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
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)

(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE 16MER GCAGNCUUAAGUCUGC CONTAINING 8-AZA-7-DEAZA-7-ETHYNYL ADENOSINE
 
Authors :  P. A. Beal, A. J. Fisher, K. J. Phelps, J. M. Ibarra-Soza, Y. Zheng
Date :  31 Oct 13  (Deposition) - 02 Jul 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Rna 16Mer Oligo, 8-Aza-7-Deaza-7-Ethynyladenosine, Position 5, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. J. Phelps, J. M. Ibarra-Soza, K. Tran, A. J. Fisher, P. A. Beal
Click Modification Of Rna At Adenosine: Structure And Reactivity Of 7-Ethynyl- And 7-Triazolyl-8-Aza-7-Deazaadenosine In Rna.
Acs Chem. Biol. V. 9 1780 2014
PubMed-ID: 24896732  |  Reference-DOI: 10.1021/CB500270X

(-) Compounds

Molecule 1 - GCAG(A7E)CUUAAGUCUGC
    ChainsA, B, C
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)A  
Biological Unit 2 (1x) BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1A7E3Mod. Nucleotide3-ETHYNYL-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-AMINE
2ARF3Ligand/IonFORMAMIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1A7E2Mod. Nucleotide3-ETHYNYL-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-AMINE
2ARF2Ligand/IonFORMAMIDE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1A7E2Mod. Nucleotide3-ETHYNYL-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-AMINE
2ARF2Ligand/IonFORMAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU A:12BINDING SITE FOR RESIDUE ARF A 101
2AC2SOFTWAREU B:12BINDING SITE FOR RESIDUE ARF B 101
3AC3SOFTWAREU C:12BINDING SITE FOR RESIDUE ARF C 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NFP)

(-) 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:16
                                               
                  4nfp A  1 GCAGaCUUAAGUCUGC 16
                                |   10      
                                |           
                                5-A7E       

Chain B from PDB  Type:RNA  Length:16
                                               
                  4nfp B  1 GCAGaCUUAAGUCUGC 16
                                |   10      
                                5-A7E       

Chain C from PDB  Type:RNA  Length:16
                                               
                  4nfp C  1 GCAGaCUUAAGUCUGC 16
                                |   10      
                                5-A7E       

   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 4NFP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    A7E  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ARF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4nfp)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) 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
  4nfp
    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 4NFP)

(-) Related Entries Specified in the PDB File

4nfo 4nfq