Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE FROM VIBRIO CHOLERAE
 
Authors :  Y. Patskovsky, R. Toro, M. Dickey, J. M. Sauder, S. K. Burley, C. D. Poult J. A. Gerlt, S. C. Almo, New York Sgx Research Center For Structu Genomics (Nysgxrc)
Date :  14 Oct 10  (Deposition) - 27 Oct 10  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Isoprenyl Synthase, Structural Genomics, Psi, Protein Structure Initiative, Nysgrc, New York Structural Genomix Research Consortium, Nysgxrc, New York Sgx Research Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. H. Wallrapp, J. J. Pan, G. Ramamoorthy, D. E. Almonacid, B. S. Hillerich, R. Seidel, Y. Patskovsky, P. C. Babbitt, S. C. Almo, M. P. Jacobson, C. D. Poulter
Prediction Of Function For The Polyprenyl Transferase Subgroup In The Isoprenoid Synthase Superfamily.
Proc. Natl. Acad. Sci. Usa V. 110 E1196 2013
PubMed-ID: 23493556  |  Reference-DOI: 10.1073/PNAS.1300632110

(-) Compounds

Molecule 1 - GERANYLTRANSTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BN-PSGX2
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: VC_0890
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: N16961

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3P8R)

(-) Sites  (0, 0)

(no "Site" information available for 3P8R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P8R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P8R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P8R)

(-) Exons   (0, 0)

(no "Exon" information available for 3P8R)

(-) 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:268
 aligned with Q9KTL2_VIBCH | Q9KTL2 from UniProtKB/TrEMBL  Length:294

    Alignment length:297
                               1                                                                                                                                                                                                                                                                                                     
                               |     7        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       
         Q9KTL2_VIBCH     - ---MIEALSSYQQRNNQQLDQWLNRIPFQTLPLIEAMRYGLLLGGKRARPYLVYITGQMLGCELSDLDTPASAVECIHAYSLIHDDLPAMDDDELRRGKPTCHIQFDEATAILTGDALQTLAFTILAEGDLSAAGETQRVAMLQALAEASGAQGMCLGQALDLAAENRLISLEELETIHRNKTGALMRCAIRLGALAAGEKGRAMLPHLDRYAEAVGLAFQVQDDILDIISDTETLGKPQGSDQELNKSTYPALLGLEGAQQKAHTLLQEALLALEAIPYNTEHLEEFARYVVERKN 294
               SCOP domains d3p8ra_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------polyprenyl_synt-3p8rA01 A:30-284                                                                                                                                                                                                                               ---------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--------------.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p8r A  -2 HHHSLEALSSYQQRNNQQLDQWLNRIPFQTLPLIEAMRYGLLLGGKRARPYLVYITGQMLGCELSDLDTPASAVECIHAYSLIHDDLPAMDD--------------DEATAILTGDALQTLAFTILAEGDLSAAGETQRVAMLQALAEASGAQGMCLGQALDLAAENRLISLEELETIHRNKTGALMRCAIRLGALAAGEKGRAMLPHLDRYAEAVGLAFQVQDDILDIISD---------------KSTYPALLGLEGAQQKAHTLLQEALLALEAIPYNTEHLEEFARYVVERKN 294
                                     7        17        27        37        47        57        67        77        87 |       -      |107       117       127       137       147       157       167       177       187       197       207       217       227 |       -       247       257       267       277       287       
                                                                                                                      89            104                                                                                                                          229             245
   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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P8R)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: polyprenyl_synt] (86)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9KTL2_VIBCH | Q9KTL2)
molecular function
    GO:0004337    geranyltranstransferase activity    Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-trans,6-trans-farnesyl diphosphate + diphosphate.
    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:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

 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
(no "Ligands, Modified Residues, Ions" information available for 3p8r)
 
  Sites
(no "Sites" information available for 3p8r)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3p8r)
 
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 | Biol. Unit 1 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
  3p8r
    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
  Q9KTL2_VIBCH | Q9KTL2
    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
  Q9KTL2_VIBCH | Q9KTL2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3P8R)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3P8R)