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(-) Description

Title :  COMPLEX STRUCTURE OF (+)-ABA-BOUND PYL1 AND ABI1
 
Authors :  P. Yin, H. Fan, Q. Hao, X. Yuan, N. Yan
Date :  23 Oct 09  (Deposition) - 10 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aba, Pyl1, Abi1, Abscisic Acid Signaling Pathway, Cell Membrane, Hydrolase, Magnesium, Manganese, Metal-Binding, Nucleus, Protein Phosphatase, Hydrolase-Hormone Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Yin, H. Fan, Q. Hao, X. Yuan, D. Wu, Y. Pang, C. Yan, W. Li, J. Wang, N. Ya
Structural Insights Into The Mechanism Of Abscisic Acid Signaling By Pyl Proteins
Nat. Struct. Mol. Biol. V. 16 1230 2009
PubMed-ID: 19893533  |  Reference-DOI: 10.1038/NSMB.1730

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN AT5G46790
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 20-221
    GeneAT5G46790
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymPYL1
 
Molecule 2 - PROTEIN PHOSPHATASE 2C 56
    ChainsB
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 119-434
    GeneABI1, AT4G26080, F20B18.190
    MutationYES
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymABI1, ATPP2C56, PROTEIN PHOSPHATASE 2C ABI1, PP2C ABI1, PROTEIN ABSCISIC ACID-INSENSITIVE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1A8S1Ligand/Ion(2Z,4E)-5-[(1S)-1-HYDROXY-2,6,6-TRIMETHYL-4-OXOCYCLOHEX-2-EN-1-YL]-3-METHYLPENTA-2,4-DIENOIC ACID
2MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:86 , PHE A:88 , VAL A:110 , ALA A:116 , PHE A:135 , ILE A:137 , LEU A:144 , TYR A:147 , PHE A:189 , VAL A:193 , ASN A:197 , HOH A:223 , HOH A:228 , HOH A:230 , HOH A:250 , HOH A:257BINDING SITE FOR RESIDUE A8S A 222
2AC2SOFTWAREASP B:177 , ASP B:347 , ASP B:413 , HOH B:466 , HOH B:488BINDING SITE FOR RESIDUE MN B 435

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:267 -B:359

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:138 -Gly A:139
2Lys B:321 -Pro B:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.P2C56_ARATH128-422  1B:128-422
2PPM_1PS01032 PPM-type phosphatase domain signature.P2C56_ARATH172-180  1B:172-180

(-) Exons   (0, 0)

(no "Exon" information available for 3KDJ)

(-) 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:179
 aligned with PYL1_ARATH | Q8VZS8 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:179
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           PYL1_ARATH    31 DLTQDEFTQLSQSIAEFHTYQLGNGRCSSLLAQRIHAPPETVWSVVRRFDRPQIYKHFIKSCNVSEDFEMRVGCTRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVTTVHRFEKEEEEERIWTVVLESYVVDVPEGNSEEDTRLFADTVIRLNLQKLASITEAMN 209
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------Polyketide_cyc2-3kdjA01 A:57-206                                                                                                                      --- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhh...hhhhh...eeeee...........eeeeee.......eeeeeeeeee....eeeeeeeeee......eeeeeeeeeeee...eeeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdj A  31 DLTQDEFTQLSQSIAEFHTYQLGNGRCSSLLAQRIHAPPETVWSVVRRFDRPQIYKHFIKSCNVSEDFEMRVGCTRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVTTVHRFEKEEEEERIWTVVLESYVVDVPEGNSEEDTRLFADTVIRLNLQKLASITEAMN 209
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         

Chain B from PDB  Type:PROTEIN  Length:270
 aligned with P2C56_ARATH | P49597 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:298
                                   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417        
          P2C56_ARATH   128 LYGFTSICGRRPEMEDAVSTIPRFLQSSSGSMLDGRFDPQSAAHFFGVYDGHGGSQVANYCRERMHLALAEEIAKEKPMLCDGDTWLEKWKKALFNSFLRVDSEIESVAPETVGSTSVVAVVFPSHIFVANCGDSRAVLCRGKTALPLSVDHKPDREDEAARIEAAGGKVIQWNGARVFGVLAMSRSIGDRYLKPSIIPDPEVTAVKRVKEDDCLILASDGVWDVMTDEEACEMARKRILLWHKKNAVAGDASLLADERRKEGKDPAAMSAAEYLSKLAIQRGSKDNISVVVVDLKPR 425
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains PP2C-3kdjB01 B:128-415                                                                                                                                                                                                                                                                          ---------- Pfam domains
         Sec.struct. author .eeeeee........eeeeee....-----------.hhhhhheeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.eeeeee...eeeeeee...eeeeee..eeee........hhhhhhhhhhh...eee...eee.........ee.hhhh.......eeeeee....eeeeeeehhhhhh..hhhhhhhhhhhhhhhhh..-----------------..hhhhhhhhhhhhhhhhhh.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PPM_2  PDB: B:128-422 UniProt: 128-422                                                                                                                                                                                                                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------PPM_1    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdj B 128 LYGFTSICGRRPEMEDAVSTIPRFL-----------FDPQSAAHFFGVYDGHGGSQVANYCRERMHLALAEEIAKEKPMLSDGDTWLEKWKKALFNSFLRVDSEIESVAPETVGSTSVVAVVFPSHIFVANCGDSRAVLCRGKTALPLSVDHKPDREDEAARIEAAGGKVIQWNGARVFGVLAMSRSIGDRYLKPSIIPDPEVTAVKRVKEDDCLILASDGVWDVMTDEEACEMARKRILLWHKK-----------------GKDPAAMSAAEYLSKLAIQRGSKDNISVVVVDLKPR 425
                                   137       147    |    -      |167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367    |    -         -  |    397       407       417        
                                                  152         164                                                                                                                                                                                                             372               390                                   

   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 3KDJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: PP2C (22)

(-) Gene Ontology  (26, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYL1_ARATH | Q8VZS8)
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.

Chain B   (P2C56_ARATH | P49597)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004722    protein serine/threonine phosphatase activity    Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
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:0009788    negative regulation of abscisic acid-activated signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of abscisic acid (ABA) signaling.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0009787    regulation of abscisic acid-activated signaling pathway    Any process that modulates the frequency, rate or extent of abscisic acid (ABA) signaling.
    GO:0010119    regulation of stomatal movement    Any process that modulates the frequency, rate or extent of stomatal movement.
    GO:0009737    response to abscisic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abscisic acid stimulus.
    GO:0009409    response to cold    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P2C56_ARATH | P495973jrq 3nmn
        PYL1_ARATH | Q8VZS83jrq 3jrs 3kay 3nef 3neg 3nmn

(-) Related Entries Specified in the PDB File

3kdh APO-PYL2
3kdi (+)-ABA BOUND PYL2