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
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  RECOMBINANT HORSERADISH PEROXIDASE C COMPLEX WITH FERULIC ACID
 
Authors :  A. Henriksen, A. T. Smith, M. Gajhede
Date :  23 Apr 99  (Deposition) - 14 Jan 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxidase, Oxidoreductase, Reducing Substrate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Henriksen, A. T. Smith, M. Gajhede
The Structures Of The Horseradish Peroxidase C-Ferulic Acid Complex And The Ternary Complex With Cyanide Suggest How Peroxidases Oxidize Small Phenolic Substrates.
J. Biol. Chem. V. 274 35005 1999
PubMed-ID: 10574977  |  Reference-DOI: 10.1074/JBC.274.49.35005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIDASE C1A
    Chains: A
    EC Number: 1.11.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ARMORACIA RUSTICANA
    Organism Taxid: 3704
    Other Details: SYNTHETIC GENE
    Synonym: HORSERADISH PEROXIDASE C1A, HRP C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2FER1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:1016BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWARETHR A:171 , ASP A:222 , THR A:225 , ILE A:228 , ASP A:230BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREARG A:31 , ALA A:34 , SER A:35 , ARG A:38 , PHE A:41 , SER A:73 , ARG A:75 , PRO A:139 , ALA A:140 , PRO A:141 , LEU A:166 , SER A:167 , GLY A:169 , HIS A:170 , PHE A:172 , GLY A:173 , LYS A:174 , ASN A:175 , GLN A:176 , PHE A:179 , PHE A:221 , ILE A:244 , SER A:246 , FER A:601 , HOH A:1004 , HOH A:1055 , HOH A:1056 , HOH A:1267 , HOH A:1401BINDING SITE FOR RESIDUE HEM A 350
4AC4SOFTWAREARG A:38 , PHE A:41 , HIS A:42 , PHE A:68 , GLY A:69 , SER A:73 , PRO A:139 , ALA A:140 , PRO A:141 , PHE A:142 , PHE A:179 , HEM A:350 , HOH A:1401 , HOH A:1402BINDING SITE FOR RESIDUE FER A 601
5CAAAUTHORASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:1401DISTAL CA BINDING SITE
6CABAUTHORTHR A:171 , ASP A:222 , THR A:225 , ILE A:228 , ASP A:230PROXIMAL CA BINDING SITE

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:91
2A:44 -A:49
3A:97 -A:301
4A:177 -A:209

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 6ATJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 6ATJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 6ATJ)

(-) Exons   (0, 0)

(no "Exon" information available for 6ATJ)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d6atja_ A: Plant peroxidase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -6atjA01 A:2-138,A:285-305  [code=1.10.520.10, no name defined]                                                                           6atjA02 A:139-284 Peroxidase, domain 2                                                                                                            6atjA01              - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhh.........hhh..........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...................hhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhh..eeehhhhhhhhh.hhh.........hhhhhhhhhh.........eee..........hhhhhhhhh.....hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 6atj A   1 QLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNS 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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 6ATJ)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FER  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    CAA  [ RasMol ]  +environment [ RasMol ]
    CAB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 6atj)
 

(-) 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
  6atj
    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
  PER1A_ARMRU | P00433
    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
  PER1A_ARMRU | P00433
    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
        PER1A_ARMRU | P00433: 1atj 1gw2 1gwo 1gwt 1gwu 1gx2 1h55 1h57 1h58 1h5a 1h5c 1h5d 1h5e 1h5f 1h5g 1h5h 1h5i 1h5j 1h5k 1h5l 1h5m 1hch 1kzm 1w4w 1w4y 2atj 2ylj 3atj 4atj 7atj

(-) Related Entries Specified in the PDB File

7atj RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND FERULIC ACID