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 :  CRYSTAL STRUCTURE OF A PROLYL 4-HYDROXYLASE FROM BACILLUS ANTHRACIS
 
Authors :  M. A. Culpepper, E. E. Scott, J. Limburg
Date :  28 Aug 09  (Deposition) - 15 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Prolyl 4-Hydroxylase, Double-Stranded Beta Helix, Alpha-Ketoglutarate Dependent Non-Heme Iron Oxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Culpepper, E. E. Scott, J. Limburg
Crystal Structure Of Prolyl 4-Hydroxylase From Bacillus Anthracis.
Biochemistry V. 49 124 2010
PubMed-ID: 19947658  |  Reference-DOI: 10.1021/BI901771Z

(-) Compounds

Molecule 1 - PROLYL 4-HYDROXYLASE, ALPHA SUBUNIT DOMAIN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BA_4459, GBAA4459, GBAA_4459, P4H
    Organism Common: ANTHRAX,ANTHRAX BACTERIUM
    Organism Scientific: BACILLUS ANTHRACIS STR.
    Organism Taxid: 198094
    Strain: AMES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:124 , HIS A:127 , ASP A:129 , HIS A:193 , TRP A:209BINDING SITE FOR RESIDUE GOL A 968
2AC2SOFTWARELYS A:35 , GLU A:37 , GLU B:158 , SER B:167 , HIS B:169BINDING SITE FOR RESIDUE PO4 A 217
3AC3SOFTWAREGLU A:158 , SER A:167 , HIS A:169 , LYS B:35 , GLU B:37BINDING SITE FOR RESIDUE PO4 B 218
4AC4SOFTWARETYR B:124 , HIS B:127 , ASP B:129 , VAL B:147 , PHE B:178 , HIS B:193BINDING SITE FOR RESIDUE GOL B 969

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:38 -Pro A:39
2Glu B:38 -Pro B:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ITQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ITQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3ITQ)

(-) 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:198
 aligned with Q81LZ8_BACAN | Q81LZ8 from UniProtKB/TrEMBL  Length:216

    Alignment length:206
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
         Q81LZ8_BACAN    11 KEQTIFDHKGNVIKTEDREIQIISKFEEPLIVVLGNVLSDEECDELIELSKSKLARSKVGSSRDVNDIRTSSGAFLDDNELTAKIEKRISSIMNVPASHGEGLHILNYEVDQQYKAHYDYFAEHSRSAANNRISTLVMYLNDVEEGGETFFPKLNLSVHPRKGMAVYFEYFYQDQSLNELTLHGGAPVTKGEKWIATQWVRRGTYK 216
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eeeeeeee....eeeee...hhhhhhhhhhhhhhhhh--------...hhhhh..ee...hhhhhhhhhhhhhhhh.hhhhh...eeeee.....eeee.......hhhhhh.eeeeeeee.....ee..eee....eee......eeeee....hhhhhhh..eee..eee..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3itq A  11 KEQTIFDHKGNVIKTEDREIQIISKFEEPLIVVLGNVLSDEECDELIELSKSKLA--------DVNDIRTSSGAFLDDNELTAKIEKRISSImNVPASHGEGLHILNYEVDQQYKAHYDYFAEHSRSAANNRISTLVmYLNDVEEGGETFFPKLNLSVHPRKGmAVYFEYFYQDQSLNELTLHGGAPVTKGEKWIATQWVRRGTYK 216
                                    20        30        40        50        60    |    -   |    80        90       100  |    110       120       130       140       150       160       170   |   180       190       200       210      
                                                                                 65       74                          103-MSE                                      148-MSE                   174-MSE                                      


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with Q81LZ8_BACAN | Q81LZ8 from UniProtKB/TrEMBL  Length:216

    Alignment length:205
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
         Q81LZ8_BACAN    12 EQTIFDHKGNVIKTEDREIQIISKFEEPLIVVLGNVLSDEECDELIELSKSKLARSKVGSSRDVNDIRTSSGAFLDDNELTAKIEKRISSIMNVPASHGEGLHILNYEVDQQYKAHYDYFAEHSRSAANNRISTLVMYLNDVEEGGETFFPKLNLSVHPRKGMAVYFEYFYQDQSLNELTLHGGAPVTKGEKWIATQWVRRGTYK 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee....eeeeeeee....eeeee...hhhhhhhhhhhhhhhh.---------..hhhhh..ee...hhhhhhhhhhhhhhhh.hhhhh...eeeee.....eeee.......hhhhhh.eeeeeeee.....ee..eee....eee......eeeee....hhhhhhh..eee..eee..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3itq B  12 EQTIFDHKGNVIKTEDREIQIISKFEEPLIVVLGNVLSDEECDELIELSKSKLA---------VNDIRTSSGAFLDDNELTAKIEKRISSImNVPASHGEGLHILNYEVDQQYKAHYDYFAEHSRSAANNRISTLVmYLNDVEEGGETFFPKLNLSVHPRKGmAVYFEYFYQDQSLNELTLHGGAPVTKGEKWIATQWVRRGTYK 216
                                    21        31        41        51        61   |     -   |    81        91       101 |     111       121       131       141      |151       161       171  |    181       191       201       211     
                                                                                65        75                         103-MSE                                      148-MSE                   174-MSE
   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 3ITQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ITQ)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q81LZ8_BACAN | Q81LZ8)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:38 - Pro A:39   [ RasMol ]  
    Glu B:38 - Pro B:39   [ RasMol ]  
 

(-) 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
  3itq
    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
  Q81LZ8_BACAN | Q81LZ8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q81LZ8_BACAN | Q81LZ8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q81LZ8_BACAN | Q81LZ8: 5hv0 5hv4 5iat 5iav 5iax

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ITQ)