Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF JUVENILE HORMONE BINDING PROTEIN FROM SILKWORM IN COMPLEX WITH JH III
 
Authors :  R. Suzuki, Z. Fujimoto, T. Shiotsuki, M. Momma, A. Tase, T. Yamazaki
Date :  27 Apr 09  (Deposition) - 05 May 10  (Release) - 19 Jun 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Juvenile Hormone, Hormone Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Suzuki, Z. Fujimoto, T. Shiotsuki, W. Tsuchiya, M. Momma, A. Tase, M. Miyazawa, T. Yamazaki
Structural Mechanism Of Jh Delivery In Hemolymph By Jhbp Of Silkworm, Bombyx Mori
Sci Rep V. 1 133 2011
PubMed-ID: 22355650  |  Reference-DOI: 10.1038/SREP00133
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOLYMPH JUVENILE HORMONE BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector: PGEX-2T
    Expression System Vector Type: VECTOR
    Fragment: UNP RESIDUES 19-243
    Organism Common: SILK MOTH,SILKWORM
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091
    Other Details: THE NUMBERING IN THE PDB FILE AND THE CONSTRAINT FILES ARE DIFFER. THIS IS BECAUSE THE PROGRAM SPARKY DOES NOT ACCEPT MINUS RESIDUE NUMBERS.
    Synonym: HJHBP

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1JH31Ligand/IonMETHYL (2E,6E)-9-[(2R)-3,3-DIMETHYLOXIRAN-2-YL]-3,7-DIMETHYLNONA-2,6-DIENOATE
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1JH31Ligand/IonMETHYL (2E,6E)-9-[(2R)-3,3-DIMETHYLOXIRAN-2-YL]-3,7-DIMETHYLNONA-2,6-DIENOATE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:17 , THR A:21 , LEU A:89 , TYR A:128 , PHE A:142 , ILE A:208 , PHE A:220BINDING SITE FOR RESIDUE JH3 A 300

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:9 -A:16
2A:151 -A:194

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Asp A:41 -Pro A:42
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Glu A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RQF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RQF)

(-) Exons   (0, 0)

(no "Exon" information available for 2RQF)

(-) Sequences/Alignments

NMR Structure
   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:227
 aligned with Q9U556_BOMMO | Q9U556 from UniProtKB/TrEMBL  Length:243

    Alignment length:227
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       
         Q9U556_BOMMO    17 ASDGDALLKPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGNNSLEPDMEPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFENLN 243
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -JHBP-2rqfA01 A:-1-221                                                                                                                                                                                                         ---- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhh.............eee..eeee......eeeeeeeeeee.....eeeeeeee....eeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeeee.....eeeee...eeeeee....eeeehhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rqf A  -2 GSDGDALLKPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGNNSLEPDMEPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFENLN 225
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       
                             ||                                                                                                                                                                                                                                
                            -1|                                                                                                                                                                                                                                
                              1
   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 2RQF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RQF)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: JHBP] (2)

(-) Gene Ontology  (1, 1)

NMR Structure(hide GO term definitions)
Chain A   (Q9U556_BOMMO | Q9U556)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 Visualization

(-) Interactive Views

NMR Structure
  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
    JH3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:41 - Pro A:42   [ RasMol ]  
    Glu A:183 - Pro A:184   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  2rqf
    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
  Q9U556_BOMMO | Q9U556
    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
  Q9U556_BOMMO | Q9U556
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9U556_BOMMO | Q9U556: 3a1z 3aos 3aot

(-) Related Entries Specified in the PDB File

3aos 3aot