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 :  CRYSTAL STRUCTURE OF AN ANOPHELES GAMBIAE ODORANT-BINDING PROTEIN AGAMOBP22A WITH BOUND ODORANT CYCLOHEXANONE
 
Authors :  H. Ren, S. Zhang
Date :  04 Feb 11  (Deposition) - 23 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Six Alpha Helix, Three Disulfate Bonds, Odorant-Binding Protein, Mosquito, Cyclohexanone, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ren, G. Yang, G. Winberg, L. Turin, S. Zhang
Crystal Structures Of An Anopheles Gambiae Odorant-Binding Protein Agamobp22A And Complexes With Bound Odorants
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ODORANT BINDING PROTEIN (AGAP010409-PA)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)-STAR-PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: AGAMOBP22A, UNP RESIDUES 22-144
    Gene: AGAMOBP22A, AGAP010409, OBP22, OBPJJ83B
    Organism Common: AFRICAN MALARIA MOSQUITO
    Organism Scientific: ANOPHELES GAMBIAE
    Organism Taxid: 180454
    Strain: PEST
    Synonym: ODORANT-BINDING PROTEIN OBPJJ83B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CYH1Ligand/IonCYCLOHEXANONE
2NH44Ligand/IonAMMONIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:63 , GLY A:67 , LEU A:72 , TYR A:73 , ASN A:84 , ALA A:121 , PHE A:125 , LEU A:128BINDING SITE FOR RESIDUE CYH A 200
2AC2SOFTWARELEU A:44 , ASP A:95 , GLU A:96 , HOH A:206BINDING SITE FOR RESIDUE NH4 A 201
3AC3SOFTWARELEU A:106 , GLU A:107 , ASN A:110 , LEU A:111 , HIS A:157 , HOH A:222BINDING SITE FOR RESIDUE NH4 A 202
4AC4SOFTWAREASN A:71 , ASP A:80 , ALA A:83 , HOH A:220 , HOH A:241BINDING SITE FOR RESIDUE NH4 A 203
5AC5SOFTWAREASN A:34 , ASN A:71 , GLU A:153 , HOH A:212 , HOH A:241BINDING SITE FOR RESIDUE NH4 A 204

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:32 -A:65
2A:61 -A:118
3A:105 -A:127

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QME)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QME)

(-) 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:119
 aligned with Q7PGA3_ANOGA | Q7PGA3 from UniProtKB/TrEMBL  Length:144

    Alignment length:120
                                                                                                                                                144 
                                    35        45        55        65        75        85        95       105       115       125       135        |-
         Q7PGA3_ANOGA    26 ESVIESCSNAVQGAANDELKVHYRANEFPDDPVTHCFVRCIGLELNLYDDKYGVDLQANWENLGNSDDADEEFVAKHRACLEAKNLETIEDLCERAYSAFQCLREDYEMYQNNNNATSE-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains PBP_GOBP-3qmeA01 A:26-133                                                                                   ------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhh..ee...eehhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.-...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qme A  26 ESVIESCSNAVQGAANDELKVHYRANEFPDDPVTHCFVRCIGLELNLYDDKYGVDLQANWENLGNSDDADEEFVAKHRACLEAKNLETIEDLCERAYSAFQCLREDYEMYQNN-ELWSHP 158
                                    35        45        55        65        75        85        95       105       115       125       135  | |  158
                                                                                                                                          138 |     
                                                                                                                                            153
   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  (0, 0)

(no "SCOP Domain" information available for 3QME)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QME)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PBP_GOBP] (36)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7PGA3_ANOGA | Q7PGA3)
molecular function
    GO:0005549    odorant binding    Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.

 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
    CYH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qme)
 

(-) 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
  3qme
    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
  Q7PGA3_ANOGA | Q7PGA3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q7PGA3_ANOGA | Q7PGA3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7PGA3_ANOGA | Q7PGA3: 3l47 3l4a 3l4l 3pji

(-) Related Entries Specified in the PDB File

3l47 AGAMOBP22A WITH TWO AU ION
3l4a AGAMOBP22A WITH A NATIVE GLYCEROL
3l4l AGAMOBP22A WITH A BINDING LIGAND BENZALDEHYDE
3pji AGAMOBP22A IN ITS OPEN STATUS