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 :  CRYSTAL STRUCTURE OF HIV-1 SUBTYPE F DIS EXTENDED DUPLEX RNA BOUND TO NEOMYCIN
 
Authors :  S. Freisz, K. Lang, R. Micura, P. Dumas, E. Ennifar
Date :  08 Feb 08  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1, Rna, Aminoglycoside, Neomycin, Extended Duplex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Freisz, K. Lang, R. Micura, P. Dumas, E. Ennifar
Binding Of Aminoglycoside Antibiotics To The Duplex Form Of The Hiv-1 Genomic Rna Dimerization Initiation Site.
Angew. Chem. Int. Ed. Engl. V. 47 4110 2008
PubMed-ID: 18435520  |  Reference-DOI: 10.1002/ANIE.200800726
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIV-1 SUBTYPE F GENOMIC RNA
    Chains: A, B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2NMY2Ligand/IonNEOMYCIN
3UMS2Mod. Nucleotide2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU A:6 , G A:7 , A A:8 , A A:9 , G A:10 , U A:11 , HOH A:27 , HOH A:32 , HOH A:33 , HOH A:37 , HOH A:38 , HOH A:40 , HOH A:45 , HOH A:57 , HOH A:62 , HOH A:66 , HOH A:67 , C B:13 , A B:14 , C B:15 , A B:16 , HOH B:27 , HOH B:29 , HOH B:30 , HOH B:46 , HOH B:69BINDING SITE FOR RESIDUE NMY A 24
2AC2SOFTWAREC A:13 , A A:14 , C A:15 , A A:16 , C A:17 , HOH A:64 , G B:7 , A B:8 , A B:9 , G B:10 , U B:11 , HOH B:26 , HOH B:30 , HOH B:33 , HOH B:40 , HOH B:57BINDING SITE FOR RESIDUE NMY B 24
3AC3SOFTWAREHOH A:28 , HOH A:33 , HOH A:51BINDING SITE FOR RESIDUE K A 25
4AC4SOFTWAREUMS B:3 , G B:4 , HOH B:63BINDING SITE FOR RESIDUE K B 25

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C7R)

(-) Exons   (0, 0)

(no "Exon" information available for 3C7R)

(-) 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:23
                                                      
                  3c7r A  1 CUxGCUGAAGUGCACACAGCAAG 23
                              |     10        20   
                              |                    
                              3-UMS                


Chain B from PDB  Type:DNA/RNA  Length:23
                                                      
                  3c7r B  1 CUxGCUGAAGUGCACACAGCAAG 23
                              |     10        20   
                              3-UMS
   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 3C7R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3C7R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C7R)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3C7R)

 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
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NMY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3c7r)
 

(-) 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
  3c7r
    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 3C7R)

(-) Related Entries Specified in the PDB File

2qek FREE SUBTYPE F EXTENDED DUPLEX
3c3z SUBTYPE F HIV-1 DIS EXTENDED DUPLEX BOUND TO RIBOSTAMYCIN
3c44 SUBTYPE F HIV-1 DIS EXTENDED DUPLEX BOUND TO PAROMOMYCIN
3c5d SUBTYPE F HIV-1 DIS EXTENDED DUPLEX BOUND TO LIVIDOMYCIN