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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF EUGENOL SYNTHASE FROM OCIMUM BASILICUM
 
Authors :  G. V. Louie, J. P. Noel, M. E. Bowman
Date :  05 Sep 07  (Deposition) - 15 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Eugenol, Phenylpropene, Pip Reductase, Short-Chain Dehydrogenase/Reductase, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. V. Louie, T. J. Baiga, M. E. Bowman, T. Koeduka, J. H. Taylor, S. M. Spassova, E. Pichersky, J. P. Noel
Structure And Reaction Mechanism Of Basil Eugenol Synthase
Plos One V. 2 E993 2007
PubMed-ID: 17912370  |  Reference-DOI: 10.1371/JOURNAL.PONE.0000993
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EUGENOL SYNTHASE 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHIS8
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EGS1
    Organism Common: SWEET BASIL
    Organism Scientific: OCIMUM BASILICUM
    Organism Taxid: 39350

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:16 , GLY A:17 , TYR A:18 , ILE A:19 , THR A:38 , ARG A:39 , SER A:42 , LYS A:44 , ALA A:82 , LEU A:83 , ALA A:84 , PHE A:85 , GLN A:87 , SER A:110 , ASP A:111 , PHE A:112 , GLY A:113 , LYS A:132 , ASN A:152 , PHE A:154 , PHE A:158 , HOH A:1002 , HOH A:1006 , HOH A:1015 , HOH A:1023 , HOH A:1041 , HOH A:1078 , HOH A:1086 , HOH A:1092 , HOH A:1126 , HOH A:1211 , HOH A:1217BINDING SITE FOR RESIDUE NDP A 401
2AC2SOFTWARETHR B:16 , GLY B:17 , TYR B:18 , ILE B:19 , THR B:38 , ARG B:39 , SER B:42 , LYS B:44 , ALA B:82 , LEU B:83 , ALA B:84 , PHE B:85 , GLN B:87 , SER B:110 , ASP B:111 , PHE B:112 , GLY B:113 , LYS B:132 , ASN B:152 , PHE B:154 , PHE B:158 , HOH B:1012 , HOH B:1018 , HOH B:1029 , HOH B:1032 , HOH B:1046 , HOH B:1061 , HOH B:1081 , HOH B:1094 , HOH B:1231 , HOH B:1543 , HOH B:1622BINDING SITE FOR RESIDUE NDP B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R6J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:253 -Pro A:254
2Glu B:253 -Pro B:254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R6J)

(-) Exons   (0, 0)

(no "Exon" information available for 2R6J)

(-) 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:310
 aligned with EGS1_OCIBA | Q15GI4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:310
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314
           EGS1_OCIBA     5 GMKSKILIFGGTGYIGNHMVKGSLKLGHPTYVFTRPNSSKTTLLDEFQSLGAIIVKGELDEHEKLVELMKKVDVVISALAFPQILDQFKILEAIKVAGNIKRFLPSDFGVEEDRINALPPFEALIERKRMIRRAIEEANIPYTYVSANCFASYFINYLLRPYDPKDEITVYGTGEAKFAMNYEQDIGLYTIKVATDPRALNRVVIYRPSTNIITQLELISRWEKKIGKKFKKIHVPEEEIVALTKELPEPENIPIAILHCLFIDGATMSYDFKENDVEASTLYPELKFTTIDELLDIFVHDPPPPASAAF 314
               SCOP domains d2r6ja_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2r6jA01 A:5-150,A:187-209,A:275-287 NAD(P)-binding Rossmann-like Domain                                                                           2r6jA02                             2r6jA01                2r6jA02 A:151-186,A:210-274,A:288-314                            2r6jA01      2r6jA02                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhh..eeee....hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh...eee.............hhhhhhhhhhhhhhhhhhhhh....eeee..eehhhhhhhhhh......eeeee.....eeeeehhhhhhhhhhhhh.hhhhh.eeee..hhh.eeehhhhhhhhhhhhh...eeeeehhhhhhhhhhhh...hhhhhhhhhhhhh.............ee.hhh.......hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6j A   5 GMKSKILIFGGTGYIGNHMVKGSLKLGHPTYVFTRPNSSKTTLLDEFQSLGAIIVKGELDEHEKLVELMKKVDVVISALAFPQILDQFKILEAIKVAGNIKRFLPSDFGVEEDRINALPPFEALIERKRMIRRAIEEANIPYTYVSANCFASYFINYLLRPYDPKDEITVYGTGEAKFAMNYEQDIGLYTIKVATDPRALNRVVIYRPSTNIITQLELISRWEKKIGKKFKKIHVPEEEIVALTKELPEPENIPIAILHCLFIDGATMSYDFKENDVEASTLYPELKFTTIDELLDIFVHDPPPPASAAF 314
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314


Chain B from PDB  Type:PROTEIN  Length:310
 aligned with EGS1_OCIBA | Q15GI4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:310
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314
           EGS1_OCIBA     5 GMKSKILIFGGTGYIGNHMVKGSLKLGHPTYVFTRPNSSKTTLLDEFQSLGAIIVKGELDEHEKLVELMKKVDVVISALAFPQILDQFKILEAIKVAGNIKRFLPSDFGVEEDRINALPPFEALIERKRMIRRAIEEANIPYTYVSANCFASYFINYLLRPYDPKDEITVYGTGEAKFAMNYEQDIGLYTIKVATDPRALNRVVIYRPSTNIITQLELISRWEKKIGKKFKKIHVPEEEIVALTKELPEPENIPIAILHCLFIDGATMSYDFKENDVEASTLYPELKFTTIDELLDIFVHDPPPPASAAF 314
               SCOP domains d2r6jb_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2r6jB01 B:5-150,B:187-209,B:275-287 NAD(P)-binding Rossmann-like Domain                                                                           2r6jB02                             2r6jB01                2r6jB02 B:151-186,B:210-274,B:288-314                            2r6jB01      2r6jB02                     CATH domains
           Pfam domains (1) -----NmrA-2r6jB01 B:10-284                                                                                                                                                                                                                                                              ------------------------------ Pfam domains (1)
           Pfam domains (2) -----NmrA-2r6jB02 B:10-284                                                                                                                                                                                                                                                              ------------------------------ Pfam domains (2)
         Sec.struct. author .....eeee.....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhh..eeee....hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh...eee.............hhhhhhhhhhhhhhhhhhhhh....eeee..eehhhhhhhhhh......eeeee.....eeeeehhhhhhhhhhhhhhhhhhh.eeee..hhh.eeehhhhhhhhhhhhh...eeeeehhhhhhhhhhhh...hhhhhhhhhhhhh.............ee.hhh.......hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6j B   5 GMKSKILIFGGTGYIGNHMVKGSLKLGHPTYVFTRPNSSKTTLLDEFQSLGAIIVKGELDEHEKLVELMKKVDVVISALAFPQILDQFKILEAIKVAGNIKRFLPSDFGVEEDRINALPPFEALIERKRMIRRAIEEANIPYTYVSANCFASYFINYLLRPYDPKDEITVYGTGEAKFAMNYEQDIGLYTIKVATDPRALNRVVIYRPSTNIITQLELISRWEKKIGKKFKKIHVPEEEIVALTKELPEPENIPIAILHCLFIDGATMSYDFKENDVEASTLYPELKFTTIDELLDIFVHDPPPPASAAF 314
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EGS1_OCIBA | Q15GI4)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009699    phenylpropanoid biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic derivatives of trans-cinnamic acid.
    GO:0009698    phenylpropanoid metabolic process    The chemical reactions and pathways involving aromatic derivatives of trans-cinnamic acid.

 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
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:253 - Pro A:254   [ RasMol ]  
    Glu B:253 - Pro B:254   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  2r6j
    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
  EGS1_OCIBA | Q15GI4
    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
  EGS1_OCIBA | Q15GI4
    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
        EGS1_OCIBA | Q15GI4: 2qw8 2qx7 2qys 2qzz 2r2g 3c3x

(-) Related Entries Specified in the PDB File

2qw8 EUGENOL SYNTHASE WITH NADP+, MONOCLINIC FORM
2qx7 EUGENOL SYNTHASE WITH NADP+, ORTHORHOMBIC FORM
2qys EUGENOL SYNTHASE, APO FORM
2qzz EUGENOL SYNTHASE WITH NADP+ AND (1S,2S)-ETHYL 2-(4-HYDROXY- 3-METHOXYPHENYL) CYCLOPROPANECARBOXYLATE