4YXH Immune System date Mar 23, 2015
title Crystal Structure Of Deer Prion Protein Complexed With Pom1
authors P.K.Baral, M.Swayampakula, M.N.G.James
compound source
Molecule: Major Prion Protein
Chain: A
Synonym: Prp
Engineered: Yes
Organism_scientific: Odocoileus Hemionus
Organism_common: Mule Deer
Organism_taxid: 9872
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 0.243 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.282 106.580 75.775 90.00 95.81 90.00
method X-Ray Diffractionresolution 2.70 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 (4yxh.pdb1.gz) 20 Kb
  • Biological Unit Coordinates (4yxh.pdb2.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 4YXH
  • CSU: Contacts of Structural Units for 4YXH
  • Structure Factors (273 Kb)
  • Retrieve 4YXH in mmCIF format [Save to disk]
  • Re-refined 4yxh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YXH 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 4YXH
  • 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
  • Fold representative 4yxh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yxh_H] [4yxh_A] [4yxh_L] [4yxh]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YXH: [IG_like] [IGv] [PRP ] by SMART
  • Other resources with information on 4YXH
  • Community annotation for 4YXH at PDBWiki (http://pdbwiki.org)

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