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 POLYPRENYL SYNTHASE FROM CAULOBACTER CRESCENTUS CB15 COMPLEXED WITH CALCIUM AND ISOPRENYL DIPHOSPHATE
 
Authors :  Y. Patskovsky, R. Toro, M. Rutter, 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 :  23 Sep 10  (Deposition) - 13 Oct 10  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isoprenyl Synthase, Psi, Protein Structure Initiative, Nysgrc, New York Structural Genomix Research Consortium, New York Sgx Research Center For Structural Genomics, Structural Genomics, Transferase, Nysgxrc (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 - TRANS-ISOPRENYL DIPHOSPHATE SYNTHASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET
    Gene: CC_2113, TRANS_IPPS_HT
    Organism Scientific: CAULOBACTER CRESCENTUS
    Organism Taxid: 155892
    Strain: CB15
    Synonym: POLYPRENYL SYNTHETASE FAMILY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2DMA2Ligand/IonDIMETHYLALLYL DIPHOSPHATE
3POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:56 , ARG A:57 , LEU A:58 , ARG A:59 , HIS A:88 , HOH A:368BINDING SITE FOR RESIDUE POP A 336
2AC2SOFTWAREGLY B:55 , LYS B:56 , ARG B:59 , HIS B:88 , ARG B:105 , THR B:182 , PHE B:218 , GLN B:219 , ASP B:222 , DMA B:339 , HOH B:340 , HOH B:342 , HOH B:343 , HOH B:344 , HOH B:353 , HOH B:437BINDING SITE FOR RESIDUE DMA B 336
3AC3SOFTWAREASP B:95 , ASP B:99 , DMA B:339 , HOH B:347 , HOH B:365BINDING SITE FOR RESIDUE CA B 337
4AC4SOFTWAREASP B:222 , DMA B:339 , HOH B:352 , HOH B:360 , HOH B:395BINDING SITE FOR RESIDUE CA B 338
5AC5SOFTWARETHR B:91 , LEU B:92 , ASP B:95 , ASP B:99 , ARG B:104 , LYS B:181 , GLN B:219 , ASP B:222 , LYS B:236 , DMA B:336 , CA B:337 , CA B:338 , HOH B:347 , HOH B:352 , HOH B:388 , HOH B:394 , HOH B:467BINDING SITE FOR RESIDUE DMA B 339

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OYR)

(-) 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:292
 aligned with Q9A6I1_CAUCR | Q9A6I1 from UniProtKB/TrEMBL  Length:338

    Alignment length:324
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
         Q9A6I1_CAUCR    13 KSGSVDRLVRLAEADMAGVNRLITDRMQSDVAIIPALAEHLIAAGGKRLRPLMTVAAARLAGADNDHFQKLAAAVEFIHTATLLHDDVVDGSQLRRGKVAAHLIWGGAQSVLVGDFLFARAFELMVETNSMKALEILARASRVIAEGEVLQLMRSHDLNLSQAVYLEIIQAKTAELFAAASEAGAVSAGVDVAKSEALRDYGLNLGLAFQLADDALDYGGATETLGKNAGDDFREGKATLPLLLAIARSGPREAEFWERAIGRREQTEADFRRARELIIGSGALDATLDLAADYADKAKAALAMFPANDWREALEELADFAVSR 336
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....---------.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..-------------------.hhhhhhhhhhh.hhhhhhhhhhh.----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oyr A  10 KSGSVDRLVRLAEADMAGVNRLITDRMQSDVAIIPALAEHLIAAGGKRLRPLMTVAAARLAGADNDHFQKLAAAVEFIHTATLLHDDVV---------VAAHLIWGGAQSVLVGDFLFARAFELMVETNSMKALEILARASRVIAEGEVLQLMRSHDLNLSQAVYLEIIQAKTAELFAAASEAGAVSAGVDVAKSEALRDYGLNLGLAFQLADDALDY-------------------ATLPLLLAIARSGPREAEFWERAIG----TEADFRRARELIIGSGALDATLDLAADYADKAKAALAMFPANDWREALEELADFAVSR 333
                                    19        29        39        49        59        69        79        89        |-       109       119       129       139       149       159       169       179       189       199       209       219       | -         -       249       259       269 |    |279       289       299       309       319       329    
                                                                                                                   98       108                                                                                                                    227                 247                     271  276                                                         


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with Q9A6I1_CAUCR | Q9A6I1 from UniProtKB/TrEMBL  Length:338

    Alignment length:328
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        
         Q9A6I1_CAUCR    11 PRKSGSVDRLVRLAEADMAGVNRLITDRMQSDVAIIPALAEHLIAAGGKRLRPLMTVAAARLAGADNDHFQKLAAAVEFIHTATLLHDDVVDGSQLRRGKVAAHLIWGGAQSVLVGDFLFARAFELMVETNSMKALEILARASRVIAEGEVLQLMRSHDLNLSQAVYLEIIQAKTAELFAAASEAGAVSAGVDVAKSEALRDYGLNLGLAFQLADDALDYGGATETLGKNAGDDFREGKATLPLLLAIARSGPREAEFWERAIGRREQTEADFRRARELIIGSGALDATLDLAADYADKAKAALAMFPANDWREALEELADFAVSRRA 338
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------polyprenyl_synt-3oyrB01 B:42-287                                                                                                                                                                                                                      ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------polyprenyl_synt-3oyrB02 B:42-287                                                                                                                                                                                                                      ------------------------------------------------ Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oyr B   8 PRKSGSVDRLVRLAEADMAGVNRLITDRMQSDVAIIPALAEHLIAAGGKRLRPLMTVAAARLAGADNDHFQKLAAAVEFIHTATLLHDDVVDGSQLRRGKVAAHLIWGGAQSVLVGDFLFARAFELMVETNSMKALEILARASRVIAEGEVLQLMRSHDLNLSQAVYLEIIQAKTAELFAAASEAGAVSAGVDVAKSEALRDYGLNLGLAFQLADDALDYGGATETLGKNAGDDFREGKATLPLLLAIARSGPREAEFWERAIGRREQTEADFRRARELIIGSGALDATLDLAADYADKAKAALAMFPANDWREALEELADFAVSRRA 335
                                    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       297       307       317       327
   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 3OYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9A6I1_CAUCR | Q9A6I1)
molecular function
    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/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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    POP  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3oyr)
 

(-) 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
  3oyr
    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
  Q9A6I1_CAUCR | Q9A6I1
    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
  Q9A6I1_CAUCR | Q9A6I1
    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 3OYR)

(-) Related Entries Specified in the PDB File

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