3BFB - JenaLib

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Description

Title :   CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN FROM APIS MELLIFERA IN COMPLEX WITH THE 9-KETO-2(E)-DECENOIC ACID

Authors :   M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. T C. Cambillau

Date :   21 Nov 07 (Deposition) - 10 Jun 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Honeybee, Apis Mellifera, Pheromone Binding Protein, Signal Transduction, Queen Mandibular Pheromone, Pheromone-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. Tegoni, C. Cambillau
Structural Basis Of The Honey Bee Pbp Pheromone And Ph-Induced Conformational Change
J. Mol. Biol. V. 380 158 2008
PubMed-ID: 18508083 | Reference-DOI: 10.1016/J.JMB.2008.04.048

Compounds

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

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 4)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	9OD	1	Ligand/Ion	(2Z)-9-OXODEC-2-ENOIC ACID
2	CL	1	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	9OD	1	Ligand/Ion	(2Z)-9-OXODEC-2-ENOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	9OD	2	Ligand/Ion	(2Z)-9-OXODEC-2-ENOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	4	Ligand/Ion	GLYCEROL

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:12 , LEU A:52 , PHE A:56 , LEU A:73 , ILE A:119	BINDING SITE FOR RESIDUE 9OD A 121
2	AC2	SOFTWARE	TRP A:4 , TRP A:116 , PHE A:117	BINDING SITE FOR RESIDUE GOL A 122
3	AC3	SOFTWARE	ASP A:3 , TRP A:4 , PHE A:117	BINDING SITE FOR RESIDUE GOL A 123

SS Bonds (3, 3)

Asymmetric Unit

No.	Residues
1	A:20	-	A:51
2	A:47	-	A:98
3	A:89	-	A:107

Cis Peptide Bonds (2, 2)

Asymmetric Unit

No.	Residues
1	Asp A:3	-	Trp A:4
2	Leu A:90	-	Pro A:91

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

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

Exons (0, 0)

(no "Exon" information available for 3BFB)

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
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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 d3bfba_ A: Pheromone-binding protein asp1                                                                             SCOP domains
               CATH domains 3bfbA00 A:3-119  [code=1.10.238.20, no name defined]                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfb A   3 DWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    12        22        32        42        52        62        72        82        92       102       112

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, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: Insect pheromone/odorant-binding proteins (68)

Family: Insect pheromone/odorant-binding proteins (50)

Protein domain: Pheromone-binding protein asp1 (14)

Honeybee (Apis mellifera) [TaxId: 7460] (14)

d3bfba_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: [code=1.10.238.20, no name defined] (55)

Honeybee (Apis mellifera) (19)

3bfbA00

A:3-119

Pfam Domains (0, 0)

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

Gene Ontology (1, 1)

Asymmetric Unit(hide GO term definitions)

Chain A (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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	Ligands, Modified Residues, Ions
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	3bfb
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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	:	3bfh 3cyz 3cz0 3cz1 3cz2 3d73 3d74 3d75 3d76 3d77 3d78 3fe6 3fe8 3fe9

Related Entries Specified in the PDB File

1r5r	THE SAME PROTEIN COMPLEXED WITH N-BUTYL BENZENESULFANAMIDE
2h8v	UNCOMPLEXED FORM OF THE SAME PROTEIN
3bfa	THE SAME PROTEIN COMPLEXED WITH THE QUEEN MANDIBULAR PHEROMONE
3bfh	THE SAME PROEIN COMPLEXED WITH HEXADECANOIC ACID