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 :  THIOSTREPTON, REDUCED AT N-CA BOND OF RESIDUE 14
 
Authors :  H. R. A. Jonker, S. Baumann, A. Wolf, S. Schoof, F. Hiller, K. W. Schulte, K. N. Kirschner, H. Schwalbe, H. -D. Arndt
Date :  27 Aug 10  (Deposition) - 02 Feb 11  (Release) - 26 Jun 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Natural Antibiotic, Thiopeptide, Antibiotic, Antimicrobial, Antibacterial, Thiazole, Thiazoline (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. R. Jonker, S. Baumann, A. Wolf, S. Schoof, F. Hiller, K. W. Schulte, K. N. Kirschner, H. Schwalbe, H. D. Arndt
Nmr Structures Of Thiostrepton Derivatives For Characterization Of The Ribosomal Binding Site.
Angew. Chem. Int. Ed. Engl. V. 50 3308 2011
PubMed-ID: 21365717  |  Reference-DOI: 10.1002/ANIE.201003582

(-) Compounds

Molecule 1 - THIOSTREPTON
    ChainsA
    MutationYES
    Organism ScientificSTREPTOMYCES AZUREUS
    Organism Taxid146537
    SynonymALANINAMIDE, BRYAMYCIN, GARGON, THIACTIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 13)

NMR Structure (8, 13)
No.NameCountTypeFull Name
1BB94Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
2DBU1Mod. Amino Acid(2Z)-2-AMINOBUT-2-ENOIC ACID
3DCY1Mod. Amino AcidD-CYSTEINE
4DHA3Mod. Amino Acid2-AMINO-ACRYLIC ACID
5DSN1Mod. Amino AcidD-SERINE
6NH21Mod. Amino AcidAMINO GROUP
7QUA1Mod. Amino Acid8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID
8TS91Mod. Amino Acid(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC ACID
NMR Structure * (8, 13)
No.NameCountTypeFull Name
1BB94Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
2DBU1Mod. Amino Acid(2Z)-2-AMINOBUT-2-ENOIC ACID
3DCY1Mod. Amino AcidD-CYSTEINE
4DHA3Mod. Amino Acid2-AMINO-ACRYLIC ACID
5DSN1Mod. Amino AcidD-SERINE
6NH21Mod. Amino AcidAMINO GROUP
7QUA1Mod. Amino Acid8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID
8TS91Mod. Amino Acid(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC ACID

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDBU A:8 , TS9 A:10BINDING SITE FOR RESIDUE DCY A 9
2AC2SOFTWAREALA A:4 , SER A:5 , BB9 A:13 , BB9 A:15BINDING SITE FOR RESIDUE DSN A 14

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L2Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L2Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L2Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2L2Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2L2Z)

(-) 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:19
 aligned with THCL_STRAJ | P0C8P8 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:19
                                            72 
                                    64       | 
            THCL_STRAJ   55 MIASASCTTCICTCSCSS-  -
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ................... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                  2l2z A  0 xIAsAScTtxicTcxcssx 18
                            |  |  | |9|| ||||||
                            |  |  | |||| 14-DSN
                            0-QUA | |||| |15-BB9
                               3-DHA|||| | 16-DHA
                                  6-BB9| |  17-DHA
                                    8-DBU|   18-NH2
                                     9-DCY     
                                     10-TS9    
                                      11-BB9   
                                        13-BB9 

   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 2L2Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L2Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L2Z)

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A   (THCL_STRAJ | P0C8P8)
biological process
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
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
    BB9  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DBU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DCY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DHA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DSN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    QUA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TS9  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2l2z)
 

(-) 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
  2l2z
    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
  THCL_STRAJ | P0C8P8
    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
  THCL_STRAJ | P0C8P8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        THCL_STRAJ | P0C8P81e9w 1oln 2jq7 2l2w 2l2x 2l2y 3cf5 4hp2

(-) Related Entries Specified in the PDB File

1e9w 2jq7 2l2w 2l2x 2l2y