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 GERANYLGERANYL PYROPHOSPHATE SYNTHASE FROM LACTOBACILLUS BREVIS ATCC 367 COMPLEXED WITH CITRATE
 
Authors :  Y. Patskovsky, R. Toro, M. Rutter, S. Chang, J. M. Sauder, C. D. Poulter, S. K. Burley, J. A. Gerlt, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)
Date :  11 Nov 10  (Deposition) - 24 Nov 10  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isoprenyl Diphosphate Synthase, Structural Genomics, Psi, Protein Structure Initiative, Nysgrc, New York Structural Genomix Research Consortium, Nysgxrc, Transferase, New York Sgx Research Center For Structural Genomics (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 - GERANYLGERANYL PYROPHOSPHATE SYNTHASE
    Atcc: ATCC 367
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BN-PSGX2(BN)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: LVIS_1638
    Organism Scientific: LACTOBACILLUS BREVIS
    Organism Taxid: 387344
    Strain: ATCC 367 / JCM 1170

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:50 , HIS A:80 , ARG A:97 , TYR A:211 , HOH A:328 , HOH A:330BINDING SITE FOR RESIDUE CIT A 326
2AC2SOFTWARETHR A:131 , ARG A:133 , HOH A:343 , HOH A:348 , HOH A:430 , HOH A:434 , THR B:131BINDING SITE FOR RESIDUE GOL A 327

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PKO)

(-) 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:331
 aligned with Q03Q08_LACBA | Q03Q08 from UniProtKB/TrEMBL  Length:325

    Alignment length:331
                                   1                                                                                                                                                                                                                                                                                                                                   
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
         Q03Q08_LACBA     - -------MDRQLWRQFPQVEPQLTALQDYLLRTVQLDNQPIHHKILALLKSGGKLLRPGYFYLFSTFGNATTPAQLQAGAAAIEILHVGTLIHDDVIDDSPTRRGVRTIQMTYGQRNAIYAGDFMFTVYFDQVLQSTTDRSLIQNHIDAMRRILQGELHQMDLNYREDITLDAYLNEIAGKTAELFALSCYQGAQLAGAPQSVIDHTREIGIAIGCAYQMLDDILDYAGDPKKTQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKLLKKKQAMTLEDIKHVQALVAQYDGVGAAKQLARDYTDRALTLIQQLPAGSAQQSLEQLTRLLLRRD 324
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pko A  -7 AHHHHHHSLRQLWRQFPQVEPQLTALQDYLLRTVQLDNQPIHHKILALLKSGGKLLRPGYFYLFSTFGNAATPAQLQAGAAAIEILHVGTLIHDDVIDDSPTRRGVRTIQMTYGQRNAIYAGDFMFTVYFDQVLKSTTDRSLIQNHIDAMHRILQGELHQMDLNYREDITLDAYLNEIAGKTAELFALSCYQGAQLAGAPQSVIDRTRDIGIAIGCAYQMLDDILDYAGDPKRTQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKLLKKKQAMTLEDIKHVQALVAQYDGVGAAKQLAQDYTDRALTLIQQLPVGSAQQSLEQLTRLLLRRD 324
                                    |3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
                                    1|                                                                                                                                                                                                                                                                                                                                 
                                     3                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:310
 aligned with Q03Q08_LACBA | Q03Q08 from UniProtKB/TrEMBL  Length:325

    Alignment length:324
                                    10        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    
         Q03Q08_LACBA     1 MDRQLWRQFPQVEPQLTALQDYLLRTVQLDNQPIHHKILALLKSGGKLLRPGYFYLFSTFGNATTPAQLQAGAAAIEILHVGTLIHDDVIDDSPTRRGVRTIQMTYGQRNAIYAGDFMFTVYFDQVLQSTTDRSLIQNHIDAMRRILQGELHQMDLNYREDITLDAYLNEIAGKTAELFALSCYQGAQLAGAPQSVIDHTREIGIAIGCAYQMLDDILDYAGDPKKTQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKLLKKKQAMTLEDIKHVQALVAQYDGVGAAKQLARDYTDRALTLIQQLPAGSAQQSLEQLTRLLLRRD 324
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------polyprenyl_synt-3pkoB01 B:34-291                                                                                                                                                                                                                                  --------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------polyprenyl_synt-3pkoB02 B:34-291                                                                                                                                                                                                                                  --------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..--------------hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pko B   1 LDRQLWRQFPQVEPQLTALQDYLLRTVQLDNQPIHHKILALLKSGGKLLRPGYFYLFSTFGNAATPAQLQAGAAAIEILHVGTLIHDDVI--------------TYGQRNAIYAGDFMFTVYFDQVLKSTTDRSLIQNHIDAMHRILQGELHQMDLNYREDITLDAYLNEIAGKTAELFALSCYQGAQLAGAPQSVIDRTRDIGIAIGCAYQMLDDILDYAGDPKRTQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKLLKKKQAMTLEDIKHVQALVAQYDGVGAAKQLAQDYTDRALTLIQQLPVGSAQQSLEQLTRLLLRRD 324
                                    10        20        30        40        50        60        70        80        90         -    |  110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    
                                                                                                                    90            105
   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 3PKO)

(-) CATH Domains  (0, 0)

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

(-) 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   (Q03Q08_LACBA | Q03Q08)
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
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pko)
 

(-) 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
  3pko
    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
  Q03Q08_LACBA | Q03Q08
    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
  Q03Q08_LACBA | Q03Q08
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q03Q08_LACBA | Q03Q08: 3n3d

(-) Related Entries Specified in the PDB File

3n3d COMPLEXED WITH SULFATE RELATED ID: NYSGXRC-20019C RELATED DB: TARGETDB