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 :  SEQUENTIAL 1H,13C AND 15N NMR ASSIGNMENTS AND SOLUTION CONFORMATION OF APOKEDARCIDIN
 
Authors :  K. L. Constantine, K. L. Colson, M. Wittekind, M. S. Friedrichs, N. Zein J. Tuttle, D. R. Langley, J. E. Leet, D. R. Schroeder, K. S. Lam, B. T. Far W. J. Metzler, R. E. Bruccoleri, L. Mueller
Date :  20 Jun 94  (Deposition) - 31 Aug 94  (Release) - 22 Feb 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
NMR Structure *:  A  (1x)
Keywords :  Antibiotic Chromoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. L. Constantine, K. L. Colson, M. Wittekind, M. S. Friedrichs, N. Zein, J. Tuttle, D. R. Langley, J. E. Leet, D. R. Schroeder, K. S. Lam, B. T. Farmer Iii, W. J. Metzler, R. E. Bruccoleri, L. Mueller
Sequential 1H, 13C, And 15N Nmr Assignments And Solution Conformation Of Apokedarcidin.
Biochemistry V. 33 11438 1994
PubMed-ID: 7918358  |  Reference-DOI: 10.1021/BI00204A006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APOKEDARCIDIN
    ChainsA
    EngineeredYES
    Organism ScientificACTINOMYCETE ATCC 53650
    Organism Taxid38989
    StrainL585-6 / ATCC 53650

 Structural Features

(-) Chains, Units

  1
NMR Structure (15x)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 1AKP)

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1S1UNKNOWNTHR A:33 , LEU A:35 , CYS A:37 , ILE A:39 , ARG A:44 , CYS A:47 , VAL A:49 , PHE A:52 , ASP A:54 , TYR A:75 , MET A:77 , GLU A:96 , VAL A:98 , TYR A:106 , ASN A:108NULL

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:37 -A:47
2A:88 -A:95

(-) Cis Peptide Bonds  (2, 30)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Ser A:8 -Pro A:9
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Gly A:80 -Pro A:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1AKP)

(-) 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:114
 aligned with KEDA_ACTSL | P41249 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
           KEDA_ACTSL     1 ASAAVSVSPATGLADGATVTVSASGFATSTSATALQCAILADGRGACNVAEFHDFSLSGGEGTTSVVVRRSFTGYVMPDGPEVGAVDCDTAPGGCEIVVGGNTGEYGNAAISFG 114
               SCOP domains d1akpa_ A: Kedarcidin                                                                                              SCOP domains
               CATH domains 1akpA00 A:1-114  [code=2.60.40.230, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee........eeeeeeeee....eeeeeeeeeee...eeeeehhhheeeee...eeeeeeee..eeeeee......eeeeehhhh..eeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1akp A   1 ASAAVSVSPATGLADGATVTVSASGFATSTSATALQCAILADGRGACNVAEFHDFSLSGGEGTTSVVVRRSFTGYVMPDGPEVGAVDCDTAPGGCEIVVGGNTGEYGNAAISFG 114
                                    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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AKP)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (KEDA_ACTSL | P41249)
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
(no "Ligands, Modified Residues, Ions" information available for 1akp)
 
  Sites
    S1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:80 - Pro A:81   [ RasMol ]  
    Ser 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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1akp
    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
  KEDA_ACTSL | P41249
    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
  KEDA_ACTSL | P41249
    Protein Disorder PredictionDisEMBL | 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 1AKP)

(-) Related Entries Specified in the PDB File

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