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 :  SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS GG
 
Authors :  L. Huang, D. M. J. Lilley
Date :  14 Oct 15  (Deposition) - 25 May 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Rna, Kink Turn, Rna Motif, Sam-I Riboswitch (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Huang, J. Wang, D. M. J. Lilley
A Critical Base Pair In K-Turns Determines The Conformational Class Adopted, And Correlates With Biological Function.
Nucleic Acids Res. V. 44 5390 2016
PubMed-ID: 27016741  |  Reference-DOI: 10.1093/NAR/GKW201

(-) Compounds

Molecule 1 - SAM-I RIBOSWITCH
    ChainsA
    FragmentSAM BINDING DOMAIN, RESIDUES 1-94
    Organism ScientificTHERMOANAEROBACTER TENGCONGENSIS
    Organism Taxid119072
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1BA11Ligand/IonBARIUM ION
2SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREA A:6 , U A:7 , C A:8 , G A:11 , A A:45 , C A:47 , U A:57 , G A:58 , C A:59 , U A:88 , G A:89 , BA A:1097BINDING SITE FOR RESIDUE SAM A1095
02AC2SOFTWAREG A:74 , HOH A:2009 , HOH A:2010BINDING SITE FOR RESIDUE BA A1096
03AC3SOFTWAREG A:11 , U A:64 , SAM A:1095BINDING SITE FOR RESIDUE BA A1097
04AC4SOFTWAREU A:64 , U A:67 , HOH A:2006 , HOH A:2007BINDING SITE FOR RESIDUE BA A1098
05AC5SOFTWAREG A:86 , HOH A:2012BINDING SITE FOR RESIDUE BA A1099
06AC6SOFTWAREG A:1 , HOH A:2001BINDING SITE FOR RESIDUE BA A1100
07AC7SOFTWAREG A:1BINDING SITE FOR RESIDUE BA A1101
08AC8SOFTWAREG A:42 , G A:43BINDING SITE FOR RESIDUE BA A1102
09AC9SOFTWAREA A:45 , HOH A:2004BINDING SITE FOR RESIDUE BA A1103
10BC1SOFTWAREG A:50 , A A:52BINDING SITE FOR RESIDUE BA A1104
11BC2SOFTWAREG A:32 , HOH A:2003BINDING SITE FOR RESIDUE BA A1105
12BC3SOFTWAREG A:18 , G A:19BINDING SITE FOR RESIDUE BA A1106

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FK2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FK2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FK2)

(-) Exons   (0, 0)

(no "Exon" information available for 5FK2)

(-) 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:94
                                                                                                                             
                  5fk2 A  1 GGCUUAUCAAGAGAGGGGGAGCGACUGGCGCGAAGAGCCCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCG 94
                                    10        20        30        40        50        60        70        80        90    

   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 5FK2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FK2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FK2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5FK2)

 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
    BA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAM  [ 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 ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5fk2)
 

(-) 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
  5fk2
    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 5FK2)

(-) Related Entries Specified in the PDB File

5fjc SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT C-2BU
5fk1 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS UG
5fk3 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS CC
5fk4 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS UU
5fk5 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS AA
5fk6 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS CA
5fkd SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS UA
5fke SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS GU
5fkf SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS UC
5fkg SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS CG
5fkh SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS CU