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

(-) Description

Title :  SOLUTION STRUCTURE OF HOLO-NEOCARZINOSTATIN
 
Authors :  H. Takashima, T. Ishino, T. Yoshida, K. Hasuda, T. Ohkubo, Y. Kobayashi
Date :  04 Oct 03  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (60x)
Keywords :  Protein-Ligand Complex, 7 Stranded Beta Barrel, Cromoprotein, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Takashima, T. Yoshida, T. Ishino, K. Hasuda, T. Ohkubo, Y. Kobayashi
Solution Nmr Structure Investigation For Releasing Mechanism Of Neocarzinostatin Chromophore From The Holoprotein
J. Biol. Chem. V. 280 11340 2005
PubMed-ID: 15640161  |  Reference-DOI: 10.1074/JBC.M411579200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEOCARZINOSTATIN
    Chains: A
    Organism Scientific: STREPTOMYCES CARZINOSTATICUS
    Organism Taxid: 1897
    Other Details: PROTEIN WAS ISOTOPE LABELED BY PRE-ENRICHED CHLORELLA AS AMINO ACIDE SOURCE.
    Synonym: NCS, MITOMALCIN, MMC

 Structural Features

(-) Chains, Units

  
NMR Structure (60x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1CHR1Ligand/IonNEOCARZINOSTATIN-CHROMOPHORE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:35 , CYS A:37 , TRP A:39 , LEU A:45 , PHE A:76 , PHE A:78 , GLN A:94 , GLY A:96 , SER A:98 , GLY A:102 , ASN A:103BINDING SITE FOR RESIDUE CHR A 114

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:37 -A:47
2A:88 -A:93

(-) Cis Peptide Bonds  (1, 60)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60Thr A:8 -Pro A:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O5P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O5P)

(-) Exons   (0, 0)

(no "Exon" information available for 1O5P)

(-) 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:113
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:113
                                    44        54        64        74        84        94       104       114       124       134       144   
           NCZS_STRCZ    35 AAPTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN 147
               SCOP domains d1o5pa_ A: Neocarzinostatin                                                                                       SCOP domains
               CATH domains 1o5pA00 A:1-113  [code=2.60.40.230, no name defined]                                                              CATH domains
               Pfam domains ---Neocarzinostat-1o5pA01 A:4-113                                                                                 Pfam domains
         Sec.struct. author ................eeeeeee.......eeeeeeeee.....eee.....eeee......eeeeeee..eeeeee....eeeeee.....eeeeee........eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1o5p A   1 AAPTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN 113
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Neocarzinostat] (3)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (NCZS_STRCZ | P0A3R9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.

 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
    CHR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:8 - Pro A:9   [ 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 - model 1, sites 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
  1o5p
    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
  NCZS_STRCZ | P0A3R9
    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
  NCZS_STRCZ | P0A3R9
    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
        NCZS_STRCZ | P0A3R9: 1j5h 1j5i 1nco 1noa 2cbm 2cbo 2cbq 2cbt 2g0k 2g0l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1O5P)