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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE DNA QUADRUPLEX D(TGGGGT)S2
 
Authors :  C. Caceres, G. Wright, C. Gouyette, G. Parkinson, J. A. Subirana
Date :  15 Jan 04  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  I,J,K,L  (1x)
Keywords :  Quadruplex Dna, Thymine Triads And Tetrads, Thallium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Caceres, G. Wright, C. Gouyette, G. Parkinson, J. A. Subirana
A Thymine Tetrad In D(Tggggt) Quadruplexes Stabilized With Tl+1/Na+1 Ions
Nucleic Acids Res. V. 32 1097 2004
PubMed-ID: 14960719  |  Reference-DOI: 10.1093/NAR/GKH269
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*TP*GP*GP*GP*GP*T)-3'
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN TETRAHYMENA.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCD        
Biological Unit 2 (1x):     EFGH    
Biological Unit 3 (1x):         IJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1NA7Ligand/IonSODIUM ION
2TL6Ligand/IonTHALLIUM (I) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2TL-1Ligand/IonTHALLIUM (I) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2TL-1Ligand/IonTHALLIUM (I) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2TL-1Ligand/IonTHALLIUM (I) ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDG E:582 , DG F:692 , DG G:802 , DG H:912 , NA H:1506 , DG I:1022 , TL I:1700 , DG J:1132 , DG K:1242 , DG L:1352BINDING SITE FOR RESIDUE NA E 1505
02AC2SOFTWAREDG E:582 , DG E:583 , NA E:1505 , TL E:1701 , DG F:692 , DG F:693 , DG G:802 , DG G:803 , DG H:912 , DG H:913BINDING SITE FOR RESIDUE NA H 1506
03AC3SOFTWAREDG E:584 , DG E:585 , DG F:694 , DG F:695 , NA F:1510 , DG G:804 , DG G:805 , DG H:914 , DG H:915BINDING SITE FOR RESIDUE NA E 1507
04AC4SOFTWAREDG E:585 , NA E:1507 , DG F:695 , DT F:696 , DG G:805 , DG H:915 , HOH H:1944BINDING SITE FOR RESIDUE NA F 1510
05AC5SOFTWAREDG I:1025 , TL I:1705 , DG J:1135 , DG K:1245 , DG L:1355BINDING SITE FOR RESIDUE NA K 1512
06AC6SOFTWAREDT A:101 , DG A:102 , DG B:212 , DT C:321 , DG C:322 , DG D:432 , TL D:1704BINDING SITE FOR RESIDUE NA A 1514
07AC7SOFTWAREDG A:104 , DG A:105 , DG B:214 , DG B:215 , TL B:1703 , DG C:324 , DG C:325 , DG D:434 , DG D:435BINDING SITE FOR RESIDUE NA A 1515
08AC8SOFTWARENA E:1505 , DG I:1022 , DG I:1023 , TL I:1702 , DG J:1132 , DG J:1133 , DG K:1242 , DG K:1243 , DG L:1352 , DG L:1353BINDING SITE FOR RESIDUE TL I 1700
09AC9SOFTWAREDG E:583 , DG E:584 , DG F:693 , DG F:694 , DG G:803 , DG G:804 , DG H:913 , DG H:914 , NA H:1506BINDING SITE FOR RESIDUE TL E 1701
10BC1SOFTWAREDG I:1023 , DG I:1024 , TL I:1700 , TL I:1705 , DG J:1133 , DG J:1134 , DG K:1243 , DG K:1244 , DG L:1353 , DG L:1354BINDING SITE FOR RESIDUE TL I 1702
11BC2SOFTWAREDG A:103 , DG A:104 , NA A:1515 , DG B:213 , DG B:214 , DG C:323 , DG C:324 , DG D:433 , DG D:434 , TL D:1704BINDING SITE FOR RESIDUE TL B 1703
12BC3SOFTWAREDG A:102 , DG A:103 , NA A:1514 , DG B:212 , DG B:213 , TL B:1703 , DG C:322 , DG C:323 , DG D:432 , DG D:433BINDING SITE FOR RESIDUE TL D 1704
13BC4SOFTWAREDG I:1024 , DG I:1025 , TL I:1702 , DG J:1134 , DG J:1135 , DG K:1244 , DG K:1245 , NA K:1512 , DG L:1354 , DG L:1355BINDING SITE FOR RESIDUE TL I 1705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S47)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S47)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S47)

(-) Exons   (0, 0)

(no "Exon" information available for 1S47)

(-) 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:6
                                       
                1s47 A  101 TGGGGT  106


Chain B from PDB  Type:DNA  Length:6
                                       
                1s47 B  211 TGGGGT  216


Chain C from PDB  Type:DNA  Length:6
                                       
                1s47 C  321 TGGGGT  326


Chain D from PDB  Type:DNA  Length:6
                                       
                1s47 D  431 TGGGGT  436


Chain E from PDB  Type:DNA  Length:6
                                       
                1s47 E  581 TGGGGT  586


Chain F from PDB  Type:DNA  Length:6
                                       
                1s47 F  691 TGGGGT  696


Chain G from PDB  Type:DNA  Length:6
                                       
                1s47 G  801 TGGGGT  806


Chain H from PDB  Type:DNA  Length:6
                                       
                1s47 H  911 TGGGGT  916


Chain I from PDB  Type:DNA  Length:6
                                       
                1s47 I 1021 TGGGGT 1026


Chain J from PDB  Type:DNA  Length:6
                                       
                1s47 J 1131 TGGGGT 1136


Chain K from PDB  Type:DNA  Length:6
                                       
                1s47 K 1241 TGGGGT 1246


Chain L from PDB  Type:DNA  Length:6
                                       
                1s47 L 1351 TGGGGT 1356
   Legend:   → Mismatch (orange background)
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  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 1S47)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1S47)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1S47)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1S47)

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  1s47
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 Related Entries

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