Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  HORF6 A NOVEL HUMAN PEROXIDASE ENZYME
 
Authors :  H. -J. Choi, S. W. Kang, C. -H. Yang, S. G. Rhee, S. -E. Ryu
Date :  03 Apr 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peroxiredoxin, Horf6, Hydrogen Peroxide, Redox Regulation, Cellular Signaling, Antioxidant (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. J. Choi, S. W. Kang, C. H. Yang, S. G. Rhee, S. E. Ryu
Crystal Structure Of A Novel Human Peroxidase Enzyme At 2. 0 A Resolution.
Nat. Struct. Biol. V. 5 400 1998
PubMed-ID: 9587003  |  Reference-DOI: 10.1038/NSB0598-400
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HORF6
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 1PRX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PRX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PRX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PRX)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.PRDX6_HUMAN5-169
 
  2A:5-169
B:5-169

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003403851aENSE00001887950chr1:173446405-173446631227PRDX6_HUMAN1-32322A:5-32
B:2-32
28
31
1.2bENST000003403852bENSE00000814648chr1:173450465-173450621157PRDX6_HUMAN32-84532A:32-84
B:32-84
53
53
1.3bENST000003403853bENSE00000789881chr1:173454500-173454646147PRDX6_HUMAN85-133492A:85-133
B:85-133 (gaps)
49
49
1.4ENST000003403854ENSE00001608679chr1:173455394-173455540147PRDX6_HUMAN134-182492A:134-182
B:134-182
49
49
1.5cENST000003403855cENSE00001161142chr1:173456874-1734579461073PRDX6_HUMAN183-224422A:183-224
B:183-224
42
42

(-) 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:220
 aligned with PRDX6_HUMAN | P30041 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:220
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
          PRDX6_HUMAN     5 LLLGDVAPNFEANTTVGRIRFHDFLGDSWGILFSHPRDFTPVCTTELGRAAKLAPEFAKRNVKLIALSIDSVEDHLAWSKDINAYNCEEPTEKLPFPIIDDRNRELAILLGMLDPAEKDEKGMPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVDWKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP 224
               SCOP domains d1prxa_ A: 1-Cys peroxiredoxin                                                                                                                                                                                               SCOP domains
               CATH domains 1prxA01 A:5-155 Glutaredoxin                                                                                                                           1prxA02 A:156-224 Antioxidant, Horf6; Chain A, domain2                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee..eeeehhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhh............eee....hhhhh...................eeeee.....eeeeee........hhhhhhhhhhhhhhhhh.....................hhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: A:5-169 UniProt: 5-169                                                                                                                           ------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:5-32      ----------------------------------------------------Exon 1.3b  PDB: A:85-133 UniProt: 85-133         Exon 1.4  PDB: A:134-182 UniProt: 134-182        Exon 1.5c  PDB: A:183-224 UniProt: 183-224 Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.2b  PDB: A:32-84 UniProt: 32-84               -------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1prx A   5 LLLGDVAPNFEANTTVGRIRFHDFLGDSWGILFSHPRDFTPVcTTELGRAAKLAPEFAKRNVKLIALSIDSVEDHLAWSKDINAYNSEEPTEKLPFPIIDDRNRELAILLGMLDPAEKDEKGMPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVDWKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP 224
                                    14        24        34        44  |     54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
                                                                     47-CSO                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with PRDX6_HUMAN | P30041 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
          PRDX6_HUMAN     2 PGGLLLGDVAPNFEANTTVGRIRFHDFLGDSWGILFSHPRDFTPVCTTELGRAAKLAPEFAKRNVKLIALSIDSVEDHLAWSKDINAYNCEEPTEKLPFPIIDDRNRELAILLGMLDPAEKDEKGMPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVDWKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP 224
               SCOP domains d1prxb_ B: 1-Cys peroxiredoxin                                                                                                                                                                                                  SCOP domains
               CATH domains 1prxB01 B:2-155 Glutaredoxin                                                                                                                              1prxB02 B:156-224 Antioxidant, Horf6; Chain A, domain2                CATH domains
           Pfam domains (1) -----AhpC-TSA-1prxB01 B:7-146                                                                                                                    -------------------1-cysPrx_C-1prxB03 B:166-205            ------------------- Pfam domains (1)
           Pfam domains (2) -----AhpC-TSA-1prxB02 B:7-146                                                                                                                    -------------------1-cysPrx_C-1prxB04 B:166-205            ------------------- Pfam domains (2)
         Sec.struct. author .............eeee..eeeehhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhh............eee....hhhhh........-----......eeeee.....eeeeee........hhhhhhhhhhhhhhhhh.....................hhhhhhh....eee..........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: B:5-169 UniProt: 5-169                                                                                                                           ------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:2-32         ----------------------------------------------------Exon 1.3b  PDB: B:85-133 (gaps) UniProt: 85-133  Exon 1.4  PDB: B:134-182 UniProt: 134-182        Exon 1.5c  PDB: B:183-224 UniProt: 183-224 Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2b  PDB: B:32-84 UniProt: 32-84               -------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1prx B   2 PGGLLLGDVAPNFEANTTVGRIRFHDFLGDSWGILFSHPRDFTPVcTTELGRAAKLAPEFAKRNVKLIALSIDSVEDHLAWSKDINAYNSEEPTEKLPFPIIDDRNRELAILLGMLDPAE-----MPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVDWKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP 224
                                    11        21        31        41     |  51        61        71        81        91       101       111       121     | 131       141       151       161       171       181       191       201       211       221   
                                                                        47-CSO                                                                   121   127                                                                                                 

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PRDX6_HUMAN | P30041)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004602    glutathione peroxidase activity    Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0000302    response to reactive oxygen species    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CSO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1prx)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1prx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1prx
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PRDX6_HUMAN | P30041
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PRDX6_HUMAN | P30041
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRDX6_HUMAN | P300415b6m 5b6n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PRX)