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

(-) Description

Title :  BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE
 
Authors :  K. Fukuyama, H. Itakura
Date :  01 Jul 97  (Deposition) - 01 Jul 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Glycoprotein, Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Itakura, Y. Oda, K. Fukuyama
Binding Mode Of Benzhydroxamic Acid To Arthromyces Ramosus Peroxidase Shown By X-Ray Crystallographic Analysis Of The Complex At 1. 6 A Resolution.
Febs Lett. V. 412 107 1997
PubMed-ID: 9257700  |  Reference-DOI: 10.1016/S0014-5793(97)00751-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Organism Scientific: 'ARTHROMYCES RAMOSUS'
    Organism Taxid: 5451

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1BHO1Ligand/IonBENZHYDROXAMIC ACID
2CA2Ligand/IonCALCIUM ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:108 , GLY A:111 , ASN A:143 , NAG A:349 , HOH A:378 , HOH A:660BINDING SITE FOR RESIDUE NAG A 348
2AC2SOFTWAREARG A:104 , ILE A:108 , NAG A:348BINDING SITE FOR RESIDUE NAG A 349
3AC3SOFTWAREASP A:57 , GLY A:75 , ASP A:77 , SER A:79 , HOH A:424 , HOH A:425BINDING SITE FOR RESIDUE CA A 346
4AC4SOFTWARESER A:185 , ASP A:202 , THR A:204 , VAL A:207 , ASP A:209BINDING SITE FOR RESIDUE CA A 347
5AC5SOFTWAREARG A:48 , LEU A:51 , PHE A:55 , GLY A:155 , LEU A:181 , ALA A:183 , HIS A:184 , LEU A:186 , ALA A:187 , SER A:188 , GLN A:189 , GLU A:190 , GLY A:191 , LEU A:192 , MET A:243 , SER A:245 , HOH A:360 , HOH A:361 , HOH A:394 , BHO A:800 , HOH A:801BINDING SITE FOR RESIDUE HEM A 345
6AC6SOFTWAREARG A:52 , PHE A:55 , HIS A:56 , ALA A:92 , PRO A:154 , GLY A:155 , PRO A:156 , HEM A:345 , HOH A:801BINDING SITE FOR RESIDUE BHO A 800
7CA1UNKNOWNCA A:346 , ASP A:57 , GLY A:75 , ASP A:77 , SER A:79 , HOH A:424 , HOH A:425ACTIVE SITE.
8CA2UNKNOWNCA A:347 , SER A:185 , ASP A:202 , THR A:204 , VAL A:207 , ASP A:209ACTIVE SITE.
9GL1UNKNOWNNAG A:348 , NAG A:349 , ASN A:143ACTIVE SITE.

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:12 -A:24
2A:23 -A:293
3A:43 -A:129
4A:257 -A:322

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.PER_ARTRA67-78  1A:47-58
2PEROXIDASE_4PS50873 Plant heme peroxidase family profile.PER_ARTRA70-317  1A:50-297
3PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.PER_ARTRA196-206  1A:176-186

(-) Exons   (0, 0)

(no "Exon" information available for 1HSR)

(-) 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:336
 aligned with PER_ARTRA | P28313 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:336
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358      
            PER_ARTRA    29 SVTCPGGQSTSNSQCCVWFDVLDDLQTNFYQGSKCESPVRKILRIVFHDAIGFSPALTAAGQFGGGGADGSIIAHSNIELAFPANGGLTDTIEALRAVGINHGVSFGDLIQFATAVGMSNCPGSPRLEFLTGRSNSSQPSPPSLIPGPGNTVTAILDRMGDAGFSPDEVVDLLAAHSLASQEGLNSAIFRSPLDSTPQVFDTQFYIETLLKGTTQPGPSLGFAEELSPFPGEFRMRSDALLARDSRTACRWQSMTSSNEVMGQRYRAAMAKMSVLGFDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDDIEVSCPSEPFPEIATASGPLPSLAPAP 364
               SCOP domains d1hsra_ A: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -----------1hsrA01 A:20-153,A:277-304  [code=1.10.520.10, no name defined]                                                                       1hsrA02 A:154-276,A:305-344 Peroxidase, domain 2                                                                           1hsrA01 A:20-153,A:277-304  1hsrA02 A:154-276,A:305-344              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) .ee.....ee......hhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhh..............hhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee..........hhhhhh...............ee........-hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhh.........ee...............ee.....................ee............ Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ee----------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------------PEROXIDASE_-------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------PEROXIDASE_4  PDB: A:50-297 UniProt: 70-317                                                                                                                                                                                                             ----------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1hsr A   9 SVTCPGGQSTSNSQCCVWFDVLDDLQTNFYQGSKCESPVRKILRIVFHDAIGFSPALTAAGQFGGGGADGSIIAHSNIELAFPANGGLTDTIEALRAVGINHGVSFGDLIQFATAVGMSNCPGSPRLEFLTGRSNSSQPSPPSLIPGPGNTVTAILDRMGDAGFSPDEVVDLLAAHSLASQEGLNSAIFRSPLDSTPQVFDTQFYIETLLKGTTQPGPSLGFAEELSPFPGEFRMRSDALLARDSRTACRWQSMTSSNEVMGQRYRAAMAKMSVLGFDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDDIEVSCPSEPFPEIATASGPLPSLAPAP 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HSR)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PER_ARTRA | P28313)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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: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: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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
    BHO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
    CA1  [ RasMol ]  +environment [ RasMol ]
    CA2  [ RasMol ]  +environment [ RasMol ]
    GL1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hsr)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1hsr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PER_ARTRA | P28313
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.11.1.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PER_ARTRA | P28313
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PER_ARTRA | P28313: 1arp 1aru 1arv 1arw 1arx 1ary 1c8i 1ck6 1gza 1gzb 2e39 2e3a 2e3b

(-) Related Entries Specified in the PDB File

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