Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  COCRYSTAL STRUCTURE OF A CLASS-I PREQ1 RIBOSWITCH
 
Authors :  D. J. Klein, T. E. Edwards, A. R. Ferre-D'Amare
Date :  13 Jan 09  (Deposition) - 03 Mar 09  (Release) - 17 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Rna; Aptamer; Riboswitch; Queuosine; Preq1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Klein, T. E. Edwards, A. R. Ferre-D'Amare
Cocrystal Structure Of A Class I Preq1 Riboswitch Reveals A Pseudoknot Recognizing An Essential Hypermodified Nucleobase
Nat. Struct. Mol. Biol. V. 16 343 2009
PubMed-ID: 19234468  |  Reference-DOI: 10.1038/NSMB.1563
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PREQ1 RIBOSWITCH
    Chains: A, B, C
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED RNA CORRESPONDING TO THE NATURAL SEQUENCE FROM BACILLUS SUBTILIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CA9Ligand/IonCALCIUM ION
2PRF3Ligand/Ion7-DEAZA-7-AMINOMETHYL-GUANINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PRF1Ligand/Ion7-DEAZA-7-AMINOMETHYL-GUANINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PRF1Ligand/Ion7-DEAZA-7-AMINOMETHYL-GUANINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PRF1Ligand/Ion7-DEAZA-7-AMINOMETHYL-GUANINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG A:5 , U A:6 , G A:11 , C A:12 , C A:17 , C A:18 , A A:30 , C A:31BINDING SITE FOR RESIDUE PRF A 101
2AC2SOFTWAREU A:7 , U A:9 , HOH A:810 , HOH A:811 , HOH A:812BINDING SITE FOR RESIDUE CA A 901
3AC3SOFTWAREC A:21 , C B:21 , HOH B:801 , HOH B:802BINDING SITE FOR RESIDUE CA A 902
4AC4SOFTWAREC A:8BINDING SITE FOR RESIDUE CA A 907
5AC5SOFTWAREG B:5 , U B:6 , G B:11 , C B:12 , C B:17 , C B:18 , A B:30 , C B:31BINDING SITE FOR RESIDUE PRF B 101
6AC6SOFTWAREU B:7 , U B:9 , HOH B:805 , HOH B:806BINDING SITE FOR RESIDUE CA B 903
7AC7SOFTWAREG C:5 , U C:6 , G C:11 , C C:12 , C C:17 , C C:18 , A C:30 , C C:31BINDING SITE FOR RESIDUE PRF C 101
8AC8SOFTWAREU C:7 , U C:9BINDING SITE FOR RESIDUE CA C 904
9AC9SOFTWAREC B:8 , C C:8BINDING SITE FOR RESIDUE CA C 905

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FU2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FU2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FU2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FU2)

(-) Exons   (0, 0)

(no "Exon" information available for 3FU2)

(-) Sequences/Alignments

Asymmetric 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:32
                                                               
                  3fu2 A  1 AGAGGUUCUAGCCACCCUCUAUAAAAAACUAA 34
                                    10 ||     22        32  
                                      12|                   
                                       15                   


Chain B from PDB  Type:DNA/RNA  Length:33
                                                                
                  3fu2 B  1 AGAGGUUCUAGCACACCCUCUAUAAAAAACUAA 34
                                    10 ||     21        31   
                                      12|                    
                                       14                    


Chain C from PDB  Type:DNA/RNA  Length:32
                                                               
                  3fu2 C  1 AGAGGUUCUAGCCACCCUCUAUAAAAAACUAA 34
                                    10 ||     22        32  
                                      12|                   
                                       15
   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 3FU2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FU2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FU2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3FU2)

 Visualization

(-) Interactive Views

Asymmetric 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PRF  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3fu2)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3fu2
    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 3FU2)

(-) Related Entries Specified in the PDB File

3fu4