5H5S Oxidoreductase Oxidoreductase Inhibitor date Nov 09, 2016
title Crystal Structure Of Human Gpx4 In Complex With Gxpep-3
authors S.Sogabe, A.Kadotani, W.Lane, G.Snell
compound source
Molecule: Phospholipid Hydroperoxide Glutathione Peroxidase Mitochondrial;
Chain: A
Synonym: Phgpx,Glutathione Peroxidase 4,Gshpx-4
Ec: 1.11.1.12
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gpx4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Gxpep-3
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Enterobacteria Phage T7
Organism_taxid: 10760
symmetry Space Group: P 1 21 1
R_factor 0.166 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
35.017 39.077 59.394 90.00 97.84 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand CSD, GOL enzyme Oxidoreductase E.C.1.11.1.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDiscovery of GPX4 inhibitory peptides from random peptide T7 phage display and subsequent structural analysis., Sakamoto K, Sogabe S, Kamada Y, Matsumoto SI, Kadotani A, Sakamoto JI, Tani A, Biochem Biophys Res Commun. 2016 Nov 9. pii: S0006-291X(16)31890-3. doi:, 10.1016/j.bbrc.2016.11.035. PMID:27836545
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (5h5s.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 5H5S
  • CSU: Contacts of Structural Units for 5H5S
  • Structure Factors (172 Kb)
  • Retrieve 5H5S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5H5S from S2C, [Save to disk]
  • Re-refined 5h5s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5H5S 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 5H5S
  • 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 5h5s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5h5s_B] [5h5s_A] [5h5s]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5H5S
  • Community annotation for 5H5S at PDBWiki (http://pdbwiki.org)

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