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(-) Description

Title :  CRYSTAL STRUCTURE OF D(G4T4G4) WITH FOUR QUADRUPLEXES IN THE ASYMMETRIC UNIT.
 
Authors :  M. P. H. Lee, G. N. Parkinson, S. Neidle
Date :  05 May 06  (Deposition) - 19 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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 :  Oxytricha, G-Quartet, G-Quadruplex, G-Tetrad, G-Tetraplex, Four Quadruplexes, Asymmetric Unit. , Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. P. H. Lee, S. Haider, G. N. Parkinson, S. Neidle
Crystal Structure Of D(G4T4G4) With Four And Six Quadruplexes In The Asymmetric Unit.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
    ChainsA, B, C, D, E, F, G, H
    EngineeredYES
    Other DetailsOXYTRICHA NOVA TELOMERIC SEQUENCE
    SyntheticYES

 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, 20)

Asymmetric Unit (1, 20)
No.NameCountTypeFull Name
1K20Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDG C:28 , DT C:29 , DT C:31 , DG C:33 , HOH C:129 , HOH C:131 , DG D:37 , DG D:48 , K D:98BINDING SITE FOR RESIDUE K C 97
02AC2SOFTWAREDG C:27 , DG C:28 , DG C:33 , DG C:34 , K C:97 , DG D:37 , DG D:38 , DG D:47 , DG D:48 , K D:99BINDING SITE FOR RESIDUE K D 98
03AC3SOFTWAREDG C:26 , DG C:27 , DG C:34 , DG C:35 , K C:100 , DG D:38 , DG D:39 , DG D:46 , DG D:47 , K D:98BINDING SITE FOR RESIDUE K D 99
04AC4SOFTWAREDG C:25 , DG C:26 , DG C:35 , DG C:36 , DG D:39 , DG D:40 , DG D:45 , DG D:46 , K D:99 , K D:101BINDING SITE FOR RESIDUE K C 100
05AC5SOFTWAREDG C:25 , DG C:36 , K C:100 , DG D:40 , DT D:41 , DT D:43 , DG D:45 , HOH D:139 , HOH D:186BINDING SITE FOR RESIDUE K D 101
06AC6SOFTWAREDG A:4 , DT A:5 , DT A:7 , DG A:9 , K A:103 , HOH A:117 , HOH A:118 , DG B:13 , DG B:24BINDING SITE FOR RESIDUE K A 102
07AC7SOFTWAREDG A:3 , DG A:4 , DG A:9 , DG A:10 , K A:102 , K A:104 , DG B:13 , DG B:14 , DG B:23 , DG B:24BINDING SITE FOR RESIDUE K A 103
08AC8SOFTWAREDG A:2 , DG A:3 , DG A:10 , DG A:11 , K A:103 , DG B:14 , DG B:15 , DG B:22 , DG B:23 , K B:105BINDING SITE FOR RESIDUE K A 104
09AC9SOFTWAREDG A:1 , DG A:2 , DG A:11 , DG A:12 , K A:104 , DG B:15 , DG B:16 , DG B:21 , DG B:22 , K B:106BINDING SITE FOR RESIDUE K B 105
10BC1SOFTWAREDG A:1 , DG A:12 , DG B:16 , DT B:17 , DT B:19 , DG B:21 , K B:105 , HOH B:167 , HOH B:171BINDING SITE FOR RESIDUE K B 106
11BC2SOFTWAREDG G:73 , DG G:84 , K G:108 , DG H:88 , DT H:89 , DT H:91 , DG H:93 , HOH H:150 , HOH H:163BINDING SITE FOR RESIDUE K H 107
12BC3SOFTWAREDG G:73 , DG G:74 , DG G:83 , DG G:84 , K G:109 , DG H:87 , DG H:88 , DG H:93 , DG H:94 , K H:107BINDING SITE FOR RESIDUE K G 108
13BC4SOFTWAREDG G:74 , DG G:75 , DG G:82 , DG G:83 , K G:108 , K G:110 , DG H:86 , DG H:87 , DG H:94 , DG H:95BINDING SITE FOR RESIDUE K G 109
14BC5SOFTWAREDG G:75 , DG G:76 , DG G:81 , DG G:82 , K G:109 , K G:111 , DG H:85 , DG H:86 , DG H:95 , DG H:96BINDING SITE FOR RESIDUE K G 110
15BC6SOFTWAREDG G:76 , DT G:77 , DT G:79 , DG G:81 , K G:110 , HOH G:119 , HOH G:122 , DG H:85 , DG H:96BINDING SITE FOR RESIDUE K G 111
16BC7SOFTWAREDG E:52 , DT E:53 , DT E:55 , DG E:57 , K E:113 , HOH E:124 , DG F:61 , DG F:72BINDING SITE FOR RESIDUE K E 112
17BC8SOFTWAREDG E:51 , DG E:52 , DG E:57 , DG E:58 , K E:112 , K E:114 , DG F:61 , DG F:62 , DG F:71 , DG F:72BINDING SITE FOR RESIDUE K E 113
18BC9SOFTWAREDG E:50 , DG E:51 , DG E:58 , DG E:59 , K E:113 , K E:115 , DG F:62 , DG F:63 , DG F:70 , DG F:71BINDING SITE FOR RESIDUE K E 114
19CC1SOFTWAREDG E:49 , DG E:50 , DG E:59 , DG E:60 , K E:114 , DG F:63 , DG F:64 , DG F:69 , DG F:70 , K F:116BINDING SITE FOR RESIDUE K E 115
20CC2SOFTWAREDG E:49 , DG E:60 , K E:115 , DG F:64 , DT F:65 , DT F:67 , DG F:69 , HOH F:127 , HOH F:144BINDING SITE FOR RESIDUE K F 116

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GWQ)

(-) 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
                                           
                  2gwq A  1 GGGGTTTTGGGG 12
                                    10  

Chain B from PDB  Type:DNA  Length:12
                                           
                  2gwq B 13 GGGGTTTTGGGG 24
                                    22  

Chain C from PDB  Type:DNA  Length:12
                                           
                  2gwq C 25 GGGGTTTTGGGG 36
                                    34  

Chain D from PDB  Type:DNA  Length:12
                                           
                  2gwq D 37 GGGGTTTTGGGG 48
                                    46  

Chain E from PDB  Type:DNA  Length:12
                                           
                  2gwq E 49 GGGGTTTTGGGG 60
                                    58  

Chain F from PDB  Type:DNA  Length:12
                                           
                  2gwq F 61 GGGGTTTTGGGG 72
                                    70  

Chain G from PDB  Type:DNA  Length:12
                                           
                  2gwq G 73 GGGGTTTTGGGG 84
                                    82  

Chain H from PDB  Type:DNA  Length:12
                                           
                  2gwq H 85 GGGGTTTTGGGG 96
                                    94  

   Legend:   → Mismatch (orange background)
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  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 2GWQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2GWQ)

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