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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GPX4 IN COMPLEX WITH GXPEP-2
 
Authors :  S. Sogabe, A. Kadotani, W. Lane, G. Snell
Date :  09 Nov 16  (Deposition) - 07 Dec 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phospholipid Hydroperoxide Glutathione Peroxidase 4, Selenocysteine, Oxidoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sakamoto, S. Sogabe, Y. Kamada, S. I. Matsumoto, A. Kadotani, J. I. Sakamoto, A. Tani
Discovery Of Gpx4 Inhibitory Peptides From Random Peptide T Phage Display And Subsequent Structural Analysis
Biochem. Biophys. Res. V. 482 195 2017 Commun.
PubMed-ID: 27836545  |  Reference-DOI: 10.1016/J.BBRC.2016.11.035

(-) Compounds

Molecule 1 - PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE, MITOCHONDRIAL
    Chains: A
    EC Number: 1.11.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GPX4
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PHGPX,GLUTATHIONE PEROXIDASE 4,GSHPX-4
 
Molecule 2 - GXPEP-2
    Chains: B
    Engineered: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T7
    Organism Taxid: 10760
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2GOL1Ligand/IonGLYCEROL
3NH21Mod. Amino AcidAMINO GROUP
4OCS1Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:151 , LYS A:152 , LYS A:154 , LYS A:178 , ARG A:179 , HOH A:395binding site for residue GOL A 201

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:901 -B:909

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5H5R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H5R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H5R)

(-) Exons   (0, 0)

(no "Exon" information available for 5H5R)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.hhhh.eee.....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhh....ee...........hhhhhhhhh.................eeee.....eeeee....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h5r A  29 SASRDDWRAARSMHEFSAKDIDGHMVNLDKYRGFVSIVTNVASQcGKTEVNYTQLVDLHARYAERGLRILAFPSNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKIEVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGVVVKRYGPMEEPLVIEKDLPHYF 197
                                    38        48        58        68    |   78        88        98       108       118       128       138       148       158       168       178       188         
                                                                       73-OCS                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ...eee..eeee... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 5h5r B 900 xCRAWYQNYCALRRx 914
                            |      909    |
                          900-ACE       914-NH2
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5H5R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H5R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H5R)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  5h5r
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  GPX4_HUMAN | P36969
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  1.11.1.12
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GPX4_HUMAN | P36969: 2gs3 2obi 5h5q 5h5s

(-) Related Entries Specified in the PDB File

5h5q 5h5s