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 :  FE(II)/(ALPHA)KETOGLUTARATE-DEPENDENT DIOXYGENASE ASQJ IN COMPLEX WITH 4-METHOXYDEHYDROCYCLOPEPTIN
 
Authors :  M. Groll, A. Braeuer
Date :  20 Aug 15  (Deposition) - 25 Nov 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Antibiotics, Biosynthesis, Alkaloids, Viridicatin, Desaturase, Epoxidase, Fragmentation, 4-Methoxydehydrocyclopeptin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Brauer, P. Beck, L. Hintermann, M. Groll
Structure Of The Dioxygenase Asqj: Mechanistic Insights Int A One-Pot Multistep Quinolone Antibiotic Biosynthesis.
Angew. Chem. Int. Ed. Engl. V. 55 422 2016
PubMed-ID: 26553478  |  Reference-DOI: 10.1002/ANIE.201507835

(-) Compounds

Molecule 1 - PHYTANOYL-COA DIOXYGENASE FAMILY PROTEIN (AFU_ORTHOLOGUE AFUA_8G00230)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 110-416
    Gene: AN9227.2, ANIA_09227
    Organism Scientific: ASPERGILLUS NIDULANS FGSC A4
    Organism Taxid: 227321
    Synonym: ASQJ

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
158J1Ligand/Ion4-METHOXYDEHYDROCYCLOPEPTIN
2BR2Ligand/IonBROMIDE ION
3K1Ligand/IonPOTASSIUM ION
4NI1Ligand/IonNICKEL (II) ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
158J2Ligand/Ion4-METHOXYDEHYDROCYCLOPEPTIN
2BR-1Ligand/IonBROMIDE ION
3K-1Ligand/IonPOTASSIUM ION
4NI-1Ligand/IonNICKEL (II) ION
5TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:134 , ASP A:136 , HIS A:211 , TRS A:403binding site for residue NI A 401
2AC2SOFTWAREASN A:70 , VAL A:72 , MET A:118 , GLN A:131 , PRO A:132 , HIS A:134 , ASP A:136 , MET A:137 , PHE A:139 , TRS A:403 , HOH A:538 , HOH A:583 , HOH A:609 , HOH A:615binding site for residue 58J A 402
3AC3SOFTWAREMET A:122 , GLN A:131 , HIS A:134 , ASP A:136 , ASN A:157 , HIS A:211 , NI A:401 , 58J A:402 , HOH A:557binding site for residue TRS A 403
4AC4SOFTWARETHR A:172 , GLY A:213 , ARG A:223binding site for residue BR A 404
5AC5SOFTWARESER A:74 , THR A:77 , GLN A:131binding site for residue BR A 405
6AC6SOFTWAREHOH A:650binding site for residue K A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DAV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DAV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DAV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DAV)

(-) Exons   (0, 0)

(no "Exon" information available for 5DAV)

(-) 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:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...hhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhhhhhh...................eeee.....hhhhhhh...hhhhhhhhhhhhh....eeeeeeeeeee................hhhhhhh.......eeeeeee...........ee..hhhhh......hhhhhee.......eeeee....ee..........eeeeeeeeee............hhhhhhh.hhhhhhhh.....................hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dav A   8 KSQIPRLSAINDLHKIWPTVEEHGAAIIESFLSLDIVRRLNEEVDPFVKIEPIPAAKTKDHPNHVLSTTTRLVNVLAPISKAYREDVLNSKVLHRICSDAFHVYGDYWVLMGAVMELAPSNPAQPLHRDMRFSHPIVEYLKPDAPATSINFLVALSPFTAENGATHVILGSHKWQNLSNVSMDATVRALMNPGDALLITDSTIHCGGAETTGTETRRLLTITMGISQLTPLESNLAVPRPVIESLTPLAQRLLGWASQRSAAPRDIGLLTIRGNSIEKTMNLKAEQPL 295
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287
   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 5DAV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DAV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DAV)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 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
    58J  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dav)
 
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
  5dav
    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
  ASQJ_EMENI | Q5AR53
    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
  ASQJ_EMENI | Q5AR53
    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
        ASQJ_EMENI | Q5AR53: 5dap 5daq 5daw 5dax

(-) Related Entries Specified in the PDB File

5dap FE(II)/(ALPHA)KETOGLUTARATE-DEPENDENT DIOXYGENASE ASQJ