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 MAIZE CYTOKININ OXIDASE/DEHYDROGENASE 4 (ZMCKO4) IN COMPLEX WITH 6-(3-METHYLPYRROL-1-YL)-9H-PURINE
 
Authors :  D. Kopecny, P. Briozzo
Date :  11 Jan 16  (Deposition) - 04 May 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Flavoenzyme, Plant Hormone Degradation, Oxidase/Dehydrogenase, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hluska, P. I. Dobrev, D. Tarkowska, J. Frebortova, D. Zalabak, D. Kopecny, O. Plihal, F. Kokas, P. Briozzo, M. Zatloukal, V. Motyka, P. Galuszka
Cytokinin Metabolism In Maize: Novel Evidence Of Cytokinin Abundance, Interconversions And Formation Of A New Trans-Zeatin Metabolic Product With A Weak Anticytokinin Activity.
Plant Sci. V. 247 127 2016
PubMed-ID: 27095406  |  Reference-DOI: 10.1016/J.PLANTSCI.2016.03.014

(-) Compounds

Molecule 1 - CYTOKININ DEHYDROGENASE 4
    Chains: A
    EC Number: 1.5.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PTYB12
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Gene: CKX4
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: CYTOKININ OXIDASE/DEHYDROGENASE 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2ZME1Ligand/Ion6-(3-METHYL-1H-PYRROL-1-YL)-9H-PURINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:57 , ALA A:95 , ARG A:96 , GLY A:97 , HIS A:98 , GLY A:99 , HIS A:100 , SER A:101 , GLN A:105 , ALA A:106 , THR A:169 , ASP A:170 , TYR A:171 , SER A:175 , GLY A:177 , GLY A:178 , THR A:179 , SER A:181 , ASN A:182 , GLY A:184 , ILE A:185 , GLY A:234 , ILE A:235 , ILE A:236 , TRP A:389 , TYR A:487 , GLN A:526 , ZME A:601 , HOH A:733 , HOH A:809 , HOH A:818 , HOH A:854binding site for residue FAD A 600
2AC2SOFTWAREASP A:170 , LEU A:452 , FAD A:600 , HOH A:800binding site for residue ZME A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HHZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:126 -Ala A:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HHZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HHZ)

(-) Exons   (0, 0)

(no "Exon" information available for 5HHZ)

(-) 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:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhh............eeee..hhhhhhhhhhhhhhh.....eeee...............eeee.........eee....eeeeeee...hhhhhhhhhhh...ee..........hhhhhhh......hhhhhhhhhh.eeeeeee.....eeeee...hhhhhhhhh.......eeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhh......eeeeeeee.hhhhhhhh..eeeeeeeeeee......hhhhhhhhhhhh........eeeeeehhhhhhhhhhhhhhhhhh.........eeeeee.hhhhhhhhhh.........eeeeeee.hhh............eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hhz A  40 GGRLSVDASDIAEASRDFGGVARAEPMAVFHPRAAGDVAGLVGAAFRSARGFRVSARGHGHSISGQAQAAGGVVVDMSRVARALPVHSAALGGHYVDVWGGELWVDVLNWTLSHGGLAPRSWTDYLYLSVGGTLSNAGISGQAFHHGPQISNVYELDVVTGKGEVVTCSETENPDLFFGVLGGLGQFGIITRARIALERAPKRVRWIRALYSNFSEFTADQERLISLGRRFDYVEGFVVAAEGLSLKHHSSVLYCLEVTKNYDDETAGSVDQDVDTLLGELNFLPGTVFTTDLPYVDFLDRVHKAELKLRAKGMWEVPHPWLNLFVPASRIADFDRGVFRGVLAGGPVLIYPMNKHKWDPRSSAVTPDEEVFYLVAFLRSALPGAPESLEALARQNQRILDFCAGTGIGAKQYLPGHKARHEWAEHFGAARWDRFARLKAEFDPRAILAAGQGIFRP 531
                                    49        59        69        79        89        99       109       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266      |280       290   ||  318       328       338       348       358       368       378       388       398       408  ||   424       434       444       454       464       474       484       494       504       514       524       
                                                                                                        118|                                                                                                                                                273|             294|                                                                                               411|                                                                                                                 
                                                                                                         126                                                                                                                                                 278              313                                                                                                418
   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 5HHZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HHZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HHZ)

(-) Gene Ontology  (8, 8)

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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:126 - Ala A:127   [ 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
  5hhz
    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
  E3T1W8_MAIZE | E3T1W8
    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)
  1.5.99.12
    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
  E3T1W8_MAIZE | E3T1W8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        E3T1W8_MAIZE | E3T1W8: 4o95 4oal 5hmr 5hqx

(-) Related Entries Specified in the PDB File

4o95 4O95 CONTAINS THE SAME PROTEIN ZMCKO4 COMPLEXED WITH CPPU
4oal 4OAL CONTAINS THE SAME PROTEIN ZMCKO4 COMPLEXED WITH CPPU