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 - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE NON-CANONICAL MCOL5 OF HYDRA NEMATOCYSTS
 
Authors :  S. Meier, S. Oezbek, S. Grzesiek
Date :  31 Jan 07  (Deposition) - 18 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Disulfide, Cis-Proline, Nematocyst, Non-Canonical Crd, Cysteine-Rich Domain, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Adamczyk, S. Meier, T. Gross, B. Hobmayer, S. Grzesiek, H. P. Bachinger, T. W. Holstein, S. Ozbek
Minicollagen-15, A Novel Minicollagen Isolated From Hydra, Forms Tubule Structures In Nematocysts.
J. Mol. Biol. V. 376 1008 2008
PubMed-ID: 18206162  |  Reference-DOI: 10.1016/J.JMB.2007.10.090
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MINICOLLAGEN-5
    Chains: A
    Engineered: YES
    Other Details: WILD TYPE SEQUENCE OBTAINED BY SOLID PHASE SYNTHESIS AND OXIDATIVE REFOLDING
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2OQ9)

(-) Sites  (0, 0)

(no "Site" information available for 2OQ9)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:13 -A:22
2A:17 -A:21

(-) Cis Peptide Bonds  (1, 10)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10Ala A:18 -Pro A:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OQ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OQ9)

(-) Exons   (0, 0)

(no "Exon" information available for 2OQ9)

(-) 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:24
 aligned with A6N8P1_HYDVU | A6N8P1 from UniProtKB/TrEMBL  Length:260

    Alignment length:24
                                   246       256    
         A6N8P1_HYDVU   237 APMQAPVQAAPACMASCAPQCCGR 260
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ........................ Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 2oq9 A   1 APMQAPVQAAPACMASCAPQCCGR  24
                                    10        20
   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 2OQ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OQ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OQ9)

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A   (A6N8P1_HYDVU | A6N8P1)
cellular component
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    GO:0042151    nematocyst    An organelle found in cnidoblast (nematoblast) cells. When matured, these stinging organelles store toxins and can deliver them when the cnidocil (a short extension of the cnidocyst) is stimulated by a prey or another stimulus.

 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
(no "Ligands, Modified Residues, Ions" information available for 2oq9)
 
  Sites
(no "Sites" information available for 2oq9)
 
  Cis Peptide Bonds
    Ala A:18 - Pro A:19   [ 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 - 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
  2oq9
    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
  A6N8P1_HYDVU | A6N8P1
    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
  A6N8P1_HYDVU | A6N8P1
    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 2OQ9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OQ9)