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 :  STRUCTURE OF THE DICKEYA DADANTII YKKC RIBOSWITCH BOUND TO GUANIDINIUM
 
Authors :  R. A. Battaglia, I. R. Price, A. Ke
Date :  02 Dec 16  (Deposition) - 01 Feb 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  B
Keywords :  Riboswitch, Ykkc, Guanidine, Guanidinium, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. A. Battaglia, I. R. Price, A. Ke
Structural Basis For Guanidine Sensing By The Ykkc Family O Riboswitches.
Rna V. 23 578 2017
PubMed-ID: 28096518  |  Reference-DOI: 10.1261/RNA.060186.116

(-) Compounds

Molecule 1 - YKKC RIBOSWITCH
    ChainsB
    EngineeredYES
    Organism ScientificDICKEYA DADANTII
    Organism Taxid204038
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric/Biological Unit (4, 27)
No.NameCountTypeFull Name
1GAI1Ligand/IonGUANIDINE
2GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3K1Ligand/IonPOTASSIUM ION
4MG24Ligand/IonMAGNESIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG B:33 , C B:76 , C B:77 , HOH B:207 , HOH B:210 , HOH B:214binding site for residue MG B 101
02AC2SOFTWAREG B:31 , MG B:113binding site for residue MG B 102
03AC3SOFTWAREG B:52binding site for residue MG B 103
04AC4SOFTWAREG B:48 , A B:50binding site for residue MG B 104
05AC5SOFTWAREG B:33 , C B:77 , MG B:112 , HOH B:203binding site for residue MG B 105
06AC6SOFTWAREA B:34binding site for residue MG B 106
07AC7SOFTWAREA B:32binding site for residue MG B 107
08AC8SOFTWAREC B:30 , G B:31 , MG B:111 , MG B:113binding site for residue MG B 110
09AC9SOFTWAREG B:31 , MG B:110 , MG B:113 , HOH B:208 , HOH B:220binding site for residue MG B 111
10AD1SOFTWAREA B:32 , G B:33 , MG B:105 , MG B:115 , HOH B:203binding site for residue MG B 112
11AD2SOFTWAREG B:31 , MG B:102 , MG B:110 , MG B:111 , HOH B:208binding site for residue MG B 113
12AD3SOFTWAREMG B:112 , HOH B:217binding site for residue MG B 115
13AD4SOFTWAREG B:33 , C B:62 , G B:63 , G B:80 , MG B:117binding site for residue MG B 116
14AD5SOFTWAREA B:20 , G B:81 , MG B:116 , HOH B:218binding site for residue MG B 117
15AD6SOFTWAREA B:82 , G B:83binding site for residue MG B 118
16AD7SOFTWAREA B:49binding site for residue MG B 119
17AD8SOFTWAREC B:65 , G B:66 , HOH B:219binding site for residue MG B 121
18AD9SOFTWAREHOH B:205 , HOH B:211 , HOH B:215 , HOH B:219binding site for residue MG B 122
19AE1SOFTWAREA B:71binding site for residue MG B 123
20AE2SOFTWAREG B:11 , U B:12 , HOH B:216binding site for residue MG B 124
21AE3SOFTWAREG B:33 , A B:34 , G B:63 , G B:64 , G B:79 , G B:81binding site for residue GAI B 125

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U3G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U3G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U3G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3G)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3G)

(-) 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 B from PDB  Type:RNA  Length:85
                                                                                                                    
                  5u3g B  1 xGUGACUAGGGUUCCGGCGAAAGCCGGUCCGAGAGUUACCGACCGCCGAAAGGCGGUUACACGGCGGGAAAAAAGCCCGGGAGGA 85
                            |       10        20        30        40        50        60        70        80     
                            |                                                                                    
                            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 5U3G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3G)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5U3G)

 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
    GAI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
    AE2  [ RasMol ]  +environment [ RasMol ]
    AE3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5u3g)
 

(-) 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
  5u3g
    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 5U3G)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5U3G)