Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  WILD TYPE HUMAN PRXV WITH DTT BOUND AS A COMPETITIVE INHIBITOR
 
Authors :  A. Hall, P. A. Karplus
Date :  21 Apr 10  (Deposition) - 04 Aug 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Peroxiredoxin, Peroxidase, Prxv, Substrate Analog, Dtt, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Hall, D. Parsonage, L. B. Poole, P. A. Karplus
Structural Evidence That Peroxiredoxin Catalytic Power Is Based On Transition-State Stabilization.
J. Mol. Biol. V. 402 194 2010
PubMed-ID: 20643143  |  Reference-DOI: 10.1016/J.JMB.2010.07.022

(-) Compounds

Molecule 1 - PEROXIREDOXIN-5, MITOCHONDRIAL
    ChainsA
    EC Number1.11.1.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30-PRX5
    Expression System StrainB834/PREP4
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneACR1, AOEB166, ARC1, PMP20, PRDX5, SBBI10
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEROXIREDOXIN V, PRX-V, PEROXISOMAL ANTIOXIDANT ENZYME, PLP, THIOREDOXIN REDUCTASE, THIOREDOXIN PEROXIDASE PMP20, ANTIOXIDANT ENZYME B166, AOEB166, TPX TYPE VI, LIVER TISSUE 2D-PAGE SPOT 71B, ALU COREPRESSOR 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1BR8Ligand/IonBROMIDE ION
2D1D1Ligand/Ion(4S,5S)-1,2-DITHIANE-4,5-DIOL
3GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2D1D2Ligand/Ion(4S,5S)-1,2-DITHIANE-4,5-DIOL
3GOL4Ligand/IonGLYCEROL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:40 , THR A:44 , GLY A:46 , CYS A:47 , ALA A:64 , GLY A:66 , ARG A:127BINDING SITE FOR RESIDUE D1D A 201
02AC2SOFTWARELYS A:63 , LYS A:93 , SER A:118BINDING SITE FOR RESIDUE BR A 301
03AC3SOFTWAREPRO A:155BINDING SITE FOR RESIDUE BR A 302
04AC4SOFTWAREGLN A:133 , LEU A:149BINDING SITE FOR RESIDUE BR A 303
05AC5SOFTWAREALA A:90 , GLU A:91BINDING SITE FOR RESIDUE BR A 304
06AC6SOFTWAREGLN A:68 , ASP A:113 , SER A:115BINDING SITE FOR RESIDUE BR A 305
07AC7SOFTWAREHIS A:88BINDING SITE FOR RESIDUE BR A 306
08AC8SOFTWAREVAL A:5BINDING SITE FOR RESIDUE BR A 307
09AC9SOFTWAREHOH A:1053 , HOH A:1122BINDING SITE FOR RESIDUE BR A 308
10BC1SOFTWARETHR A:150 , CYS A:151 , HOH A:1154 , HOH A:1195BINDING SITE FOR RESIDUE GOL A 401
11BC2SOFTWAREHOH A:1142 , HOH A:1211 , HOH A:1241 , HOH A:1250 , HOH A:1256BINDING SITE FOR RESIDUE GOL A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MNG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MNG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036406F157LPRDX5_HUMANUnclassified  ---AF104L
2CancerSNPVAR_PRDX5_HUMAN_CCDS8069_1_01 *F157LPRDX5_HUMANDisease (Breast cancer)  ---AF104L
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036406F157LPRDX5_HUMANUnclassified  ---AF104L
2CancerSNPVAR_PRDX5_HUMAN_CCDS8069_1_01 *F157LPRDX5_HUMANDisease (Breast cancer)  ---AF104L
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.PRDX5_HUMAN56-214  1A:3-161
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.PRDX5_HUMAN56-214  2A:3-161

(-) Exons   (6, 6)

Asymmetric Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002654621ENSE00001265861chr11:64085569-64085858290PRDX5_HUMAN1-57571A:1-44
1.2ENST000002654622ENSE00001317366chr11:64087206-64087340135PRDX5_HUMAN58-102451A:5-4945
1.3ENST000002654623ENSE00001291509chr11:64088133-64088264132PRDX5_HUMAN103-146441A:50-9344
1.4ENST000002654624ENSE00001313724chr11:64088337-6408837539PRDX5_HUMAN147-159131A:94-10613
1.5ENST000002654625ENSE00000992394chr11:64088479-6408854062PRDX5_HUMAN160-180211A:107-12721
1.6ENST000002654626ENSE00001195244chr11:64089058-64089282225PRDX5_HUMAN180-214351A:127-16135

(-) Sequences/Alignments

Asymmetric 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:161
 aligned with PRDX5_HUMAN | P30044 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:161
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
          PRDX5_HUMAN    54 APIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL 214
               SCOP domains d3mnga_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Redoxin-3mngA01 A:4-155                                                                                                                                 ------ Pfam domains
         Sec.struct. author ............eee......eeehhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh......eeee...hhhhhhhh......hhhhhh......eeeeee..eeeeeee..........hhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------------------------------------L--------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------L--------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --THIOREDOXIN_2  PDB: A:3-161 UniProt: 56-214                                                                                                                     PROSITE
           Transcript 1 (1) 1.1 Exon 1.2  PDB: A:5-49 UniProt: 58-102        Exon 1.3  PDB: A:50-93 UniProt: 103-146     Exon 1.4     Exon 1.5             ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:127-161            Transcript 1 (2)
                 3mng A   1 APIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFTPGCSKTHLPGFVEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNRRLKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 

   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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MNG)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)
Chain A   (PRDX5_HUMAN | P30044)
molecular function
    GO:0001016    RNA polymerase III regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    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:0043027    cysteine-type endopeptidase inhibitor activity involved in apoptotic process    Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    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:0072541    peroxynitrite reductase activity    Catalysis of the reaction: 2 R-SH + ONOO- = R-SS-R + NO2- + H2O.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0008379    thioredoxin peroxidase activity    Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O.
biological process
    GO:0070995    NADPH oxidation    A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADPH, to the oxidized form, NADP.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0034614    cellular response to reactive oxygen species    Any process that results in a change in state or activity of a cell (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.
    GO:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0051354    negative regulation of oxidoreductase activity    Any process that stops or reduces the rate of oxidoreductase activity, the 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.
    GO:0016480    negative regulation of transcription from RNA polymerase III promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase III promoter.
    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:0032967    positive regulation of collagen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    GO:2001057    reactive nitrogen species metabolic process    The chemical reactions and pathways involving a reactive nitrogen species.
    GO:0060785    regulation of apoptosis involved in tissue homeostasis    Any process that modulates the occurrence or rate of cell death by apoptosis that results in the maintenance of the steady-state number of cells within a tissue.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

 Visualization

(-) Interactive Views

Asymmetric 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
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    D1D  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mng)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) 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
  3mng
    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
  PRDX5_HUMAN | P30044
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.11.1.15
    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
  PRDX5_HUMAN | P30044
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRDX5_HUMAN | P300441h4o 1hd2 1oc3 1urm 2vl2 2vl3 2vl9 4k7i 4k7n 4k7o 4mmm

(-) Related Entries Specified in the PDB File

1h4o THE SAME PROTEIN BOUND TO BENZOATE AT 2.0 A RESOLUTION.
1hd2 THE SAME PROTEIN BOUND TO BENZOATE AT 1.5 A RESOLUTION.
1oc3 THE SAME PROTEIN BOUND TO BENZOATE AT 2.0 A RESOLUTION.
1urm THE C47S MUTANT OF THE SAME PROTEIN BOUND TO BENZOATE AT 1.7 A RESOLUTION.
2vl2 THE SAME PROTEIN BOUND TO BENZOATE AT 1.9 A RESOLUTION.
2vl3 THE SAME PROTEIN AT 1.8 A RESOLUTION.