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 :  DIMERIC CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN FROM APIS MELLIFERA IN COMPLEX WITH 9-KETO-2(E)-DECENOIC ACID AT PH 7.0
 
Authors :  M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. T C. Cambillau
Date :  27 Apr 08  (Deposition) - 28 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Honeybee, Apis Mellifera, Pheromone Binding Protein, Signal Transduction, Queen Mandibular Pheromone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, V. Campanacci, M. Tegoni, C. Cambillau
Queen Bee Pheromone Binding Protein Ph-Induced Domain Swapping Favors Pheromone Release
J. Mol. Biol. V. 390 981 2009
PubMed-ID: 19481550  |  Reference-DOI: 10.1016/J.JMB.2009.05.067

(-) Compounds

Molecule 1 - PHEROMONE-BINDING PROTEIN ASP1
    Chains: A, B
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PHIL-D2
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-144
    Organism Common: HONEYBEE
    Organism Scientific: APIS MELLIFERA
    Organism Taxid: 7460

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
19OD3Ligand/Ion(2Z)-9-OXODEC-2-ENOIC ACID
2CL4Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:24 , HOH A:165 , HOH A:202 , SER B:93 , GLY B:94BINDING SITE FOR RESIDUE CL A 120
02AC2SOFTWAREHOH A:159 , TYR B:102 , HOH B:130 , HOH B:213BINDING SITE FOR RESIDUE CL A 121
03AC3SOFTWAREVAL A:65 , PRO A:91 , THR A:92 , HOH A:168 , HOH A:208BINDING SITE FOR RESIDUE CL A 122
04AC4SOFTWAREHOH A:277 , HOH A:278 , HOH A:279 , HOH A:280 , HOH B:243 , HOH B:244BINDING SITE FOR RESIDUE MG A 123
05AC5SOFTWAREASN B:64 , VAL B:65 , PRO B:91 , THR B:92 , HOH B:195BINDING SITE FOR RESIDUE CL B 120
06AC6SOFTWAREMET A:49 , MET A:86 , PHE A:117 , ILE A:119 , HOH A:214 , HOH A:285BINDING SITE FOR RESIDUE 9OD A 124
07AC7SOFTWARELEU B:53 , VAL B:85 , ALA B:112 , PHE B:117 , 9OD B:122BINDING SITE FOR RESIDUE 9OD B 121
08AC8SOFTWARELYS B:17 , ILE B:31 , ASP B:35 , TYR B:48 , MET B:49 , LEU B:52 , LEU B:104 , ALA B:105 , ILE B:119 , 9OD B:121 , HOH B:212 , HOH B:249BINDING SITE FOR RESIDUE 9OD B 122
09AC9SOFTWAREGLU B:67 , GLN B:83 , MET B:86 , GLY B:87 , LEU B:90BINDING SITE FOR RESIDUE GOL B 123
10BC1SOFTWAREGLU A:15 , LEU B:78 , HOH B:234BINDING SITE FOR RESIDUE GOL B 124

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:20 -A:51
2A:47 -A:98
3A:89 -A:107
4B:20 -B:51
5B:47 -B:98
6B:89 -B:107

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:90 -Pro A:91
2Leu B:90 -Pro B:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CYZ)

(-) 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:116
 aligned with Q9U9J6_APIME | Q9U9J6 from UniProtKB/TrEMBL  Length:144

    Alignment length:116
                                    38        48        58        68        78        88        98       108       118       128       138      
         Q9U9J6_APIME    29 WVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3cyza_ A: Pheromone-binding protein asp1                                                                            SCOP domains
               CATH domains 3cyzA00 A:4-119  [code=1.10.238.20, no name defined]                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyz A   4 WVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    13        23        33        43        53        63        73        83        93       103       113      


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with Q9U9J6_APIME | Q9U9J6 from UniProtKB/TrEMBL  Length:144

    Alignment length:115
                                    39        49        59        69        79        89        99       109       119       129       139     
         Q9U9J6_APIME    30 VPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3cyzb_ B: Pheromone-binding protein asp1                                                                           SCOP domains
               CATH domains 3cyzB00 B:5-119  [code=1.10.238.20, no name defined]                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyz B   5 VPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    14        24        34        44        54        64        74        84        94       104       114
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9U9J6_APIME | Q9U9J6)
molecular function
    GO:0005549    odorant binding    Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.

 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
    9OD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:90 - Pro A:91   [ RasMol ]  
    Leu B:90 - Pro B:91   [ RasMol ]  
 

(-) 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
  3cyz
    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
  Q9U9J6_APIME | Q9U9J6
    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
  Q9U9J6_APIME | Q9U9J6
    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
        Q9U9J6_APIME | Q9U9J6: 2h8v 3bfa 3bjh 3cab 3cdn
UniProtKB/TrEMBL
        Q9U9J6_APIME | Q9U9J6: 3bfb 3bfh 3cz0 3cz1 3cz2 3d73 3d74 3d75 3d76 3d77 3d78 3fe6 3fe8 3fe9

(-) Related Entries Specified in the PDB File

2h8v THE APO FORM OF THE SAME PROTEIN AT PH 5.5
3bfa THE SAME PROTEIN IN COMPLEX WITH THE QUEEN MANDIBULAR PHEROMONE AT PH 5.5
3bfb THE SAME PROTEIN IN COMPLEX WITH THE 9-KETO-2(E)-DECENOIC ACID AT PH 5.5
3bfh THE SAME PROTEIN IN COMPLEX WITH THE HEXADECANOIC ACID AT PH 5.5
3bjh THE SAME PROTEIN IN COMPLEX WITH THE N BUTYL BENZENE SULFONAMIDE AT PH 5.5
3cab THE SAME PROTEIN SOAKED AT PH 7.0
3cdn THE APO FORM OF THE SAME PROTEIN AT PH 4.0
3cz0 THE SAME PROTEIN IN COMPLEX WITH THE QUEEN MANDIBULAR PHEROMONE AT PH 7.0
3cz1 THE SAME PROTEIN IN COMPLEX WITH THE N BUTYL BENZENE SULFONAMIDE AT PH 7.0
3cz2 THE APO FORM OF THE SAME PROTEIN AT PH 7.0