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 UBIX Y169F IN COMPLEX WITH A COVALENT ADDUCT FORMED BETWEEN REDUCED FMN AND DIMETHYLALLYL MONOPHOSPHATE
 
Authors :  M. D. White, D. Leys
Date :  14 Apr 15  (Deposition) - 17 Jun 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Prenyl Transferase, Flavin Binding, Ubix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. White, K. A. Payne, K. Fisher, S. A. Marshall, D. Parker, N. J. Rattray, D. K. Trivedi, R. Goodacre, S. E. Rigby, N. S. Scrutton, S. Hay, D. Leys
Ubix Is A Flavin Prenyltransferase Required For Bacterial Ubiquinone Biosynthesis.
Nature V. 522 497 2015
PubMed-ID: 26083743  |  Reference-DOI: 10.1038/NATURE14559

(-) Compounds

Molecule 1 - UBIX
    Chains: A
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PA4019
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
14LS1Ligand/Ion1-DEOXY-1-[7,8-DIMETHYL-5-(3-METHYLBUT-2-EN-1-YL)-2,4-DIOXO-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-5-O-PHOSPHONO-D-RIBITOL
2NA1Ligand/IonSODIUM ION
3PO41Ligand/IonPHOSPHATE ION
4SCN3Ligand/IonTHIOCYANATE ION
Biological Unit 1 (3, 60)
No.NameCountTypeFull Name
14LS12Ligand/Ion1-DEOXY-1-[7,8-DIMETHYL-5-(3-METHYLBUT-2-EN-1-YL)-2,4-DIOXO-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-5-O-PHOSPHONO-D-RIBITOL
2NA-1Ligand/IonSODIUM ION
3PO412Ligand/IonPHOSPHATE ION
4SCN36Ligand/IonTHIOCYANATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:12 , GLY A:13 , ALA A:14 , SER A:15 , SER A:39 , ALA A:41 , VAL A:45 , TRP A:84 , ALA A:89 , SER A:104 , THR A:105 , THR A:107 , CYS A:116 , ARG A:122 , ARG A:139 , TRP A:200 , PO4 A:306 , HOH A:448 , HOH A:461 , HOH A:497 , HOH A:509 , HOH A:514 , HOH A:516binding site for residue 4LS A 301
2AC2SOFTWAREGLN A:62 , THR A:66 , ALA A:71 , ALA A:72 , GLY A:74 , GLN A:75 , ILE A:76 , HOH A:401 , HOH A:457binding site for residue SCN A 302
3AC3SOFTWAREGLN A:59 , HOH A:444 , HOH A:499binding site for residue SCN A 303
4AC4SOFTWAREASN A:96 , ALA A:97 , PRO A:133binding site for residue SCN A 304
5AC5SOFTWARELYS A:40 , HOH A:404 , HOH A:552binding site for residue NA A 305
6AC6SOFTWARESER A:90 , GLY A:91 , ARG A:122 , LYS A:129 , ARG A:139 , GLU A:140 , PHE A:169 , ARG A:185 , 4LS A:301 , HOH A:406binding site for residue PO4 A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZAZ)

(-) 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 4ZAZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZAZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZAZ)

(-) 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
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4zaz A   1 MSGPERITLAMTGASGAQYGLRLLDCLVQEEREVHFLISKAAQLVMATETDVALPAKPQAMQAFLTEYCGAAAGQIRVFGQNDWMAPPASGSSAPNAMVICPCSTGTLSAVATGACNNLIERAADVALKERRPLVLVPREAPFSSIHLENMLKLSNLGAVILPAAPGFFHQPQSVEDLVDFVVARILNTLGIPQDMLPRWGEQHLVS 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  (0, 0)

(no "SCOP Domain" information available for 4ZAZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZAZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZAZ)

(-) Gene Ontology  (4, 4)

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
    4LS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SCN  [ 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
    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
  4zaz
    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)
  4.1.1.-
    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: 3zqu 4zaf 4zag 4zal 4zan 4zav 4zaw 4zax 4zay

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZAZ)