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(-) Description

Title :  DIMERIC CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN FROM APIS MELLIFERA IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE 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 :  1.70
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, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
19OD3Ligand/Ion(2Z)-9-OXODEC-2-ENOIC ACID
2CL4Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:65 , PRO A:91 , THR A:92 , HOH A:215 , HOH A:216BINDING SITE FOR RESIDUE CL A 120
2AC2SOFTWAREHIS A:24 , HOH A:164 , SER B:93 , GLY B:94BINDING SITE FOR RESIDUE CL A 121
3AC3SOFTWAREHOH A:138 , HOH A:185 , TYR B:102 , HOH B:186BINDING SITE FOR RESIDUE CL A 122
4AC4SOFTWAREHOH A:247 , HOH A:248 , HOH A:249 , HOH A:250 , HOH B:278 , HOH B:279BINDING SITE FOR RESIDUE MG A 123
5AC5SOFTWAREVAL B:65 , PRO B:91 , THR B:92 , HOH B:221BINDING SITE FOR RESIDUE CL B 120
6AC6SOFTWAREMET A:49 , MET A:86 , PHE A:117 , HOH A:252 , HOH A:263BINDING SITE FOR RESIDUE 9OD A 124
7AC7SOFTWAREARG B:81 , ALA B:112 , PHE B:117 , 9OD B:122BINDING SITE FOR RESIDUE 9OD B 121
8AC8SOFTWARELYS B:17 , ASP B:35 , LEU B:52 , LEU B:53 , LEU B:104 , VAL B:118 , ILE B:119 , 9OD B:121 , HOH B:218 , HOH B:294BINDING SITE FOR RESIDUE 9OD B 122
9AC9SOFTWAREGLU B:67 , GLN B:83 , MET B:86 , GLY B:87 , LEU B:90 , HOH B:290BINDING SITE FOR RESIDUE GOL B 123

(-) 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 3CZ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CZ0)

(-) Exons   (0, 0)

(no "Exon" information available for 3CZ0)

(-) 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:118
 aligned with Q9U9J6_APIME | Q9U9J6 from UniProtKB/TrEMBL  Length:144

    Alignment length:118
                                    36        46        56        66        76        86        96       106       116       126       136        
         Q9U9J6_APIME    27 PDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3cz0a_ A: Pheromone-binding protein asp1                                                                              SCOP domains
               CATH domains 3cz0A00 A:2-119  [code=1.10.238.20, no name defined]                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeehhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3cz0 A   2 PDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    11        21        31        41        51        61        71        81        91       101       111        


Chain B 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 d3cz0b_ B: Pheromone-binding protein asp1                                                                            SCOP domains
               CATH domains 3cz0B00 B:4-119  [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
                 3cz0 B   4 WVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    13        23        33        43        53        63        73        83        93       103       113
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  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 3CZ0)

(-) 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.

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  3cz0
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 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 3cyz 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
3cyz THE SAME PROTEIN IN COMPLEX WITH THE 9-KETO-2(E)-DECENOIC ACID 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