Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  BOMBYX MORI PHEROMONE BINDING PROTEIN
 
Authors :  B. H. Sandler, L. Nikonova, W. S. Leal, J. Clardy
Date :  04 Jan 00  (Deposition) - 10 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Helical Bundle, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. H. Sandler, L. Nikonova, W. S. Leal, J. Clardy
Sexual Attraction In The Silkworm Moth: Structure Of The Pheromone-Binding-Protein-Bombykol Complex.
Chem. Biol. V. 7 143 2000
PubMed-ID: 10662696  |  Reference-DOI: 10.1016/S1074-5521(00)00078-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHEROMONE-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: DOMESTIC SILKWORM
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091
    Synonym: PBP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1BOM2Ligand/IonHEXADECA-10,12-DIEN-1-OL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:12 , SER A:56 , HOH A:338BINDING SITE FOR RESIDUE BOM A 300
2AC2SOFTWAREPHE B:12 , SER B:56 , MET B:61 , LEU B:68 , PHE B:118BINDING SITE FOR RESIDUE BOM B 400

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:19 -A:54
2A:50 -A:108
3A:97 -A:117
4B:19 -B:54
5B:50 -B:108
6B:97 -B:117

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DQE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DQE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DQE)

(-) Exons   (0, 0)

(no "Exon" information available for 1DQE)

(-) 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:137
 aligned with PBP_BOMMO | P34174 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:137
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       
            PBP_BOMMO    23 SQEVMKNLSLNFGKALDECKKEMTLTDAINEDFYNFWKEGYEIKNRETGCAIMCLSTKLNMLDPEGNLHHGNAMEFAKKHGADETMAQQLIDIVHGCEKSTPANDDKCIWTLGVATCFKAEIHKLNWAPSMDVAVGE 159
               SCOP domains d1dqea_ A: Moth pheromone-binding protein, PBP                                                                                            SCOP domains
               CATH domains 1dqeA00 A:1-137  [code=1.10.238.20, no name defined]                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.........hhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dqe A   1 SQEVMKNLSLNFGKALDECKKEMTLTDAINEDFYNFWKEGYEIKNRETGCAIMCLSTKLNMLDPEGNLHHGNAMEFAKKHGADETMAQQLIDIVHGCEKSTPANDDKCIWTLGVATCFKAEIHKLNWAPSMDVAVGE 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain B from PDB  Type:PROTEIN  Length:137
 aligned with PBP_BOMMO | P34174 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:137
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       
            PBP_BOMMO    23 SQEVMKNLSLNFGKALDECKKEMTLTDAINEDFYNFWKEGYEIKNRETGCAIMCLSTKLNMLDPEGNLHHGNAMEFAKKHGADETMAQQLIDIVHGCEKSTPANDDKCIWTLGVATCFKAEIHKLNWAPSMDVAVGE 159
               SCOP domains d1dqeb_ B: Moth pheromone-binding protein, PBP                                                                                            SCOP domains
               CATH domains 1dqeB00 B:1-137  [code=1.10.238.20, no name defined]                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dqe B   1 SQEVMKNLSLNFGKALDECKKEMTLTDAINEDFYNFWKEGYEIKNRETGCAIMCLSTKLNMLDPEGNLHHGNAMEFAKKHGADETMAQQLIDIVHGCEKSTPANDDKCIWTLGVATCFKAEIHKLNWAPSMDVAVGE 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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, 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 1DQE)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PBP_BOMMO | P34174)
molecular function
    GO:0005549    odorant binding    Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.
    GO:0005550    pheromone binding    Interacting selectively and non-covalently with a pheromone, a substance, or characteristic mixture of substances, that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process.
biological process
    GO:0019236    response to pheromone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BOM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dqe)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1dqe
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PBP_BOMMO | P34174
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PBP_BOMMO | P34174
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PBP_BOMMO | P34174: 1gm0 1ls8 1xfr 2fjy 2p70 2p71

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DQE)