Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  NMR AND MD SOLUTION STRUCTURE OF A GAMMA-METHYLATED PNA DUPLEX
 
Authors :  W. He, M. J. Crawford, S. Rapireddy, M. Madrid, R. R. Gil, D. H. Ly, C. Achi
Date :  15 Mar 10  (Deposition) - 12 May 10  (Release) - 22 Sep 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (11x)
NMR Structure *:  A,B  (1x)
Keywords :  Pna, Gamma-Methylated Pna, Methyl Modified Pna, Peptide Nucleic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. He, M. J. Crawford, S. Rapireddy, M. Madrid, R. R. Gil, D. H. Ly, C. Achim
The Structure Of A Gamma-Modified Peptide Nucleic Acid Duplex.
Mol Biosyst V. 6 1619 2010
PubMed-ID: 20386807  |  Reference-DOI: 10.1039/C002254C

(-) Compounds

Molecule 1 - GAMMA-MODIFIED PEPTIDE NUCLEIC ACID
    Chains: A, B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
NMR Structure (11x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 20)

NMR Structure (6, 20)
No.NameCountTypeFull Name
140A2OTHERN-[(2S)-2-AMINOPROPYL]-N-[(6-AMINO-9H-PURIN-9-YL)ACETYL]GLYCINE
240C6OTHERN-[(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)ACETYL]-N-[(2S)-2-AMINOPROPYL]GLYCINE
340G6OTHERN-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ACETYL]-N-[(2S)-2-AMINOPROPYL]GLYCINE
440T2OTHERN-[(2S)-2-AMINOPROPYL]-N-[(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)ACETYL]GLYCINE
5ACE2Mod. Amino AcidACETYL GROUP
6NME2OTHERMETHYLAMINE
NMR Structure * (6, 20)
No.NameCountTypeFull Name
140A2OTHERN-[(2S)-2-AMINOPROPYL]-N-[(6-AMINO-9H-PURIN-9-YL)ACETYL]GLYCINE
240C6OTHERN-[(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)ACETYL]-N-[(2S)-2-AMINOPROPYL]GLYCINE
340G6OTHERN-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ACETYL]-N-[(2S)-2-AMINOPROPYL]GLYCINE
440T2OTHERN-[(2S)-2-AMINOPROPYL]-N-[(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)ACETYL]GLYCINE
5ACE2Mod. Amino AcidACETYL GROUP
6NME2OTHERMETHYLAMINE

(-) Sites  (0, 0)

(no "Site" information available for 2KVJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KVJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KVJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KVJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KVJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2KVJ)

(-) Sequences/Alignments

NMR Structure
   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:OTHER/PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  2kvj A  1 xxxxxxxxxx 10
                            ||||||||10
                            ||||||||9-40C
                            1-ACE|||10-NME
                             2-40G||  
                              3-40G|  
                               4-40C  
                                5-40A 
                                 6-40T
                                  7-40G
                                   8-40C


Chain B from PDB  Type:OTHER/PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  2kvj B 11 xxxxxxxxxx 20
                            ||||||||20
                            |||||||19-40C
                           11-ACE|||20-NME
                            12-40G||  
                             13-40G|  
                              14-40C  
                               15-40A 
                                16-40T
                                 17-40G
                                  18-40C
   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 2KVJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KVJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KVJ)

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 2KVJ)

 Visualization

(-) Interactive Views

NMR Structure
  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
    40A  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    40C  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    40G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    40T  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2kvj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2kvj)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2kvj
    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 (structure derived) | HSSP (homology derived)
    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 2KVJ)

(-) Related Entries Specified in the PDB File

2k4g GAMMA-METHYLATED PNA DUPLEX