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 APICAL DOMAIN OF INSECTICIDAL GROEL FROM XENORHAPDUS NEMATOPHILA
 
Authors :  R. Viswanathan, A. Arockiasamy
Date :  10 Sep 10  (Deposition) - 05 Oct 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha, Beta, Apical Domain, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Viswanathan, B. Krishnadas, K. Shashi, L. M. Iyer, L. Aravind, B. Nirupama, A. Arockiasamy
Crystal Structure Of Apical Domain Of Insecticidal Groel From Xenorhapdus Nematophila
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 60 KDA CHAPERONIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: APICAL DOMAIN (UNP RESIDUES 191-376)
    Gene: GROEL, GROL
    Organism Scientific: XENORHABDUS NEMATOPHILA
    Organism Taxid: 628

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3OSX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OSX)

(-) 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:190
 aligned with Q6Y3X3_XENNE | Q6Y3X3 from UniProtKB/TrEMBL  Length:548

    Alignment length:190
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379
         Q6Y3X3_XENNE   190 VEGMQFDRGYLSPYFINKPESGSVELENPYILLVDKKISNIRELLPVLEGVAKASKPLVIIAEDVEGEALATLVVNNMRGIVKVASVKAPGFGDRRKAMLQDIATLTNGTVISEEIGLELEKATLEDLGQAKRVVINKDTTTIIDGVGEEGAIAARVTQIRQQIEESTSDYDREKLQERVAKLAGGVAVI 379
               SCOP domains d3osxa_ A: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....hhhhh.......eeee..eeeeeeeee.hhhhhhhhhhhhhh....eeeeeeeehhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhheeeeeeee....eeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3osx A 190 SEGMQFDRGYLSPYFINKPESGSVELENPYILLVDKKISNIRELLPVLEGVAKASKPLVIIAEDVEGEALATLVVNNMRGIVKVASVKAPGFGDRRKAMLQDIATLTNGTVISEEIGLELEKATLEDLGQAKRVVINKDTTTIIDGVGEEGAIAARVTQIRQQIEESTSDYDREKLQERVAKLAGGVKLN 379
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6Y3X3_XENNE | Q6Y3X3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0042026    protein refolding    The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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 3osx)
 
  Sites
(no "Sites" information available for 3osx)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3osx)
 

(-) 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
  3osx
    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
  Q6Y3X3_XENNE | Q6Y3X3
    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
  Q6Y3X3_XENNE | Q6Y3X3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3OSX)

(-) Related Entries Specified in the PDB File

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