James
compound source
Molecule: Major Prion Protein
Chain: A
Synonym: Prp
Engineered: Yes
Organism_scientific: Cervus Elaphus Nelsoni
Organism_common: North American Elk
Organism_taxid: 9864
Gene: Prnp, Prp
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Pom1 Fab Heavy Chain
Chain: H
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_taxid: 10090

Molecule: Pom1 Fab Light Chain
Chain: L
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_taxid: 10090
symmetry Space Group: C 1 2 1
R_factor 0.300 R_Free 0.353
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.674 105.509 76.112 90.00 95.22 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceX-ray structural and molecular dynamical studies of the globular domains of cow, deer, elk and Syrian hamster prion proteins., Baral PK, Swayampakula M, Aguzzi A, James MN, J Struct Biol. 2015 Oct;192(1):37-47. doi: 10.1016/j.jsb.2015.08.014. Epub 2015, Aug 28. PMID:26320075
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (4yxk.pdb1.gz) 20 Kb
  • Biological Unit Coordinates (4yxk.pdb2.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 4YXK
  • CSU: Contacts of Structural Units for 4YXK
  • Structure Factors (228 Kb)
  • Retrieve 4YXK in mmCIF format [Save to disk]
  • Re-refined 4yxk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YXK 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 4YXK
  • 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
  • Fold representative 4yxk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yxk] [4yxk_A] [4yxk_L] [4yxk_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YXK: [IG_like] [IGv] [PRP ] by SMART
  • Other resources with information on 4YXK
  • Community annotation for 4YXK at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science