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 :  COMPLEX OF RICE BLAST (MAGNAPORTHE ORYZAE) EFFECTOR PROTEIN AVR-PIKD WITH THE HMA DOMAIN OF PIKP1 FROM RICE (ORYZA SATIVA)
 
Authors :  A. Maqbool, H. Saitoh, M. Franceschetti, C. E. Stevenson, A. Uemura, H. S. Kamoun, R. Terauchi, M. J. Banfield
Date :  01 Jul 15  (Deposition) - 26 Aug 15  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Antiviral Protein, Rice Blast Disease, Plant Disease Resistance, Effector Protein, Integrated Hma Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Maqbool, H. Saitoh, M. Franceschetti, C. E. Stevenson, A. Uemura, H. Kanzaki, S. Kamoun, R. Terauchi, M. J. Banfield
Structural Basis Of Pathogen Recognition By An Integrated Hma Domain In A Plant Nlr Immune Receptor.
Elife V. 4 2015
PubMed-ID: 26304198  |  Reference-DOI: 10.7554/ELIFE.08709

(-) Compounds

Molecule 1 - RESISTANCE PROTEIN PIKP-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINS3C
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: SHUFFLE
    Expression System Vector Type: PLASMID
    Fragment: PIKP-HMA, UNP RESIDUES 186-258
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530
    Strain: K60
 
Molecule 2 - AVR-PIK PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINA
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: SHUFFLE
    Expression System Vector Type: PLASMID
    Fragment: AVR-PIKD, UNP RESIDUES 22-113
    Organism Scientific: MAGNAPORTHE ORYZAE
    Organism Taxid: 318829
    Strain: SASA2

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER C:73 , ASP C:90 , ASP C:91 , HOH C:2075BINDING SITE FOR RESIDUE SO4 C 1114
2AC2SOFTWARELEU B:254 , LEU C:35 , TRP C:84 , HOH C:2007 , HOH C:2043 , HOH C:2066BINDING SITE FOR RESIDUE EDO C 1115
3AC3SOFTWAREASN C:62 , ASN C:83 , TRP C:84 , HOH C:2030BINDING SITE FOR RESIDUE EDO C 1116
4AC4SOFTWAREVAL B:257 , HOH B:2039 , ASP C:77 , HIS C:86 , HOH C:2042BINDING SITE FOR RESIDUE EDO C 1117
5AC5SOFTWAREVAL B:192 , LYS B:228 , LEU B:255 , GLN B:256 , HOH B:2024 , HOH B:2040 , TRP C:56BINDING SITE FOR RESIDUE EDO B 1259

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1C:54 -C:93

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A6W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A6W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A6W)

(-) Exons   (0, 0)

(no "Exon" information available for 5A6W)

(-) 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:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhh...eeeeeee.....eeeeee...hhhhhhhhhhhhh..eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 5a6w A 187 LKQKIVIKVAMENNCRSKAMALVASTGGVDSVALVGDLRDKIEVVGYGIDPIKLISALRKKVGDAELLQVS 258
                                   196 ||    207       217       227       237       247       257 
                                     198|                                                          
                                      200                                                          


Chain B from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee...hhhhhhhhhhhh...eeeeeee.....eeeeee...hhhhhhhhhhhhh..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5a6w B 184 GPGLKQKIVIKVAMENCRSKAMALVASTGGVDSVALVGDLRDKIEVVGYGIDPIKLISALRKKVGDAELLQVS 258
                                   193    || 205       215       225       235       245       255   
                                        198|                                                         
                                         201                                                         


Chain C from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeeee..eeeeeeee...eeeeeee..eeeeeee.....ee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 5a6w C  31 RAIDLSRERDPNFFDHPGIPVPECFWFMFKNNVRQDAGTCYSSWKMDMKVGPNWVHIKSDDNCNLSGDFPPGWIVLGKKRPGF 113
                                    40        50        60        70        80        90       100       110
   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 5A6W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A6W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A6W)

(-) Gene Ontology  (3, 3)

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
    EDO  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5a6w)
 

(-) 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
  5a6w
    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
  C4B8B8_MAGOR | C4B8B8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  E9KPB5_ORYSJ | E9KPB5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  C4B8B8_MAGOR | C4B8B8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  E9KPB5_ORYSJ | E9KPB5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        E9KPB5_ORYSJ | E9KPB5: 5a6p

(-) Related Entries Specified in the PDB File

5a6p HEAVY METAL ASSOCIATED DOMAIN OF NLR-TYPE IMMUNE RECEPTOR PIKP1 FROM RICE (ORYZA SATIVA)