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 :  CRYSTAL STRUCTURE OF ORYZA SATIVA DWARF14 (D14) IN COMPLEX WITH PMSF
 
Authors :  M. Kagiyama, Y. Hirano, T. Mori, S. Y. Kim, J. Kyozuka, Y. Seto, S. Yamagu T. Hakoshima
Date :  19 Oct 12  (Deposition) - 23 Jan 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Strigolactone Signaling, Alpha/Beta Hydrolase, Strigolactone Hydrolysis, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kagiyama, Y. Hirano, T. Mori, S. Y. Kim, J. Kyozuka, Y. Seto, S. Yamaguchi, T. Hakoshima
Structures Of D14 And D14L In The Strigolactone And Karriki Signaling Pathways
Genes Cells V. 18 147 2013
PubMed-ID: 23301669  |  Reference-DOI: 10.1111/GTC.12025

(-) Compounds

Molecule 1 - DWARF 88 ESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET47B
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 55-318
    Gene: D88, LOC_OS03G10620, OS03G0203200
    Organism Common: JAPANESE RICE
    Organism Scientific: ORYZA SATIVA JAPONICA GROUP
    Organism Taxid: 39947
    Synonym: HYDROLASE, ALPHA/BETA FOLD FAMILY PROTEIN, EXPRESSED, OS03G0203200 PROTEIN

 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  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2PMS2Ligand/IonPHENYLMETHANESULFONIC ACID
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2PMS1Ligand/IonPHENYLMETHANESULFONIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2PMS1Ligand/IonPHENYLMETHANESULFONIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:78 , SER A:147 , VAL A:148 , PHE A:176 , VAL A:244 , PHE A:245BINDING SITE FOR RESIDUE PMS A 401
2AC2SOFTWARETYR A:182 , HIS A:183 , SER A:274 , VAL A:275BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWAREPHE A:186 , TYR A:209 , SER A:270 , HOH A:657BINDING SITE FOR RESIDUE EDO A 403
4AC4SOFTWAREARG A:97 , LEU A:136 , HOH A:610 , HOH A:655 , ARG B:94BINDING SITE FOR RESIDUE EDO A 404
5AC5SOFTWAREMET A:198 , GLY A:199 , ASN A:201 , TYR A:202 , PRO A:234 , HOH A:538 , PRO B:90 , TYR B:91BINDING SITE FOR RESIDUE EDO A 405
6AC6SOFTWAREPHE B:78 , SER B:147 , VAL B:148 , MET B:151 , PHE B:176 , VAL B:244 , PHE B:245 , HIS B:297BINDING SITE FOR RESIDUE PMS B 401
7AC7SOFTWAREASP B:181 , TYR B:182 , HIS B:183 , SER B:274 , VAL B:275 , HOH B:574BINDING SITE FOR RESIDUE EDO B 402
8AC8SOFTWAREASP B:120 , HIS B:239 , GLN B:242 , THR B:243 , LYS B:246BINDING SITE FOR RESIDUE EDO B 403
9AC9SOFTWARESER A:203 , TYR B:91 , SER B:305 , GLN B:309 , HOH B:517 , HOH B:625BINDING SITE FOR RESIDUE EDO B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W05)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W05)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W05)

(-) Exons   (0, 0)

(no "Exon" information available for 3W05)

(-) 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:264
 aligned with D14_ORYSJ | Q10QA5 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:264
                                    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    
            D14_ORYSJ    55 KLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..eeee....eeeee.....hhhhhh.hhhhh....eeee.........hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhh...eeeee.........hhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w05 A  55 KLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
                                    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:264
 aligned with D14_ORYSJ | Q10QA5 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:264
                                    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    
            D14_ORYSJ    55 KLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..eeee....eeeee.....hhhhhh.hhhhh....eeee.........hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...eeeee.........hhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w05 B  55 KLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
                                    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  (0, 0)

(no "SCOP Domain" information available for 3W05)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W05)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W05)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (D14_ORYSJ | Q10QA5)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0010223    secondary shoot formation    The process that gives rise to secondary (or auxiliary or axillary) shoots in plants. This process pertains to the initial formation of a structure from unspecified parts. These secondary shoots originate from secondary meristems initiated in the axils of leaf primordia. Axillary meristems function like the shoot apical meristem of the primary shoot initating the development of lateral organs.
    GO:1901601    strigolactone biosynthetic process    The chemical reactions and pathways resulting in the formation of strigolactone.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PMS  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3w05)
 
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
  3w05
    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
  D14_ORYSJ | Q10QA5
    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
  D14_ORYSJ | Q10QA5
    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
        D14_ORYSJ | Q10QA5: 3vxk 3w04 3wio 4ih9 4iha 5dj5

(-) Related Entries Specified in the PDB File

3w04 3w06