Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF AN ALL-RNA MINIMAL HAIRPIN RIBOZYME WITH MUTATION G8A AT THE CLEAVAGE SITE
 
Authors :  J. E. Wedekind
Date :  20 Apr 05  (Deposition) - 14 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hairpin Ribozyme, All-Rna, Cobalt Hexaamine, Mutation, Junctionless, Low Salt, S-Turn, E-Loop, Ribose Zipper, Catalytic Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Salter, J. Krucinska, S. Alam, V. Grum-Tokars, J. E. Wedekind
Water In The Active Site Of An All-Rna Hairpin Ribozyme And Effects Of Gua8 Base Variants On The Geometry Of Phosphoryl Transfer.
Biochemistry V. 45 686 2006
PubMed-ID: 16411744  |  Reference-DOI: 10.1021/BI051887K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'
    Chains: A
    Engineered: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*GP*GP*UP*GP*AP*AP*AP*AP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Mutation: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 3 - 5'- R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
    Chains: C
    Engineered: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 4 - 5'- R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) -3'
    Chains: D
    Engineered: YES
    Mutation: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NCO1Ligand/IonCOBALT HEXAMMINE(III)
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:2 , HOH A:104BINDING SITE FOR RESIDUE SO4 A 102
2AC2SOFTWAREA C:20 , G C:21 , A D:40 , U D:41BINDING SITE FOR RESIDUE NCO D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZFV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZFV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZFV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZFV)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZFV)

(-) 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:13
                                            
                  1zfv A  1 UCCCAGUCCACCG 13
                                    10   


Chain B from PDB  Type:RNA  Length:12
                                           
                  1zfv B  2 CGGUGAAAAGGG 13
                                    11  


Chain C from PDB  Type:RNA  Length:17
                                                
                  1zfv C 15 GGCAGAGAAACACACGA 31
                                    24       


Chain D from PDB  Type:RNA  Length:19
                                                  
                  1zfv D 31 UCGUGGUACAUUACCUGCC 49
                                    40
   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 1ZFV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZFV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZFV)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1ZFV)

 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
    NCO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zfv)
 

(-) 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
  1zfv
    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 1ZFV)

(-) Related Entries Specified in the PDB File

1x9c ALL-RNA HAIRPIN RIBOZYME WITH MUTATION U39C (LOW SALT)
1x9k ALL-RNA HAIRPIN RIBOZYME WITH MUTATION U39C (HIGH SALT)
1zfr ALL-RNA HAIRPIN RIBOZYME WITH MUTATION U39C (LOW SALT)
1zft ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8I AND U39C (LOW SALT).
1zfx ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8U AND U39C (LOW SALT).