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(-) Description

Title :  CRYSTAL STRUCTURE OF D(G4T4G4) WITH SIX QUADRUPLEXES IN THE ASYMMETRIC UNIT.
 
Authors :  M. P. H. Lee, S. Haider, G. N. Parkinson, S. Neidle
Date :  04 May 06  (Deposition) - 19 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Biol. Unit 5:  I,J  (1x)
Biol. Unit 6:  K,L  (1x)
Keywords :  Oxytricha, G-Quartet, G-Quadruplex, G-Tetrad, G-Tetraplex, Six 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, I, J, K, L
    EngineeredYES
    Other DetailsOXYTRICHA NOVA TELOMERIC SEQUENCE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (1x)AB          
Biological Unit 2 (1x)  CD        
Biological Unit 3 (1x)    EF      
Biological Unit 4 (1x)      GH    
Biological Unit 5 (1x)        IJ  
Biological Unit 6 (1x)          KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 30)

Asymmetric Unit (1, 30)
No.NameCountTypeFull Name
1K30Ligand/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
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDG C:28 , DT C:29 , DT C:31 , DG C:33 , K C:146 , HOH C:211 , DG D:37 , DG D:48BINDING SITE FOR RESIDUE K C 145
02AC2SOFTWAREDG C:27 , DG C:28 , DG C:33 , DG C:34 , K C:145 , K C:147 , DG D:37 , DG D:38 , DG D:47 , DG D:48BINDING SITE FOR RESIDUE K C 146
03AC3SOFTWAREDG C:26 , DG C:27 , DG C:34 , DG C:35 , K C:146 , K C:148 , DG D:38 , DG D:39 , DG D:46 , DG D:47BINDING SITE FOR RESIDUE K C 147
04AC4SOFTWAREDG C:25 , DG C:26 , DG C:35 , DG C:36 , K C:147 , DG D:39 , DG D:40 , DG D:45 , DG D:46 , K D:149BINDING SITE FOR RESIDUE K C 148
05AC5SOFTWAREDG C:25 , DG C:36 , K C:148 , DG D:40 , DT D:41 , DT D:43 , DG D:45 , HOH D:197BINDING SITE FOR RESIDUE K D 149
06AC6SOFTWAREDG E:49 , DG E:60 , K E:151 , DG F:64 , DT F:65 , DT F:67 , DG F:69 , HOH F:206 , HOH F:208BINDING SITE FOR RESIDUE K F 150
07AC7SOFTWAREDG E:49 , DG E:50 , DG E:59 , DG E:60 , DG F:63 , DG F:64 , DG F:69 , DG F:70 , K F:150 , K F:152BINDING SITE FOR RESIDUE K E 151
08AC8SOFTWAREDG E:50 , DG E:51 , DG E:58 , DG E:59 , K E:151 , K E:153 , DG F:62 , DG F:63 , DG F:70 , DG F:71BINDING SITE FOR RESIDUE K F 152
09AC9SOFTWAREDG E:51 , DG E:52 , DG E:57 , DG E:58 , K E:154 , DG F:61 , DG F:62 , DG F:71 , DG F:72 , K F:152BINDING SITE FOR RESIDUE K E 153
10BC1SOFTWAREDG E:52 , DT E:53 , DT E:55 , DG E:57 , K E:153 , HOH E:176 , HOH E:269 , DG F:61 , DG F:72BINDING SITE FOR RESIDUE K E 154
11BC2SOFTWAREDG I:97 , DG I:108 , K I:156 , DG J:112 , DT J:113 , DT J:115 , DG J:117 , HOH J:175BINDING SITE FOR RESIDUE K J 155
12BC3SOFTWAREDG I:97 , DG I:98 , DG I:107 , DG I:108 , DG J:111 , DG J:112 , DG J:117 , DG J:118 , K J:155 , K J:157BINDING SITE FOR RESIDUE K I 156
13BC4SOFTWAREDG I:98 , DG I:99 , DG I:106 , DG I:107 , K I:156 , DG J:110 , DG J:111 , DG J:118 , DG J:119 , K J:158BINDING SITE FOR RESIDUE K J 157
14BC5SOFTWAREDG I:99 , DG I:100 , DG I:105 , DG I:106 , K I:159 , DG J:109 , DG J:110 , DG J:119 , DG J:120 , K J:157BINDING SITE FOR RESIDUE K J 158
15BC6SOFTWAREDG I:100 , DT I:101 , DT I:103 , DG I:105 , DG J:109 , DG J:120 , K J:158 , HOH J:198BINDING SITE FOR RESIDUE K I 159
16BC7SOFTWAREDG A:1 , DG A:12 , K A:161 , DG B:16 , DT B:17 , DT B:19 , DG B:21 , HOH B:177BINDING SITE FOR RESIDUE K B 160
17BC8SOFTWAREDG A:1 , DG A:2 , DG A:11 , DG A:12 , K A:162 , DG B:15 , DG B:16 , DG B:21 , DG B:22 , K B:160BINDING SITE FOR RESIDUE K A 161
18BC9SOFTWAREDG A:2 , DG A:3 , DG A:10 , DG A:11 , K A:161 , K A:163 , DG B:14 , DG B:15 , DG B:22 , DG B:23BINDING SITE FOR RESIDUE K A 162
19CC1SOFTWAREDG A:3 , DG A:4 , DG A:9 , DG A:10 , K A:162 , K A:164 , DG B:13 , DG B:14 , DG B:23 , DG B:24BINDING SITE FOR RESIDUE K A 163
20CC2SOFTWAREDG A:4 , DT A:5 , DT A:7 , DG A:9 , K A:163 , HOH A:195 , HOH A:227 , DG B:13 , DG B:24BINDING SITE FOR RESIDUE K A 164
21CC3SOFTWAREDG G:73 , DG G:84 , K G:166 , DG H:88 , DT H:89 , DT H:91 , DG H:93 , HOH H:180 , HOH H:193BINDING SITE FOR RESIDUE K H 165
22CC4SOFTWAREDG G:73 , DG G:74 , DG G:83 , DG G:84 , K G:167 , DG H:87 , DG H:88 , DG H:93 , DG H:94 , K H:165BINDING SITE FOR RESIDUE K G 166
23CC5SOFTWAREDG G:74 , DG G:75 , DG G:82 , DG G:83 , K G:166 , K G:168 , DG H:86 , DG H:87 , DG H:94 , DG H:95BINDING SITE FOR RESIDUE K G 167
24CC6SOFTWAREDG G:75 , DG G:76 , DG G:81 , DG G:82 , K G:167 , K G:169 , DG H:85 , DG H:86 , DG H:95 , DG H:96BINDING SITE FOR RESIDUE K G 168
25CC7SOFTWAREDG G:76 , DT G:77 , DT G:79 , DG G:81 , K G:168 , HOH G:235 , DG H:85 , DG H:96BINDING SITE FOR RESIDUE K G 169
26CC8SOFTWAREDG K:124 , DT K:125 , DT K:127 , DG K:129 , K K:171 , HOH K:182 , HOH K:190 , DG L:133 , DG L:144BINDING SITE FOR RESIDUE K K 170
27CC9SOFTWAREDG K:123 , DG K:124 , DG K:129 , DG K:130 , K K:170 , K K:172 , DG L:133 , DG L:134 , DG L:143 , DG L:144BINDING SITE FOR RESIDUE K K 171
28DC1SOFTWAREDG K:122 , DG K:123 , DG K:130 , DG K:131 , K K:171 , DG L:134 , DG L:135 , DG L:142 , DG L:143 , K L:173BINDING SITE FOR RESIDUE K K 172
29DC2SOFTWAREDG K:121 , DG K:122 , DG K:131 , DG K:132 , K K:172 , DG L:135 , DG L:136 , DG L:141 , DG L:142 , K L:174BINDING SITE FOR RESIDUE K L 173
30DC3SOFTWAREDG K:121 , DG K:132 , HOH K:178 , DG L:136 , DT L:137 , DT L:139 , DG L:141 , K L:173BINDING SITE FOR RESIDUE K L 174

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GWE)

(-) 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
                                            
                 2gwe A   1 GGGGTTTTGGGG  12
                                    10  

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

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

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

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

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

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

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

Chain I from PDB  Type:DNA  Length:12
                                            
                 2gwe I  97 GGGGTTTTGGGG 108
                                   106  

Chain J from PDB  Type:DNA  Length:12
                                            
                 2gwe J 109 GGGGTTTTGGGG 120
                                   118  

Chain K from PDB  Type:DNA  Length:12
                                            
                 2gwe K 121 GGGGTTTTGGGG 132
                                   130  

Chain L from PDB  Type:DNA  Length:12
                                            
                 2gwe L 133 GGGGTTTTGGGG 144
                                   142  

   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 2GWE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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