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 :  CRYSTAL STRUCTURES OF THE SMK BOX (SAM-III) RIBOSWITCH WITH SE-SAM
 
Authors :  C. Lu
Date :  13 Aug 08  (Deposition) - 07 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Smk Sam Riboswitch Shine-Delgarno Translation Regulation, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Lu, A. M. Smith, R. T. Fuchs, F. Ding, K. Rajashankar, T. M. Henkin, A. Ke
Crystal Structures Of The Sam-Iii/S(Mk) Riboswitch Reveal The Sam-Dependent Translation Inhibition Mechanism.
Nat. Struct. Mol. Biol. V. 15 1076 2008
PubMed-ID: 18806797  |  Reference-DOI: 10.1038/NSMB.1494
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMK BOX (SAM-III) RIBOSWITCH FOR RNA
    ChainsA
    EngineeredYES
    Other DetailsTHE RNA IS PREPARED BY IN VITRO TRANSCRIPTION
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1EEM1Ligand/Ion[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM
2GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3SR15Ligand/IonSTRONTIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:46BINDING SITE FOR RESIDUE SR A 204
02AC2SOFTWAREG A:19 , A A:21BINDING SITE FOR RESIDUE SR A 206
03AC3SOFTWAREC A:6 , HOH A:219BINDING SITE FOR RESIDUE SR A 207
04AC4SOFTWAREU A:34 , G A:36 , HOH A:217BINDING SITE FOR RESIDUE SR A 208
05AC5SOFTWAREA A:38BINDING SITE FOR RESIDUE SR A 209
06AC6SOFTWAREG A:19BINDING SITE FOR RESIDUE SR A 211
07AC7SOFTWAREGTP A:1BINDING SITE FOR RESIDUE SR A 212
08AC8SOFTWAREU A:14 , G A:15 , HOH A:223BINDING SITE FOR RESIDUE SR A 213
09AC9SOFTWAREA A:38 , A A:39BINDING SITE FOR RESIDUE SR A 215
10BC1SOFTWAREG A:7 , U A:30 , G A:31 , G A:36 , U A:37 , A A:38 , G A:47 , G A:48BINDING SITE FOR RESIDUE EEM A 216

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E5F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E5F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E5F)

(-) Exons   (0, 0)

(no "Exon" information available for 3E5F)

(-) 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:RNA  Length:53
                                                                                    
                  3e5f A  1 gUUCCCGAAAGGAUGGCGGAAACGCCAGAUGCCUUGUAACCGAAAGGGGGAAU 53
                            |       10        20        30        40        50   
                            |                                                    
                            1-GTP                                                

   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 3E5F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E5F)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3E5F)

 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
    EEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3e5f)
 

(-) 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
  3e5f
    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 | HSSP
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3E5F)

(-) Related Entries Specified in the PDB File

3e5c SAME RNA WITH SAM
3e5e SAME RNA WITH SAH