3D73 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN MUTANT D35A, 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 :   2.03

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)

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NBB	3	Ligand/Ion	N-BUTYL-BENZENESULFONAMIDE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	NBB	3	Ligand/Ion	N-BUTYL-BENZENESULFONAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NBB	1	Ligand/Ion	N-BUTYL-BENZENESULFONAMIDE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	NBB	2	Ligand/Ion	N-BUTYL-BENZENESULFONAMIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:49 , LEU A:53 , MET A:70 , TRP A:116 , PHE A:117 , VAL A:118 , HOH A:184	BINDING SITE FOR RESIDUE NBB A 120
2	AC2	SOFTWARE	MET B:49 , LEU B:52 , LEU B:53 , VAL B:115 , TRP B:116 , PHE B:117 , VAL B:118	BINDING SITE FOR RESIDUE NBB B 120
3	AC3	SOFTWARE	TRP B:4 , PRO B:6 , VAL B:9 , LEU B:12 , LEU B:58 , ASP B:68 , MET B:70 , GLY B:72 , LEU B:73 , LEU B:74 , PRO B:75 , PHE B:117	BINDING SITE FOR RESIDUE NBB B 121

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Leu A:90	-	Pro A:91
2	Leu B:90	-	Pro B:91

(no "SAP(SNP)/Variant" information available for 3D73)

(no "PROSITE Motif" information available for 3D73)

(no "Exon" information available for 3D73)

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 d3d73a_ A: automated matches                                                                                            SCOP domains
               CATH domains 3d73A00 A:1-119  [code=1.10.238.20, no name defined]                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh.hhhhhhhh.......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3d73 A   1 APDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVAKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 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 d3d73b_ B: automated matches                                                                                            SCOP domains
               CATH domains 3d73B00 B:1-119  [code=1.10.238.20, no name defined]                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3d73 B   1 APDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVAKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    10        20        30        40        50        60        70        80        90       100       110

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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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: automated matches (12)

Honeybee (Apis mellifera) [TaxId: 7460] (6)

1a	d3d73a_	A:
1b	d3d73b_	B:

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)

1a	3d73A00	A:1-119
1b	3d73B00	B:1-119

(no "Pfam Domain" information available for 3D73)

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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		Leu A:90 - Pro A:91	[ RasMol ]
		Leu B:90 - Pro B:91	[ RasMol ]

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

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
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
3d78	THE DIMERIC STRUCTURE OF THE SAME MUTANT D35N PROTEIN IN COMPLEX WITH THE N-BUTYL BENZENE SULFONAMIDE AT PH 7.0

Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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CATH Domains (1, 2)

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Gene Ontology (1, 1)

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