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 N-TERMINAL DOMAIN OF HUMAN CONSERVED DOPAMINE NEUROTROPHIC FACTOR (CDNF)
 
Authors :  C. Latge, K. M. S. Cabral, D. Foguel, J. R. M. Pires, M. S. Almeida
Date :  15 Feb 12  (Deposition) - 20 Feb 13  (Release) - 22 May 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Nerve Growth Factor, Neurotrophic Factor, Intercellular Signaling Protein, Nerve Tissue Protein, Neuronal Growth-Associated, Hormone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Latge, K. M. Cabral, M. S. Almeida, D. Foguel
(1)H-, (13)C- And (15)N-Nmr Assignment Of The N-Terminal Domain Of Human Cerebral Dopamine Neurotrophic Factor (Cdnf).
Biomol. Nmr Assign. V. 7 101 2013
PubMed-ID: 22528768  |  Reference-DOI: 10.1007/S12104-012-9388-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CEREBRAL DOPAMINE NEUROTROPHIC FACTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainROSETTA GAMI B (DE3)
    Expression System Taxid562
    Expression System VectorPET25B
    FragmentUNP RESIDUES 27-131
    GeneCDNF, ARMETL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymARMET-LIKE PROTEIN 1, CONSERVED DOPAMINE NEUROTROPHIC FACTOR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2LPN)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:11 -A:98
2A:14 -A:87
3A:45 -A:56

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LPN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2LPN)

(-) 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:105
 aligned with CDNF_HUMAN | Q49AH0 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           CDNF_HUMAN    27 QEAGGRPGADCEVCKEFLNRFYKSLIDRGVNFSLDTIEKELISFCLDTKGKENRLCYYLGATKDAATKILSEVTRPMSVHMPAMKICEKLKKLDSQICELKYEKT 131
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2lpn A   1 QEAGGRPGADCEVCKEFLNRFYKSLIDRGVNFSLDTIEKELISFCLDTKGKENRLCYYLGATKDAATKILSEVTRPMSVHMPAMKICEKLKKLDSQICELKYEKT 105
                                    10        20        30        40        50        60        70        80        90       100     

   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 2LPN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A   (CDNF_HUMAN | Q49AH0)
molecular function
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
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

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 2lpn)
 
  Sites
(no "Sites" information available for 2lpn)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2lpn)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2lpn
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CDNF_HUMAN | Q49AH0
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CDNF_HUMAN | Q49AH0
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CDNF_HUMAN | Q49AH02w50 4bit

(-) Related Entries Specified in the PDB File

2w50 STRUCTURE SOLVED BY X-RAY CRYSTALLOGRAPHY. RECOMBINANT PROTEIN PRODUCED IN SPODOPTERA FRUGIPERDA. RELATED ID: 18269 RELATED DB: BMRB