Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE REV BINDING ELEMENT OF HIV-1
 
Authors :  L. -W. Hung, E. L. Holbrook, S. R. Holbrook
Date :  18 Jan 00  (Deposition) - 16 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Rre, Hiv-1, Rev Binding Domain, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Hung, E. L. Holbrook, S. R. Holbrook
The Crystal Structure Of The Rev Binding Element Of Hiv-1 Reveals Novel Base Pairing And Conformational Variability.
Proc. Natl. Acad. Sci. Usa V. 97 5107 2000
PubMed-ID: 10792052  |  Reference-DOI: 10.1073/PNAS.090588197
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THE REV BINDING ELEMENT
    Chains: A, C, E, G
    Engineered: YES
    Fragment: SHORT CHAIN
    Other Details: SEQUENCE FROM HIV-1. SYNTHESIZED BY OLIGOS, ETC.
    Synthetic: YES
 
Molecule 2 - THE REV BINDING ELEMENT
    Chains: B, D, F, H
    Engineered: YES
    Fragment: LONG CHAIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1NA10Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG D:220 , A D:221 , C D:222BINDING SITE FOR RESIDUE NA D 901
02AC2SOFTWAREG G:406 , HOH G:635 , G H:423 , G H:424 , HOH H:602BINDING SITE FOR RESIDUE NA H 902
03AC3SOFTWAREG H:420 , A H:421 , C H:422BINDING SITE FOR RESIDUE NA H 903
04AC4SOFTWAREG C:206 , HOH C:631 , G D:223 , G D:224 , HOH D:601BINDING SITE FOR RESIDUE NA C 904
05AC5SOFTWAREG G:401 , C G:402BINDING SITE FOR RESIDUE NA G 905
06AC6SOFTWAREG C:201 , C C:202BINDING SITE FOR RESIDUE NA C 906
07AC7SOFTWAREG A:106 , HOH A:603 , G B:123 , G B:124BINDING SITE FOR RESIDUE NA B 911
08AC8SOFTWAREG E:306 , G F:323 , G F:324 , A F:326BINDING SITE FOR RESIDUE NA E 912
09AC9SOFTWAREC B:117 , G C:201 , C C:202 , C D:230 , U G:403BINDING SITE FOR RESIDUE NA C 913
10BC1SOFTWAREU C:203 , C F:317 , G G:401 , C G:402 , C H:430BINDING SITE FOR RESIDUE NA G 914

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DUQ)

(-) 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:RNA  Length:12
                                            
                 1duq A 101 GCUGGGCGCAGG 112
                                   110  


Chain B from PDB  Type:RNA  Length:14
                                              
                 1duq B 117 CCUGACGGUACAGC 130
                                   126    


Chain C from PDB  Type:RNA  Length:12
                                            
                 1duq C 201 GCUGGGCGCAGG 212
                                   210  


Chain D from PDB  Type:RNA  Length:14
                                              
                 1duq D 217 CCUGACGGUACAGC 230
                                   226    


Chain E from PDB  Type:RNA  Length:12
                                            
                 1duq E 301 GCUGGGCGCAGG 312
                                   310  


Chain F from PDB  Type:RNA  Length:14
                                              
                 1duq F 317 CCUGACGGUACAGC 330
                                   326    


Chain G from PDB  Type:RNA  Length:12
                                            
                 1duq G 401 GCUGGGCGCAGG 412
                                   410  


Chain H from PDB  Type:RNA  Length:14
                                              
                 1duq H 417 CCUGACGGUACAGC 430
                                   426
   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 1DUQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    NA  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1duq)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 4 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
  1duq
    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 1DUQ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DUQ)