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 PXY-TDIF/CLE41
 
Authors :  J. J. Chai, H. Q. Zhang
Date :  08 Aug 16  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.77
Chains :  Asym./Biol. Unit :  B,C
Keywords :  Pxy, Tdif, Cle Peptides, Leucine Rich Repeat, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Q. Zhang, X. Y. Lin, Z. F. Han, L. J. Qu, J. J. Chai
Crystal Structure Of Pxy-Tdif Complex Reveals A Conserved Recognition Mechanism Among Cle Peptide-Receptor Pairs
Cell Res. V. 26 543 2016
PubMed-ID: 27055373  |  Reference-DOI: 10.1038/CR.2016.45

(-) Compounds

Molecule 1 - LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE TDR
    ChainsB
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    FragmentUNP RESIDUES 31-629
    GenePXY
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymPXY
 
Molecule 2 - TDIF/CLE41
    ChainsC
    EngineeredYES
    Organism ScientificARABIDOPSIS
    Organism Taxid3701
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1HYP2Mod. Amino Acid4-HYDROXYPROLINE
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:89 , HIS B:90 , TYR B:109 , ASN B:111 , THR B:133 , ASP B:135binding site for Mono-Saccharide NAG B 701 bound to ASN B 111
2AC2SOFTWAREGLN B:267 , ASN B:271binding site for Mono-Saccharide NAG B 702 bound to ASN B 271
3AC3SOFTWAREASN B:356 , SER B:380binding site for Mono-Saccharide NAG B 703 bound to ASN B 356
4AC4SOFTWAREASN B:355 , ASN B:378 , HOH B:802binding site for Mono-Saccharide NAG B 704 bound to ASN B 378
5AC5SOFTWARETRP B:420 , ASN B:442binding site for Mono-Saccharide NAG B 705 bound to ASN B 442
6AC6SOFTWARESER B:449 , TYR B:469 , ASN B:471 , GLU B:518 , HOH B:825 , HOH B:827 , HOH B:831binding site for Mono-Saccharide NAG B 706 bound to ASN B 471
7AC7SOFTWAREGLU B:504 , ASN B:525 , GLY B:526binding site for Mono-Saccharide NAG B 707 bound to ASN B 525
8AC8SOFTWAREGLN B:520 , ASN B:542 , ASP B:564 , ASP B:566binding site for Mono-Saccharide NAG B 708 bound to ASN B 542

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1B:69 -B:76
2B:390 -B:416
3B:511 -B:535
4B:620 -B:628

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GR9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GR9)

(-) Exons   (0, 0)

(no "Exon" information available for 5GR9)

(-) 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 B from PDB  Type:PROTEIN  Length:595
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhee.hhhhhh.......hhhhhh..eee......eeeee......ee..hhhhhhh....eee..........hhhhhhh....eee............hhhhh....eee......eee.hhhhhhh....eee....eeee..hhhhhhh....eee....eeeee.hhhhhhh....eee....eee...hhhhhhh....eee......eee.hhhhhhh....eee....eeee..hhhhhhh....eee....eeee..hhhhhhh....eee....eeee..hhhhhh.....eee....ee...............eee.....................eee......eee.hhhhhhh....eee....eee.....hhhhh....eee..........hhhhhhh....eee..........hhhhhhh....eee......eee...........eee....eee.....hhhhh....eee..........hhhhhhh....eee..........hhhhhhh....eee......eee...hhhhhhhhhhhh...eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gr9 B  31 KFSPQLLSLLSLKTSLSGPPSAFQDWKVPVDAVWCSWSGVVCDNVTAQVISLDLSHRNLSGRIPIQIRYLSSLLYLNLSGNSLEGSFPTSIFDLTKLTTLDISRNSFDSSFPPGISKLKFLKVFNAFSNNFEGLLPSDVSRLRFLEELNFGGSYFEGEIPAAYGGLQRLKFIHLAGNVLGGKLPPRLGLLTELQHMEIGYNHFNGNIPSEFALLSNLKYFDVSNCSLSGSLPQELGNLSNLETLFLFQNGFTGEIPESYSNLKSLKLLDFSSNQLSGSIPSGFSTLKNLTWLSLISNNLSGEVPEGIGELPELTTLFLWNNNFTGVLPHKLGSNGKLETMDVSNNSFTGTIPSSLCHGNKLYKLILFSNMFEGELPKSLTRCESLWRFRSQNNRLNGTIPIGFGSLRNLTFVDLSNNRFTDQIPADFATAPVLQYLNLSTNFFHRKLPENIWKAPNLQIFSASFSNLIGEIPNYVGCKSFYRIELQGNSLNGTIPWDIGHCEKLLCLNLSQNHLNGIIPWEISTLPSIADVDLSHNLLTGTIPSDFGSSKTITTFNVSYNQLIGPIPSGSFAHLNPSFFSSNEGLCGDLVGKPCN 629
                                    40        50        60|       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       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624     
                                                        60|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                         65                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    

Chain C from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5gr9 C  93 HEVpSGpNPISN 104
                               |  |102  
                              96-HYP    
                                 99-HYP 

   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 5GR9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GR9)

(-) Gene Ontology  (26, 32)

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
    HYP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5gr9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5gr9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CLE41_ARATH | Q84W98
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TDR_ARATH | Q9FII5
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CLE41_ARATH | Q84W98
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TDR_ARATH | Q9FII5
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CLE41_ARATH | Q84W985gij 5jfi
        TDR_ARATH | Q9FII55gij 5gqr 5jfi 5jfk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5GR9)