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 :  ELUCIDATION OF THE STRUCTURE AND REACTION MECHANISM OF SORGHUM BICOLOR HYDROXYCINNAMOYLTRANSFERASE AND ITS STRUCTURAL RELATIONSHIP TO OTHER COA-DEPENDENT TRANSFERASES AND SYNTHASES
 
Authors :  A. M. Walker, R. P. Hayes, B. Youn, W. Vermerris, S. E. Sattler, C. Kang
Date :  25 Apr 13  (Deposition) - 15 May 13  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydroxycinnamoyl Transferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Walker, R. P. Hayes, B. Youn, W. Vermerris, S. E. Sattler, C. Kang
Elucidation Of The Structure And Reaction Mechanism Of Sorghum Hydroxycinnamoyltransferase And Its Structural Relationship To Other Coenzyme A-Dependent Transferases And Synthases.
Plant Physiol. V. 162 640 2013
PubMed-ID: 23624856  |  Reference-DOI: 10.1104/PP.113.217836

(-) Compounds

Molecule 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SB04G025760, SORBIDRAFT_04G025760
    Organism Common: BROOMCORN,MILO
    Organism Scientific: SORGHUM BICOLOR
    Organism Taxid: 4558
    Synonym: PROTEIN SB04G025760

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PG43Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:37 , GLY A:408 , ILE A:409 , ALA A:410 , PHE A:416 , PG4 A:503BINDING SITE FOR RESIDUE PG4 A 501
2AC2SOFTWAREALA A:298 , THR A:299 , ASP A:300 , ARG A:304 , ARG A:388 , PG4 A:503BINDING SITE FOR RESIDUE PG4 A 502
3AC3SOFTWAREHIS A:162 , GLY A:167 , ASP A:300 , THR A:384 , LEU A:389 , PG4 A:501 , PG4 A:502 , HOH A:822BINDING SITE FOR RESIDUE PG4 A 503
4AC4SOFTWARETYR A:270 , SER A:385 , VAL A:387 , ARG A:388 , HOH A:852BINDING SITE FOR RESIDUE GOL A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KE4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:201 -Pro A:202
2Gln A:306 -Pro A:307
3Cys A:378 -Pro A:379

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KE4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KE4)

(-) Exons   (0, 0)

(no "Exon" information available for 4KE4)

(-) 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:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........eee..hhhhhh.....eeeeeee..................hhhhhhhhhhhhh..hhhhhheeee.....eeeee....eeeeeeee...hhhhhh....hhhhhhhh.............eeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhh..........hhhhhh..........hhhhh............eeeeeeeehhhhhhhhhhh............hhhhhhhhhhhhhhhhhh......eeeeeeeee.................eeee..eeehhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhh.hhhhhh...eeeee.................eeee.......eeeeee.......eeeeeeeehhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ke4 A   1 MKITVRGSEMVYPAAETPRRRLWNSGPDLVVPRFHTPSVYFFRRRDADGNDLTAADGSFFDGARMRRALAEALVPFYPMAGRLARDEDGRVEIDCNAAGVLFQEADAPDATIDYFGDFAPTMELKRLIPTVDFSDDTAFPLLVLQVTHFKCGGVAIGVGMQHHVADGFSGLHFINSWADLCRGVPIAVMPFIDRSLLRARDPPAPVYPHVEYQPAPAMLSSATPPAAVAIFKLSRAELGRLRSQVPAREREGAPRFSTYAVLAAHVWRCASLARGLPADQPTKLYCATDGRQRLQPPLPEGYFGNVIFTATPLANAGTVTAGVAEGAAVIQAALDRMDDGYCRSALDYLELQPDLSALVRGAHTFRCPNLGLTSWVRLPIHDADFGWGRPVFMGPGGIAYEGLAFVLPSANRDGSLSVAISLQAEHMEKFRKLIYDF 448
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220||     241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       
                                                                                                                                                                                                                                                      221|                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                       233
   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 4KE4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KE4)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:201 - Pro A:202   [ RasMol ]  
    Cys A:378 - Pro A:379   [ RasMol ]  
    Gln A:306 - Pro A:307   [ RasMol ]  
 

(-) 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
  4ke4
    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
  C5XXB7_SORBI | C5XXB7
    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
  C5XXB7_SORBI | C5XXB7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        C5XXB7_SORBI | C5XXB7: 4kec

(-) Related Entries Specified in the PDB File

4kec