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 :  3.5 A STRUCTURE OF FRAGMENT I FROM E. COLI 5S RRNA
 
Authors :  C. C. Correll, B. Freeborn, P. B. Moore, T. A. Steitz
Date :  09 Oct 97  (Deposition) - 01 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  U-Rna, Double Helix, Kinked, Internal Loop, Overhanging Base, Modified, Mismatched (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. C. Correll, B. Freeborn, P. B. Moore, T. A. Steitz
Metals, Motifs, And Recognition In The Crystal Structure Of A 5S Rrna Domain.
Cell(Cambridge, Mass. ) V. 91 705 1997
PubMed-ID: 9393863  |  Reference-DOI: 10.1016/S0092-8674(00)80457-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA-DNA (5'-R(*UP*GP*DCP)-D(*CP(S)*)- R(*UP*GP*GP*CP*GP*GP*C)-3')
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Organelle: CYTOSOL
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - RNA (5'- R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G*UP*C)- 3')
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Organelle: CYTOSOL
    Expression System Plasmid: PKK5-1 RRNB 5S CISTRON
    Expression System Strain: HB101
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 3 - RNA (5'- R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP* GP*CP*CP*AP*GP*GP*CP*AP*U)-3')
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Organelle: CYTOSOL
    Expression System Plasmid: PKK5-1 RRNB 5S CISTRON
    Expression System Strain: HB101
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1HG1Ligand/IonMERCURY (II) ION
2MG8Ligand/IonMAGNESIUM ION
3SSU1Mod. NucleotideURIDINE-5'-PHOSPHOROTHIOATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG B:75 , A C:99BINDING SITE FOR RESIDUE MG B 62
2AC2SOFTWAREU B:74 , A C:99BINDING SITE FOR RESIDUE MG C 63
3AC3SOFTWAREG C:100BINDING SITE FOR RESIDUE MG C 64
4AC4SOFTWAREG C:98BINDING SITE FOR RESIDUE MG C 65
5AC5SOFTWAREA B:78 , G B:79BINDING SITE FOR RESIDUE MG B 66
6AC6SOFTWAREA C:119BINDING SITE FOR RESIDUE MG C 68
7AC7SOFTWAREA B:73 , U B:74BINDING SITE FOR RESIDUE HG B 89

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 357D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 357D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 357D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 357D)

(-) Exons   (0, 0)

(no "Exon" information available for 357D)

(-) 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:DNA/RNA  Length:11
                                           
                 357d A   1 UGCCuGGCGGC  11
                                |   10 
                                |      
                                5-SSU  


Chain B from PDB  Type:RNA  Length:19
                                                   
                 357d B  70 CCGAUGGUAGUGUGGGGUC  88
                                    79         


Chain C from PDB  Type:DNA/RNA  Length:31
                                                               
                 357d C  90 CCCCAUGCGAGAGUAGGGAACUGCCAGGCAU 120
                                    99       109       119
   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 357D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 357D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 357D)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 357D)

 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
    HG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SSU  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 357d)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  357d
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP | HSSP
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB 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 Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 357D)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 357D)