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 :  MINIMAL HAIRPIN RIBOZYME IN THE TRANSITION STATE WITH G8I VARIATION
 
Authors :  J. A. Liberman, J. L. Jenkins, J. Krucinska, J. E. Wedekind
Date :  19 Jul 12  (Deposition) - 15 Aug 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.83
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rna, Structure-Activity Relationship, Nucleic Acid Conformation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Liberman, M. Guo, J. L. Jenkins, J. Krucinska, Y. Chen, P. R. Carey J. E. Wedekind
A Transition-State Interaction Shifts Nucleobase Ionization Toward Neutrality To Facilitate Small Ribozyme Catalysis.
J. Am. Chem. Soc. V. 134 16933 2012
PubMed-ID: 22989273  |  Reference-DOI: 10.1021/JA3070528

(-) Compounds

Molecule 1 - LOOP A SUBSTRATE STRAND
    ChainsA
    EngineeredYES
    SyntheticYES
 
Molecule 2 - LOOP A RIBOZYME STRAND
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - LOOP B RIBOZYME STRAND
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 4 - LOOP B S-TURN STRAND
    ChainsD
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
13DA1Mod. Nucleotide3'-DEOXYADENOSINE-5'-MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:2 , C A:3 , HOH A:202BINDING SITE FOR RESIDUE SO4 A 101
2AC2SOFTWAREHOH A:201 , HOH A:202 , HOH B:201 , HOH B:202 , HOH B:203 , HOH B:204BINDING SITE FOR RESIDUE MG B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G6R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G6R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G6R)

(-) Exons   (0, 0)

(no "Exon" information available for 4G6R)

(-) 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
                                            
                  4g6r A  1 UCCCaGUCCACCG 13
                                |   10   
                                |        
                                5-3DA    

Chain B from PDB  Type:RNA  Length:11
                                          
                  4g6r B  2 CGGUGAAAGGG 13
                                 || 12 
                                 7|    
                                  9    

Chain C from PDB  Type:RNA  Length:17
                                                
                  4g6r C 15 GGCAGAGAAACACACGA 31
                                    24       

Chain D from PDB  Type:RNA  Length:19
                                                  
                  4g6r 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 4G6R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G6R)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4G6R)

 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
    3DA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 4g6r)
 

(-) 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
  4g6r
    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 4G6R)

(-) Related Entries Specified in the PDB File

4g6p 4g6s