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 THE ARABIDOPSIS RECEPTOR KINASE HAESA LRR ECTDOMAIN IN COMPLEX WITH THE PEPTIDE HORMONE IDA.
 
Authors :  J. Santiago, M. Hothorn
Date :  23 Mar 16  (Deposition) - 20 Apr 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Membrane Receptor Kinase, Peptide Hormone Receptor, Signaling Complex, Plant Development, Organ Shedding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Santiago, B. Brandt, M. Wildhagen, U. Hohmann, L. A. Hothorn, M. A. Butenko, M. Hothorn
Mechanistic Insight Into A Peptide Hormone Signaling Comple Mediating Floral Organ Abscission.
Elife V. 5 2016
PubMed-ID: 27058169  |  Reference-DOI: 10.7554/ELIFE.15075

(-) Compounds

Molecule 1 - RECEPTOR-LIKE PROTEIN KINASE 5
    Chains: A
    EC Number: 2.7.10.1, 2.7.11.1
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PBAC3MOD
    Expression System Strain: BTI38
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: ECTODOMAIN, RESIDUES 20-620
    Gene: RLK5, HAE, AT4G28490, F21O9.180
    Organ: FLOWER
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PROTEIN HAESA
    Tissue: ABSCISSION ZONE
 
Molecule 2 - PROTEIN IDA
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 58-69
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PROTEIN INFLORESCENCE DEFICIENT IN ABSCISSION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric/Biological Unit (6, 17)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3HYP1Mod. Amino Acid4-HYDROXYPROLINE
4MAN1Ligand/IonALPHA-D-MANNOSE
5MG2Ligand/IonMAGNESIUM ION
6NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:326binding site for residue MG A 714
02AC2SOFTWARESER A:435 , ARG A:457 , ILE A:458 , SER A:459 , SER A:481 , LYS A:571binding site for residue MG A 715
03AC3SOFTWAREGLU A:566 , LYS B:66 , ARG B:67 , HIS B:68binding site for residue EDO B 2000
04AC4SOFTWAREMET A:18 , SER A:74 , MET A:76 , ASN A:98binding site for Poly-Saccharide residues NAG A 701 through NAG A 702 bound to ASN A 98
05AC5SOFTWAREVAL A:78 , ASN A:102binding site for Mono-Saccharide NAG A 703 bound to ASN A 102
06AC6SOFTWAREASN A:150 , PHE A:174 , MAN A:710binding site for Poly-Saccharide residues NAG A 704 through NAG A 705 bound to ASN A 150
07AC7SOFTWARESER A:182 , ASN A:185 , GLN A:207binding site for Mono-Saccharide NAG A 706 bound to ASN A 185
08AC8SOFTWAREASN A:223 , PHE A:245 , ASN A:246 , ASN A:269 , MET A:293 , GLU A:514 , LYS A:541 , NAG A:705 , ARG B:67binding site for Poly-Saccharide residues NAG A 707 through MAN A 710 bound to ASN A 269
09AC9SOFTWARETHR A:257 , GLN A:258 , ASN A:282binding site for Mono-Saccharide NAG A 711 bound to ASN A 282
10AD1SOFTWARESER A:555 , SER A:556 , ASN A:576 , TYR A:579binding site for Poly-Saccharide residues NAG A 712 through NAG A 713 bound to ASN A 576

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:61
2A:86 -A:113
3A:376 -A:402
4A:606 -A:613

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IXQ)

(-) 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:595
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.......hhhhh..hhhhh..eee.....eeeee......ee..hhhhhhh....eee....eeeee..hhhhh......eee....eeeee...hhhhhh....eee....eee...hhhhhhh....eee..........hhhhhhh....eee...........hhhhhhh....eee......ee..hhhhhhh....eee....eeee..hhhhhhh....eee....eeee..hhhhhhh....eee....ee..............eee......ee..hhhhhhh....eee....eeeee............eee....eeee.............eee....eeee..hhhhhhh....eee....eeeee.hhhhhhh....eee....eeee..hhhhhhh....eee....eeee..hhhhhhh....eee....eeeee.hhhhhhh....eee....eeee.............eee....ee....hhhhhhh....eee......eee.hhhhhhh...eee....eeeee.hhhhhhhhhhhhh.....eeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ixq A  18 MGSLNQDATILRQAKLGLSDPAQSLSSWSDVTPCKWLGVSCDATSNVVSVDLSSFMLVGPFPSILCHLPSLHSLSLYNNSINGSLSADDFDTCHNLISLDLSENLLVGSIPKSLPFNLPNLKFLEISGNNLSDTIPSSFGEFRKLESLNLAGNFLSGTIPASLGNVTTLKELKLAYNLFSPSQIPSQLGNLTELQVLWLAGCNLVGPIPPSLSRLTSLVNLDLTFNQLTGSIPSWITQLKTVEQIELFNNSFSGELPESMGNMTTLKRFDASMNKLTGKIPDNLNLLNLESLNLFENMLEGPLPESITRSKTLSELKLFNNRLTGVLPSQLGANSPLQYVDLSYNRFSGEIPANVCGEGKLEYLILIDNSFSGEISNNLGKCKSLTRVRLSNNKLSGQIPHGFWGLPRLSLLELSDNSFTGSIPKTIIGAKNLSNLRISKNRFSGSIPNEIGSLNGIIEISGAENDFSGEIPESLVKLKQLSRLDLSKNQLSGEIPRELRGWKNLNELNLANNHLSGEIPKEVGILPVLNYLDLSSNQFSGEIPLELQNLKLNVLNLSYNHLSGKIPPLYANKIYAHDFIGNPGLCVDLDGLCRK 615
                                    27        37        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610     
                                                       46|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                        50                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B 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
                 5ixq B  58 PIPPSApSKRHN  69
                                  | 67  
                                 64-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 5IXQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 27)

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
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HYP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ixq)
 

(-) 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
  5ixq
    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
  IDA_ARATH | Q8LAD7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RLK5_ARATH | P47735
    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)
  2.7.10.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.11.1
    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
  IDA_ARATH | Q8LAD7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RLK5_ARATH | P47735
    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
        IDA_ARATH | Q8LAD7: 5ixt 5iyx
        RLK5_ARATH | P47735: 5ixo 5ixt 5iyv 5iyx

(-) Related Entries Specified in the PDB File

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