5YGP Apoptosis date Sep 25, 2017
title Human Tnfrsf25 Death Domain Mutant-D412e
authors X.Yin, T.C.Jin
compound source
Molecule: Tnfrsf25 Death Domain
Chain: A, B, C, D
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 1 21 1
R_factor 0.218 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.620 155.020 74.030 90.00 90.18 90.00
method X-Ray Diffractionresolution 2.09 Å
ligand GLC, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • carbohydrate transmembrane t...


  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (574 Kb) [Save to disk]
  • Biological Unit Coordinates (5ygp.pdb1.gz) 144 Kb
  • Biological Unit Coordinates (5ygp.pdb2.gz) 145 Kb
  • Biological Unit Coordinates (5ygp.pdb3.gz) 144 Kb
  • Biological Unit Coordinates (5ygp.pdb4.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 5YGP
  • CSU: Contacts of Structural Units for 5YGP
  • Structure Factors (3854 Kb)
  • Retrieve 5YGP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YGP from S2C, [Save to disk]
  • View 5YGP 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 5YGP
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ygp_B] [5ygp_A] [5ygp_C] [5ygp_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YGP
  • Community annotation for 5YGP at PDBWiki (http://pdbwiki.org)

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