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(-) Description

Title :  DIMERIC CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN MUTANT D35N, FROM APIS MELLIFERA, AT PH 7.0
 
Authors :  M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. Tegoni, C. Cambillau
Date :  20 May 08  (Deposition) - 26 May 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Pheromone Binding Protein, Honey Bee, Apis Mellifera, Signal Transduction, Queen Mandibular Protein, Ph (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
(for further references see the PDB file header)

(-) 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
    Mutation: YES
    Organism Common: HONEYBEE
    Organism Scientific: APIS MELLIFERA
    Organism Taxid: 7460

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2NBB3Ligand/IonN-BUTYL-BENZENESULFONAMIDE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2NBB3Ligand/IonN-BUTYL-BENZENESULFONAMIDE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2NBB1Ligand/IonN-BUTYL-BENZENESULFONAMIDE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NBB2Ligand/IonN-BUTYL-BENZENESULFONAMIDE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:49 , VAL A:115 , TRP A:116 , PHE A:117 , VAL A:118 , ILE A:119 , EDO A:122BINDING SITE FOR RESIDUE NBB A 120
2AC2SOFTWAREARG A:81 , SER A:84 , VAL A:85 , SER A:111 , HOH A:130 , HOH B:132BINDING SITE FOR RESIDUE EDO A 121
3AC3SOFTWAREMET A:70 , VAL A:85 , MET A:86 , TRP A:116 , NBB A:120BINDING SITE FOR RESIDUE EDO A 122
4AC4SOFTWAREVAL A:9 , LEU A:73 , LEU A:74 , PHE A:117BINDING SITE FOR RESIDUE EDO A 123
5AC5SOFTWAREMET A:21 , SER A:22 , GLY A:25 , THR A:26 , HOH A:200 , HOH A:232BINDING SITE FOR RESIDUE EDO A 124
6AC6SOFTWARETYR A:102 , HOH A:169 , HOH A:175BINDING SITE FOR RESIDUE EDO A 125
7AC7SOFTWAREMET B:49 , LEU B:52 , LEU B:53 , VAL B:115 , PHE B:117 , VAL B:118BINDING SITE FOR RESIDUE NBB B 120
8AC8SOFTWARETRP B:4 , VAL B:9 , LEU B:12 , LEU B:58 , ASP B:68 , MET B:70 , LEU B:73 , LEU B:74 , PRO B:75 , PHE B:117BINDING SITE FOR RESIDUE NBB B 121
9AC9SOFTWAREASN B:41 , HOH B:159BINDING SITE FOR RESIDUE EDO B 122

(-) SS Bonds  (6, 6)

Asymmetric 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 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 3D78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D78)

(-) Exons   (0, 0)

(no "Exon" information available for 3D78)

(-) Sequences/Alignments

Asymmetric 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:119
 aligned with Q9U9J6_APIME | Q9U9J6 from UniProtKB/TrEMBL  Length:144

    Alignment length:119
                                    35        45        55        65        75        85        95       105       115       125       135         
         Q9U9J6_APIME    26 APDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3d78a_ A: automated matches                                                                                            SCOP domains
               CATH domains 3d78A00 A:1-119  [code=1.10.238.20, no name defined]                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3d78 A   1 APDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVNKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with Q9U9J6_APIME | Q9U9J6 from UniProtKB/TrEMBL  Length:144

    Alignment length:119
                                    35        45        55        65        75        85        95       105       115       125       135         
         Q9U9J6_APIME    26 APDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3d78b_ B: automated matches                                                                                            SCOP domains
               CATH domains 3d78B00 B:1-119  [code=1.10.238.20, no name defined]                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3d78 B   1 APDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVNKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    10        20        30        40        50        60        70        80        90       100       110
   Legend:   → Mismatch (orange background)
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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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D78)

(-) Gene Ontology  (1, 1)

Asymmetric 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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  3d78
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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 3cz1 3cz2 3d73 3d74 3d75 3d76 3d77 3fe6 3fe8 3fe9

(-) Related Entries Specified in the PDB File

2h8v THE APO FORM OF THE SAME NATIVE PROTEIN AT PH 5.5
3bfa THE SAME NATIVE PROTEIN IN COMPLEX WITH THE QUEEN MANDIBULAR PHEROMONE AT PH 5.5
3bfb THE SAME NATIVE PROTEIN IN COMPLEX WITH THE 9-KETO-2(E)- DECENOIC ACID AT PH 5.5
3bfh THE SAME NATIVE PROTEIN IN COMPLEX WITH THE HEXADECANOIC ACID AT PH 5.5
3bjh THE SAME NATIVE PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE AT PH 5.5
3cab THE SAME NATIVE PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE SOAKED AT PH 7.0
3cdn THE APO FORM OF THE SAME NATIVE PROTEIN SOAKED AT PH 4.0
3cyz THE SAME NATIVE PROTEIN IN COMPLEX WITH THE 9-KETO-2(E)- DECENOIC ACID AT PH 7.0
3cz0 THE SAME NATIVE PROTEIN IN COMPLEX WITH THE QUEEN MANDIBULAR PHEROMONE AT PH 7.0
3cz1 THE SAME NATIVE PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE AT PH 7.0
3cz2 THE APO FORM OF THE SAME NATIVE PROTEIN AT PH 7.0
3d73 THE D35A MUTANT PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE AT PH 7.0
3d74 THE D35A MUTANT PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE SOAKED AT PH 5.5
3d75 THE SAME MUTANT D35N PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE AT PH 5.5
3d76 THE SAME MUTANT D35N PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE SOAKED AT PH 7.0
3d77 THE SAME MUTANT D35N PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE SOAKED AT PH 4.0