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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 :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Honey Bee, 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
1CL3Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4NBB3Ligand/IonN-BUTYL-BENZENESULFONAMIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:246 , HOH A:248 , HOH A:267 , HOH B:329 , HOH B:330 , HOH B:331BINDING SITE FOR RESIDUE MG A 120
02AC2SOFTWAREPHE A:10 , ASP A:11 , GLU A:15BINDING SITE FOR RESIDUE CL A 121
03AC3SOFTWAREASN B:64 , VAL B:65 , PRO B:91 , THR B:92 , HOH B:276BINDING SITE FOR RESIDUE CL B 120
04AC4SOFTWAREHIS A:24 , HOH A:218 , SER B:93 , GLY B:94BINDING SITE FOR RESIDUE CL B 121
05AC5SOFTWAREMET A:49 , LEU A:52 , PHE A:117 , VAL A:118 , ILE A:119 , HOH A:274BINDING SITE FOR RESIDUE NBB A 122
06AC6SOFTWAREMET B:49 , LEU B:52 , LEU B:53 , ILE B:119BINDING SITE FOR RESIDUE NBB B 122
07AC7SOFTWAREMET B:70 , LEU B:73 , ARG B:81 , ALA B:82 , MET B:86 , VAL B:108 , ALA B:112 , VAL B:115 , PHE B:117BINDING SITE FOR RESIDUE NBB B 123
08AC8SOFTWAREARG A:19 , SER A:22 , HOH A:148 , HOH A:187 , HOH A:217 , GLN B:77BINDING SITE FOR RESIDUE GOL A 123
09AC9SOFTWAREALA B:14 , ALA B:18 , MET B:21 , GLN B:28 , ILE B:31BINDING SITE FOR RESIDUE GOL B 124
10BC1SOFTWAREHOH A:208 , HIS B:24 , PRO B:43 , HOH B:320 , HOH B:363BINDING SITE FOR RESIDUE GOL B 125

(-) 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 3CZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3CZ1)

(-) 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:117
 aligned with Q9U9J6_APIME | Q9U9J6 from UniProtKB/TrEMBL  Length:144

    Alignment length:117
                                    37        47        57        67        77        87        97       107       117       127       137       
         Q9U9J6_APIME    28 DWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3cz1a_ A: Pheromone-binding protein asp1                                                                             SCOP domains
               CATH domains 3cz1A00 A:3-119  [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
                 3cz1 A   3 DWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    12        22        32        42        52        62        72        82        92       102       112       


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 d3cz1b_ B: Pheromone-binding protein asp1                                                                           SCOP domains
               CATH domains 3cz1B00 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
                 3cz1 B   5 VPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    14        24        34        44        54        64        74        84        94       104       114
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  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 3CZ1)

(-) 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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    Leu A:90 - Pro A:91   [ RasMol ]  
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  3cz1
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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 3cz0 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 IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE SOAKED AT PH 7.0
3cdn THE APO FORM OF THE SAME PROTEIN SOAKED AT PH 4.0
3cyz THE SAME PROTEIN IN COMPLEX WITH THE 9-KETO-2(E)-DECENOIC ACID AT PH 7.0
3cz0 THE SAME PROTEIN IN COMPLEX WITH THE QUEEN MANDIBULAR PHEROMONE AT PH 7.0
3cz2 THE APO FORM OF THE SAME PROTEIN AT PH 7.0