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
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)

(-) Description

Title :  A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6042 IN A LARGE UNIT CELL
 
Authors :  N. H. Campbell, G. Parkinson, S. Neidle
Date :  10 Oct 08  (Deposition) - 02 Dec 08  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Quadruplex, Oxytricha Nova, Bsu-6042, Bsu6042, Anti- Parallel, Bimolecular, Macromolecule, Dna, G-Quadruplex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. H. Campbell, M. Patel, A. B. Tofa, R. Ghosh, G. N. Parkinson, S. Neidle
Selectivity In Ligand Recognition Of G-Quadruplex Loops.
Biochemistry V. 48 1675 2009
PubMed-ID: 19173611  |  Reference-DOI: 10.1021/BI802233V
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'
    Chains: A, B, C, D
    Engineered: YES
    Other Details: BIMOLECULAR ANTI-PARALLEL-STRANDED DNA QUADRUPLEX
    Other Details - Source: THIS SEQUENCE OCCURS NATURALLY IN OXYTRICHA NOVA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1K8Ligand/IonPOTASSIUM ION
2NC51Ligand/Ion3-[(2R)-2-ETHYLPIPERIDIN-1-YL]-N-[6-({3-[(2S)-2-ETHYLPIPERIDIN-1-YL]PROPANOYL}AMINO)ACRIDIN-3-YL]PROPANAMIDE
3NCI1Ligand/Ion3,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE
4SPM1Ligand/IonSPERMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2NC51Ligand/Ion3-[(2R)-2-ETHYLPIPERIDIN-1-YL]-N-[6-({3-[(2S)-2-ETHYLPIPERIDIN-1-YL]PROPANOYL}AMINO)ACRIDIN-3-YL]PROPANAMIDE
3NCI-1Ligand/Ion3,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE
4SPM1Ligand/IonSPERMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2NC5-1Ligand/Ion3-[(2R)-2-ETHYLPIPERIDIN-1-YL]-N-[6-({3-[(2S)-2-ETHYLPIPERIDIN-1-YL]PROPANOYL}AMINO)ACRIDIN-3-YL]PROPANAMIDE
3NCI1Ligand/Ion3,6-BIS{3-[(2R)-(2-ETHYLPIPERIDINO)]PROPIONAMIDO}ACRIDINE
4SPM-1Ligand/IonSPERMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDG A:1 , DG A:2 , DG A:11 , DG A:12 , K A:51 , DG B:15 , DG B:16 , DG B:21 , DG B:22 , K B:49BINDING SITE FOR RESIDUE K A 50
02AC2SOFTWAREDG A:2 , DG A:3 , DG A:10 , DG A:11 , K A:50 , K A:52 , DG B:14 , DG B:15 , DG B:22 , DG B:23BINDING SITE FOR RESIDUE K A 51
03AC3SOFTWAREDG A:3 , DG A:4 , DG A:9 , DG A:10 , K A:51 , DG B:13 , DG B:14 , DG B:23 , DG B:24BINDING SITE FOR RESIDUE K A 52
04AC4SOFTWAREDT A:6 , DT A:7 , DT A:8 , DG A:9 , HOH A:63 , HOH A:97 , DG B:13 , DG B:24 , DT D:44 , DG D:46BINDING SITE FOR RESIDUE NC5 A 57
05AC5SOFTWAREDG A:1 , DG A:12 , K A:50 , DG B:16 , DT B:17 , DT B:19 , DG B:21 , HOH B:66BINDING SITE FOR RESIDUE K B 49
06AC6SOFTWAREDT B:17 , DT B:18 , DT B:19 , DG C:35 , DG C:36BINDING SITE FOR RESIDUE SPM B 59
07AC7SOFTWAREDG C:25 , DG C:26 , DG C:35 , DG C:36 , K C:55 , DG D:39 , DG D:40 , DG D:45 , DG D:46 , K D:53BINDING SITE FOR RESIDUE K C 54
08AC8SOFTWAREDG C:26 , DG C:27 , DG C:34 , DG C:35 , K C:54 , K C:56 , DG D:38 , DG D:39 , DG D:46 , DG D:47BINDING SITE FOR RESIDUE K C 55
09AC9SOFTWAREDG C:27 , DG C:28 , DG C:33 , DG C:34 , K C:55 , DG D:37 , DG D:38 , DG D:47 , DG D:48BINDING SITE FOR RESIDUE K C 56
10BC1SOFTWAREDT B:20 , DG B:21 , DG B:22 , DT C:30 , DT C:31 , DT C:32 , DG C:33 , HOH C:105 , DG D:37 , DG D:48BINDING SITE FOR RESIDUE NCI C 58
11BC2SOFTWAREDG C:25 , DG C:36 , K C:54 , DG D:40 , DT D:41 , DT D:43 , DG D:45 , HOH D:130BINDING SITE FOR RESIDUE K D 53

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EUI)

(-) 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  Length:12
                                           
                  3eui A  1 GGGGTTTTGGGG 12
                                    10  


Chain B from PDB  Type:DNA  Length:12
                                           
                  3eui B 13 GGGGTTTTGGGG 24
                                    22  


Chain C from PDB  Type:DNA  Length:12
                                           
                  3eui C 25 GGGGTTTTGGGG 36
                                    34  


Chain D from PDB  Type:DNA  Length:12
                                           
                  3eui D 37 GGGGTTTTGGGG 48
                                    46
   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 3EUI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NC5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NCI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SPM  [ 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 ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3eui)
 
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
[ 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 ](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
  3eui
    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 3EUI)

(-) Related Entries Specified in the PDB File

1jpq SAME QUADRUPLEX STRUCTURE IN ITS NATIVE FORM (LIGAND-FREE)
1jrn SAME QUADRUPLEX STRUCTURE IN ITS NATIVE FORM (LIGAND-FREE)
1l1h SAME QUADRUPLEX STRUCTURE BOUND WITH A DIFFERENT LIGAND BSU -6039
3ce5 A BIMOLECULAR PARALLEL-STRANDED HUMAN TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6,9-TRISUBSTITUTED ACRIDINE MOLECULAR BRACO19
3em2 A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6038
3eqw A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6042 IN SMALL UNIT CELL
3eru A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6045
3es0 A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6048
3et8 A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6054
3eum A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6066