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 :  STRUCTURE OF A PROBABLE AROMATIC ACID DECARBOXYLASE
 
Authors :  J. Kopec, R. Schnell, G. Schneider
Date :  11 Jun 11  (Deposition) - 02 Nov 11  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kopec, R. Schnell, G. Schneider
Structure Of Pa4019, A Putative Aromatic Acid Decarboxylase From Pseudomonas Aeruginosa
Acta Crystallogr. , Sect. F V. 67 1184 2011
PubMed-ID: 22102023  |  Reference-DOI: 10.1107/S174430911102923X

(-) Compounds

Molecule 1 - PROBABLE AROMATIC ACID DECARBOXYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FNR1Ligand/Ion1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 36)
No.NameCountTypeFull Name
1FNR12Ligand/Ion1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
2SO424Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:12 , GLY A:13 , ALA A:14 , SER A:15 , SER A:39 , ALA A:41 , LEU A:44 , VAL A:45 , TRP A:84 , SER A:104 , THR A:105 , THR A:107 , CYS A:116 , ARG A:122 , ARG A:139 , HOH A:2026 , HOH A:2063 , HOH A:2067 , HOH A:2136BINDING SITE FOR RESIDUE FNR A1208
2AC2SOFTWARESER A:90 , GLY A:91 , ARG A:122 , LYS A:129 , ARG A:139 , GLU A:140 , TYR A:169 , ARG A:185 , HOH A:2112 , HOH A:2120 , HOH A:2137 , HOH A:2138BINDING SITE FOR RESIDUE SO4 A1209
3AC3SOFTWARESER A:39 , LYS A:40 , GLN A:81 , ASN A:118 , HOH A:2026BINDING SITE FOR RESIDUE SO4 A1210

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Cys A:101 -Pro A:102
2Ala A:141 -Pro A:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZQU)

(-) 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:207
 aligned with UBIX_PSEAE | Q9HX08 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           UBIX_PSEAE     1 MSGPERITLAMTGASGAQYGLRLLDCLVQEEREVHFLISKAAQLVMATETDVALPAKPQAMQAFLTEYCGAAAGQIRVFGQNDWMAPPASGSSAPNAMVICPCSTGTLSAVATGACNNLIERAADVALKERRPLVLVPREAPFSSIHLENMLKLSNLGAVILPAAPGFYHQPQSVEDLVDFVVARILNTLGIPQDMLPRWGEQHLVS 207
               SCOP domains d3zqua_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh......hhhhhhhhhhhhhh.....eee.......hhhhh......eeeeeeehhhhhhhhhhh...hhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.ee............hhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zqu A   1 MSGPERITLAMTGASGAQYGLRLLDCLVQEEREVHFLISKAAQLVMATETDVALPAKPQAMQAFLTEYCGAAAGQIRVFGQNDWMAPPASGSSAPNAMVICPCSTGTLSAVATGACNNLIERAADVALKERRPLVLVPREAPFSSIHLENMLKLSNLGAVILPAAPGFYHQPQSVEDLVDFVVARILNTLGIPQDMLPRWGEQHLVS 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (UBIX_PSEAE | Q9HX08)
molecular function
    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:0004659    prenyltransferase activity    Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0051188    cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein.

 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
    FNR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:141 - Pro A:142   [ RasMol ]  
    Cys A:101 - Pro A:102   [ RasMol ]  
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  3zqu
    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
  UBIX_PSEAE | Q9HX08
    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)
  (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
  UBIX_PSEAE | Q9HX08
    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
        UBIX_PSEAE | Q9HX08: 4zaf 4zag 4zal 4zan 4zav 4zaw 4zax 4zay 4zaz

(-) Related Entries Specified in the PDB File

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