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 :  X-RAY CRYSTAL STRUCTURE OF THE PY13 -PYRABACTIN COMPLEX
 
Authors :  X. Zhang, Q. Zhang, G. Wang, Z. Chen
Date :  23 Aug 10  (Deposition) - 10 Aug 11  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Abscisic Acid Receptor, Crystal, Pp2C, Pyl3, Pyrabactin, Hormone Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhang, Q. Zhang, Q. Xin, L. Yu, Z. Wang, W. Wu, L. Jiang, G. Wang, W. Tian, Z. Deng, Y. Wang, Z. Liu, J. Long, Z. Gong, Z. Chen
Complex Structures Of The Abscisic Acid Receptor Pyl3/Rcar1 Reveal A Unique Regulatory Mechanism
Structure V. 20 780 2012
PubMed-ID: 22579247  |  Reference-DOI: 10.1016/J.STR.2012.02.019

(-) Compounds

Molecule 1 - ABSCISIC ACID RECEPTOR PYL3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX 4T-2
    Expression System Strain: ROSETTA 2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PYL3
    Organism Common: THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PYR1-LIKE PROTEIN 3, REGULATORY COMPONENTS OF ABA RECEPTOR 13

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PYV2Ligand/Ion4-BROMO-N-(PYRIDIN-2-YLMETHYL)NAPHTHALENE-1-SULFONAMIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:81 , ILE A:82 , LEU A:111 , ALA A:113 , SER A:116 , GLU A:118 , LEU A:141 , PHE A:188 , HOH A:307 , HOH A:312BINDING SITE FOR RESIDUE PYV A 210
2AC2SOFTWARESO4 B:2 , PHE B:81 , ILE B:82 , GLU B:118 , LEU B:141 , TYR B:144 , VAL B:192 , HOH B:217 , HOH B:270BINDING SITE FOR RESIDUE PYV B 210
3AC3SOFTWAREHIS A:63 , ALA B:113 , SER B:114 , THR B:115 , GLU B:138 , HIS B:139 , ARG B:140 , HOH B:244 , HOH B:286BINDING SITE FOR RESIDUE SO4 B 1
4AC4SOFTWARELYS B:79 , PHE B:132 , TYR B:144 , SER B:146 , GLU B:170 , ASN B:196 , PYV B:210 , HOH B:270 , HOH B:339 , HOH B:377BINDING SITE FOR RESIDUE SO4 B 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OJI)

(-) 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:181
 aligned with PYL3_ARATH | Q9SSM7 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:186
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           PYL3_ARATH    21 TPYGLTKDEFSTLDSIIRTHHTFPRSPNTCTSLIAHRVDAPAHAIWRFVRDFANPNKYKHFIKSCTIRVNGNGIKEIKVGTIREVSVVSGLPASTSVEILEVLDEEKRILSFRVLGGEHRLNNYRSVTSVNEFVVLEKDKKKRVYSVVLESYIVDIPQGNTEEDTRMFVDTVVKSNLQNLAVISTA 206
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.....-.eeeeeeeeee..hhhhhhhhhh...hhhhh...eeeeee...----.......eeeeee.......eeeeeeeeee....eeeeeeee........eeeeeeeeeeee.....eeeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oji A  21 TPYGLTKDEFSTLDSIIRTHHTFPRS-NTCTSLIAHRVDAPAHAIWRFVRDFANPNKYKHFIKSCTIRVN----KEIKVGTIREVSVVSGLPASTSVEILEVLDEEKRILSFRVLGGEHRLNNYRSVTSVNEFVVLEKDKKKRVYSVVLESYIVDIPQGNTEEDTRMFVDTVVKSNLQNLAVISTA 206
                                    30        40     | |50        60        70        80        90    |  100       110       120       130       140       150       160       170       180       190       200      
                                                    46 |                                        90   95                                                                                                               
                                                      48                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with PYL3_ARATH | Q9SSM7 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:189
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           PYL3_ARATH    21 TPYGLTKDEFSTLDSIIRTHHTFPRSPNTCTSLIAHRVDAPAHAIWRFVRDFANPNKYKHFIKSCTIRVNGNGIKEIKVGTIREVSVVSGLPASTSVEILEVLDEEKRILSFRVLGGEHRLNNYRSVTSVNEFVVLEKDKKKRVYSVVLESYIVDIPQGNTEEDTRMFVDTVVKSNLQNLAVISTASPT 209
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh........eeeeeeeeee..hhhhhhhhhh...hhhhh...eeeee..----.........eeeeee.......eeeeeeeeee....eeeeee..........eeeeeeeeeeee.....eeeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oji B  21 TPYGLTKDEFSTLDSIIRTHHTFPRSPNTCTSLIAHRVDAPAHAIWRFVRDFANPNKYKHFIKSCTIR----GIKEIKVGTIREVSVVSGLPASTSVEILEVLDEEKRILSFRVLGGEHRLNNYRSVTSVNEFVVLEKDKKKRVYSVVLESYIVDIPQGNTEEDTRMFVDTVVKSNLQNLAVISTASPT 209
                                    30        40        50        60        70        80       | -  |    100       110       120       130       140       150       160       170       180       190       200         
                                                                                              88   93
   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 3OJI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYL3_ARATH | Q9SSM7)
molecular function
    GO:0010427    abscisic acid binding    Interacting selectively and non-covalently with abscisic acid, plant hormones that regulate aspects of plant growth.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004864    protein phosphatase inhibitor activity    Stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0009738    abscisic acid-activated signaling pathway    A series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0080163    regulation of protein serine/threonine phosphatase activity    Any process that modulates the frequency, rate or extent of protein serine/threonine phosphatase activity: catalysis of the reaction: protein serine/threonine phosphate + H2O = protein serine/threonine + phosphate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
    PYV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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
(no "Cis Peptide Bonds" information available for 3oji)
 

(-) 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
  3oji
    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
  PYL3_ARATH | Q9SSM7
    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
  PYL3_ARATH | Q9SSM7
    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
        PYL3_ARATH | Q9SSM7: 3klx 4ds8 4dsb 4dsc 4jda 5jo1 5jo2

(-) Related Entries Specified in the PDB File

3kl1 3klx