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

(-) Description

Title :  CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE, WITH MUTATION V321A, COMPLEXED WITH 2',5'-ADP
 
Authors :  M. Myllykoski, A. Raasakka, P. Kursula
Date :  08 Sep 14  (Deposition) - 23 Sep 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Myelin, Nervous System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Raasakka, M. Myllykoski, S. Laulumaa, M. Lehtimaki, M. Hartlein, M. Moulin, I. Kursula, P. Kursula
Determinants Of Ligand Binding And Catalytic Activity In Th Myelin Enzyme 2', 3'-Cyclic Nucleotide 3'-Phosphodiesterase.
Sci Rep V. 5 16520 2015
PubMed-ID: 26563764  |  Reference-DOI: 10.1038/SREP16520

(-) Compounds

Molecule 1 - 2',3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
    Chains: A
    EC Number: 3.1.4.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PTH27
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 179-378
    Gene: CNP, CNP1
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: CNPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1A2P1Ligand/IonADENOSINE-2'-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:167 , TYR A:168 , HIS A:230 , THR A:232 , PHE A:235 , HIS A:309 , THR A:311 , PRO A:320 , ALA A:321 , HOH A:566binding site for residue A2P A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WDF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WDF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WDF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WDF)

(-) Exons   (0, 0)

(no "Exon" information available for 4WDF)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh........eeeeee.hhhh..hhhhhhhhhhhhhhh..eeeeeeeeeee...eeeeeee.hhhhhh........hhhhh........eeeeee......hhhhhhhhhhhhhhh........eee..eeeee.....eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wdf A 163 DFLPLYFGWFLTKKSSETLRKAGQVFLEELGNHKAFKKELRHFISGDEKLELVSYFGKRPPGVLHCTTKFCDYGKAAGAEEYAQQEVVKRSYGKAFKLSISALFVTPKTAGAQVVLTDQELQLWPSDLDKPSASEGLPPGSRAHVTLGCAADVQPAQTGLDLLDILQQVKGGSQGEAVGELPRGKLYSLGKGRWMLSLTKKMEVKAIFTGYYG 378
                                   172       182       192       202      |215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375   
                                                                        209|                                                                                                                                                                     
                                                                         213
   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 4WDF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WDF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WDF)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    A2P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4wdf)
 

(-) 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 | Asym./Biol. Unit - sites 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
  4wdf
    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
  CN37_MOUSE | P16330
    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)
  3.1.4.37
    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
  CN37_MOUSE | P16330
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CN37_MOUSE | P16330: 2xmi 2y1p 2y3x 2ydb 2ydc 2ydd 2yoz 2yp0 2ypc 2ype 2yph 2yq9 3zbr 3zbs 3zbz 4wbi 4wbl 4wc9 4wca 4wcb 4wcc 4wda 4wdb 4wdd 4wde 4wdg 4wdh 4wex 4wfr 5ae0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4WDF)