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 :  SOLUTION STRUCTURE OF THE PKD DOMAIN FROM HUMAN VPS10 DOMAIN-CONTAINING RECEPTOR SORCS2
 
Authors :  E. Chikayama, T. Kigawa, N. Tochio, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Polycystic Kidney Disease, Pkd, Structural Genomics, Kiaa1329 Protein, Riken Structural Genomics/Proteomics Initiative, Rsgi, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Chikayama, T. Kigawa, N. Tochio, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Pkd Domain From Human Vps10 Domain-Containing Receptor Sorcs2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VPS10 DOMAIN-CONTAINING RECEPTOR SORCS2
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040119-67
    Expression System Vector Type: PLASMID
    Fragment: PKD DOMAIN
    Gene: KAZUSA CDNA FH14788
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1WGO)

(-) Sites  (0, 0)

(no "Site" information available for 1WGO)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WGO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WGO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WGO)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PKDPS50093 Polycystic kidney disease (PKD) domain profile.SORC2_HUMAN816-876  1A:64-120

(-) Exons   (0, 0)

(no "Exon" information available for 1WGO)

(-) 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:123
 aligned with SORC2_HUMAN | Q96PQ0 from UniProtKB/Swiss-Prot  Length:1159

    Alignment length:160
                                   725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875
          SORC2_HUMAN   716 SSSESSTNKCSANFWFNPLSPPDDCALGQTYTSSLGYRKVVSNVCEGGVDMQQSQVQLQCPLTPPRGLQVSIQGEAVAVRPGEDVLFVVRQEQGDVLTTKYQVDLGDGFKAMYVNLTLTGEPIRHRYESPGIYRVSVRAENTAGHDEAVLFVQVNSPLQA 875
               SCOP domains d1wgoa_                                      A: VPS10 domain-containing receptor SorCS2                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------PKD-1wgoA01 A:35-111                                                         ------------ Pfam domains
         Sec.struct. author .......-------------------------------------.......................eeeee............eeeeeee........eeeee.....eeeeehhhhhh..eee.......eeeeeeee....eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------PKD  PDB: A:64-120 UniProt: 816-876                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wgo A   1 GSSGSSG-------------------------------------CEGGVDMQQSQVQLQCPLTPPRGLQVSIQGEAVAVRPGEDVLFVVRQEQGDVLTTKYQVDLGDGFKAMYVNLTLTGEPIRHRYESPGIYRVSVRAENTAGHDEAVLFVQVSGPSSG 123
                                  |  -         -         -         -    |   13        23        33        43        53        63        73        83        93       103       113       123
                                  7                                     8
   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)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WGO)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: E-set (290)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (SORC2_HUMAN | Q96PQ0)
molecular function
    GO:0008188    neuropeptide receptor activity    Combining with a neuropeptide to initiate a change in cell activity.
biological process
    GO:0007218    neuropeptide signaling pathway    The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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 1wgo)
 
  Sites
(no "Sites" information available for 1wgo)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wgo)
 

(-) 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
  1wgo
    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
  SORC2_HUMAN | Q96PQ0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  SORC2_HUMAN | Q96PQ0
    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 1WGO)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WGO)