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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BOMBYX MORI LOW MOLECULAR WEIGHT LIPOPROTEIN 7 (BMLP7)
 
Authors :  J. -P. Yang, X. -X. Ma, Y. -X. He, W. -F. Li, Y. Kang, R. Bao, Y. Chen, C. -Z. Z
Date :  03 Dec 10  (Deposition) - 01 Jun 11  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Trefoil Fold, Haemolymph, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. -P. Yang, X. -X. Ma, Y. -X. He, W. -F. Li, Y. Kang, R. Bao, Y. Chen, C. -Z. Zhou
Crystal Structure Of The 30 K Protein From The Silkworm Bombyx Mori Reveals A New Member Of The Beta-Trefoil Superfamily
J. Struct. Biol. V. 175 97 2011
PubMed-ID: 21514389  |  Reference-DOI: 10.1016/J.JSB.2011.04.003

(-) Compounds

Molecule 1 - 30KDA PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SILK MOTH, SILKWORM
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091
    Synonym: LOW MOLECULAR WEIGHT LIPOPROTEIN 7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3PUB)

(-) Sites  (0, 0)

(no "Site" information available for 3PUB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PUB)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PUB)

(-) 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:235
 aligned with E5EVW2_BOMMO | E5EVW2 from UniProtKB/TrEMBL  Length:256

    Alignment length:235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         E5EVW2_BOMMO    22 VPNDILEEQLYNSIVVADYDSAVEKSKHLYEEKKSEVITNVVNKLIRNNKMNCMEYAYQLWLQGSKDIVRDCFPVEFRLIFAENAIKLMYKRDGLALTLSNDVHGNDGRLAFGDGKDKTSPKVSWKFIALWENNKVYFKILNTERNQYLVLGVGTNPNGDHMAFGVNSVDSFRAQWYLQPAKYDKDNLFYIYNREYSKALTLSRTLETSGNRMAWGYNGRVIGSPEHYAWGVKAF 256
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeee....eeeee.........eeeee......hhhh.eeeeeeee..eeeeeeee....eeeeeeeee.....eeeeee....hhhh.eeeeeeee..eeeeeeee.....eeee.........eeeeee......hhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pub A  50 VPNDILEEQLYNSIVVADYDSAVEKSKHLYEEKKSEVITNVVNKLIRNNKMNCMEYAYQLWLQGSKDIVRDCFPVEFRLIFAENAIKLMYKRDGLALTLSNDVHGNDGRLAFGDGKDKTSPKVSWKFIALWENNKVYFKILNTERNQYLVLGVGTNPNGDHMAFGVNSVDSFRAQWYLQPAKYDKDNLFYIYNREYSKALTLSRTLETSGNRMAWGYNGRVIGSPEHYAWGVKAF 284
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     


Chain B from PDB  Type:PROTEIN  Length:236
 aligned with E5EVW2_BOMMO | E5EVW2 from UniProtKB/TrEMBL  Length:256

    Alignment length:236
                                                                                                                                                                                                                                                                    256 
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    | 
         E5EVW2_BOMMO    22 VPNDILEEQLYNSIVVADYDSAVEKSKHLYEEKKSEVITNVVNKLIRNNKMNCMEYAYQLWLQGSKDIVRDCFPVEFRLIFAENAIKLMYKRDGLALTLSNDVHGNDGRLAFGDGKDKTSPKVSWKFIALWENNKVYFKILNTERNQYLVLGVGTNPNGDHMAFGVNSVDSFRAQWYLQPAKYDKDNLFYIYNREYSKALTLSRTLETSGNRMAWGYNGRVIGSPEHYAWGVKAF-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Lipoprotein_11-3pubB01 B:50-284                                                                                                                                                                                                            - Pfam domains (1)
           Pfam domains (2) Lipoprotein_11-3pubB02 B:50-284                                                                                                                                                                                                            - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeee....eeeee....hhhhheeeeee.....hhhh.eeeeeeee..eeeeeeee....eeeeeeeee.....eeeeee....hhhh.eeeeeeee..eeeeeeee.....eeeeeeee.....eeeeee......hhhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pub B  50 VPNDILEEQLYNSIVVADYDSAVEKSKHLYEEKKSEVITNVVNKLIRNNKMNCMEYAYQLWLQGSKDIVRDCFPVEFRLIFAENAIKLMYKRDGLALTLSNDVHGNDGRLAFGDGKDKTSPKVSWKFIALWENNKVYFKILNTERNQYLVLGVGTNPNGDHMAFGVNSVDSFRAQWYLQPAKYDKDNLFYIYNREYSKALTLSRTLETSGNRMAWGYNGRVIGSPEHYAWGVKAFA 285
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
   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 3PUB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Lipoprotein_11] (1)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (E5EVW2_BOMMO | E5EVW2)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
(no "Ligands, Modified Residues, Ions" information available for 3pub)
 
  Sites
(no "Sites" information available for 3pub)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pub)
 

(-) 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 ](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
  3pub
    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
  E5EVW2_BOMMO | E5EVW2
    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
  E5EVW2_BOMMO | E5EVW2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        E5EVW2_BOMMO | E5EVW2: 4efp 4efq 4efr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3PUB)