1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hwang, G.S.
Jones, G.B.
Goldberg, I.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C31 H31 N O7
529.580
SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI)
non-polymer
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
N
C
N
12
R
C
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
N
N
72
R
C
N
73
R
C
N
74
N
O
N
75
S
C
N
76
N
O
N
77
R
C
N
78
N
C
N
79
N
O
N
80
N
O
N
81
R
C
N
82
N
O
N
83
S
C
N
84
N
C
N
85
S
C
N
86
S
C
Y
87
N
C
Y
88
N
C
Y
89
N
C
Y
90
N
C
Y
91
N
C
Y
92
N
C
Y
93
N
C
Y
94
N
C
Y
95
N
C
Y
96
N
C
N
97
N
C
N
98
N
O
N
99
S
C
Y
100
N
C
Y
101
N
C
Y
102
N
C
Y
103
N
C
Y
104
N
C
Y
105
N
C
N
106
N
C
N
107
N
C
N
108
N
C
N
109
N
O
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
O
N
142
N
P
N
143
N
O
N
144
N
O
N
145
N
O
N
146
N
C
N
147
R
C
N
148
N
O
N
149
S
C
N
150
N
O
N
151
N
C
N
152
R
C
Y
153
N
N
Y
154
N
C
Y
155
N
N
Y
156
N
C
N
157
N
C
N
158
N
O
N
159
N
N
N
160
N
C
N
161
N
N
N
162
N
N
Y
163
N
C
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
O
N
179
N
P
N
180
N
O
N
181
N
O
N
182
N
O
N
183
N
C
N
184
R
C
N
185
N
O
N
186
S
C
N
187
N
O
N
188
N
C
N
189
R
C
N
190
N
N
N
191
N
C
N
192
N
O
N
193
N
N
N
194
N
C
N
195
N
O
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
Y
111
N
doub
Y
112
N
sing
Y
113
N
sing
N
114
N
sing
Y
115
N
doub
Y
116
N
sing
Y
117
N
sing
N
118
N
sing
Y
119
N
doub
N
120
N
sing
Y
121
N
sing
N
122
N
sing
Y
123
N
doub
N
124
N
sing
Y
125
N
sing
Y
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
doub
N
130
N
sing
N
131
N
sing
Y
132
N
doub
Y
133
N
sing
Y
134
N
sing
N
135
N
sing
Y
136
N
doub
N
137
N
sing
Y
138
N
sing
N
139
N
sing
Y
140
N
doub
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
Y
173
N
sing
Y
174
N
sing
Y
175
N
doub
N
176
N
sing
Y
177
N
sing
N
178
N
sing
Y
179
N
doub
N
180
N
doub
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
doub
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
doub
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
doub
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
doub
N
219
N
sing
N
220
N
sing
N
221
N
doub
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
42
8472
8483
10.1021/bi030072d
12859193
Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA
2003
10.2210/pdb1p96/pdb
pdb_00001p96
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
4265.780
5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3'
1
syn
polymer
3694.402
5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3'
1
syn
polymer
529.580
SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI)
1
syn
non-polymer
no
no
(DC)(DA)(DC)(DG)(DC)(DA)(DG)(DT)(DT)(DC)(DG)(DG)(DA)(DC)
CACGCAGTTCGGAC
A
polydeoxyribonucleotide
no
no
(DG)(DT)(DC)(DC)(DG)(DA)(DT)(DG)(DC)(DG)(DT)(DG)
GTCCGATGCGTG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-4.621
1
19
A
1
B
12
2.782
A_DC1:DG12_B
1
18.115
0.274
0.713
-0.043
21.060
1
20
A
2
B
11
0.902
A_DA2:DT11_B
2
15.436
-0.185
1.407
-0.293
-14.788
1
19
A
3
B
10
-4.544
A_DC3:DG10_B
3
9.927
0.342
-0.016
-0.031
16.739
1
19
A
4
B
9
-4.336
A_DG4:DC9_B
4
8.890
-0.324
0.127
-0.015
-16.767
1
19
A
5
B
8
-3.863
A_DC5:DG8_B
5
24.556
0.285
0.227
-0.061
4.308
A
6
B
7
-23.263
A_DA6:DT7_B
6
36.893
0.013
0.409
0.597
-13.078
A
9
B
6
8.034
A_DT9:DA6_B
7
-3.940
0.253
-0.441
0.321
-31.018
1
19
A
10
B
5
-7.150
A_DC10:DG5_B
8
9.511
0.061
1.820
-0.481
8.820
1
19
A
11
B
4
-1.719
A_DG11:DC4_B
9
12.094
-0.319
0.769
-0.146
8.609
1
19
A
12
B
3
-5.043
A_DG12:DC3_B
10
12.246
-0.309
-0.120
-0.060
24.966
1
20
A
13
B
2
-6.049
A_DA13:DT2_B
11
6.230
-0.006
1.362
-0.194
3.070
1
19
A
14
B
1
-14.169
A_DC14:DG1_B
12
18.967
0.452
-1.074
-0.474
3.122
37.641
A
A
1
2
-20.213
B
B
12
11
3.327
-12.772
-0.343
0.111
AA_DC1DA2:DT11DG12_BB
1
-4.280
6.773
35.230
1.867
-0.037
5.764
37.601
A
A
2
3
-6.446
B
B
11
10
5.976
-4.130
-0.884
-0.322
AA_DA2DC3:DG10DT11_BB
2
6.096
-9.515
36.898
0.475
2.810
2.537
35.882
A
A
3
4
-20.271
B
B
10
9
2.721
-12.252
-0.060
0.092
AA_DC3DG4:DC9DG10_BB
3
-0.716
1.185
33.783
1.606
0.012
4.170
38.479
A
A
4
5
19.559
B
B
9
8
4.880
12.655
0.523
-1.276
AA_DG4DC5:DG8DC9_BB
4
-2.875
4.443
36.303
-4.180
-1.304
4.019
28.646
A
A
5
6
-1.839
B
B
8
7
4.119
-0.909
-1.867
0.199
AA_DC5DA6:DT7DG8_BB
5
1.378
-2.787
28.599
0.658
4.161
5.068
43.872
A
A
9
10
3.570
B
B
6
5
4.846
2.615
-1.464
0.353
AA_DT9DC10:DG5DA6_BB
6
-15.334
20.937
41.149
0.082
-0.326
2.399
32.232
A
A
10
11
-8.445
B
B
5
4
2.409
-4.667
0.258
-0.007
AA_DC10DG11:DC4DG5_BB
7
2.885
-5.220
31.774
0.603
-0.085
3.821
36.874
A
A
11
12
12.838
B
B
4
3
3.913
8.031
-0.056
0.218
AA_DG11DG12:DC3DC4_BB
8
5.490
-8.777
35.611
-0.965
0.985
3.198
37.208
A
A
12
13
-4.079
B
B
3
2
3.261
-2.592
0.241
-0.154
AA_DG12DA13:DT2DC3_BB
9
-5.390
8.481
36.741
0.101
-1.090
4.843
43.687
A
A
13
14
-27.407
B
B
2
1
5.545
-19.617
-0.397
-0.005
AA_DA13DC14:DG1DT2_BB
10
7.789
-10.882
38.470
3.192
1.804
database_2
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2003-08-26
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-02-23
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_spectrometer.model
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
The complexed structure of the bulge DNA and natural product with a similar aglycone structure.
RCSB
Y
RCSB
2003-05-09
REL
DDI
SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI)
This sequence was synthesized by DNA synthesizer.
sample
This sequence was synthesized by DNA synthesizer.
sample
This structure was determined using 2D homonuclear and heteronuclear techniques.
all calculated structures submitted
10
10
2D NOESY
2D TOCSY
DQF-COSY
H-P COSY
COSY-45
0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA
6.5
ambient
298
K
The structures are based on a total of 694 NOE restranints and 166 dihedral angle restraints.
distance geometry
sinulated annealing
1
all calculated structures submited have the least restraint violation and the lowst energy.
1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20
90% H20/10% D20; 99.96% D20
Delaglio, F.
processing
NMRPipe
2002.044.17.08
Goddard, T.D. and Kneller, D.G.
data analysis
Sparky
3.106
Brunger, A.T. et al
refinement
CNS
1.0
600
Bruker
AVANCE
750
Varian
INOVA
500
Varian
INOVA
DDI
1
3
DDI
DDI
21
A
CYT
1
n
1
DC
1
A
ADE
2
n
2
DA
2
A
CYT
3
n
3
DC
3
A
GUA
4
n
4
DG
4
A
CYT
5
n
5
DC
5
A
ADE
6
n
6
DA
6
A
GUA
7
n
7
DG
7
A
THY
8
n
8
DT
8
A
THY
9
n
9
DT
9
A
CYT
10
n
10
DC
10
A
GUA
11
n
11
DG
11
A
GUA
12
n
12
DG
12
A
ADE
13
n
13
DA
13
A
CYT
14
n
14
DC
14
A
GUA
1
n
1
DG
1
B
THY
2
n
2
DT
2
B
CYT
3
n
3
DC
3
B
CYT
4
n
4
DC
4
B
GUA
5
n
5
DG
5
B
ADE
6
n
6
DA
6
B
THY
7
n
7
DT
7
B
GUA
8
n
8
DG
8
B
CYT
9
n
9
DC
9
B
GUA
10
n
10
DG
10
B
THY
11
n
11
DT
11
B
GUA
12
n
12
DG
12
B
author_defined_assembly
2
dimeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
C27
DDI
21
WRONG HAND
1
A
C28
DDI
21
WRONG HAND
1
A
C29
DDI
21
WRONG HAND
1
A
C30
DDI
21
WRONG HAND
1
A
C26
DDI
21
WRONG HAND
1
A
C25
DDI
21
WRONG HAND
1
A
C12
DDI
21
WRONG HAND
1
A
C11
DDI
21
WRONG HAND
1
A
C9
DDI
21
WRONG HAND
2
A
C27
DDI
21
WRONG HAND
2
A
C28
DDI
21
WRONG HAND
2
A
C29
DDI
21
WRONG HAND
2
A
C30
DDI
21
WRONG HAND
2
A
C26
DDI
21
WRONG HAND
2
A
C25
DDI
21
WRONG HAND
2
A
C12
DDI
21
WRONG HAND
2
A
C11
DDI
21
WRONG HAND
2
A
C9
DDI
21
WRONG HAND
3
A
C27
DDI
21
WRONG HAND
3
A
C28
DDI
21
WRONG HAND
3
A
C29
DDI
21
WRONG HAND
3
A
C30
DDI
21
WRONG HAND
3
A
C26
DDI
21
WRONG HAND
3
A
C25
DDI
21
WRONG HAND
3
A
C12
DDI
21
WRONG HAND
3
A
C11
DDI
21
WRONG HAND
3
A
C9
DDI
21
WRONG HAND
4
A
C27
DDI
21
WRONG HAND
4
A
C28
DDI
21
WRONG HAND
4
A
C29
DDI
21
WRONG HAND
4
A
C30
DDI
21
WRONG HAND
4
A
C26
DDI
21
WRONG HAND
4
A
C25
DDI
21
WRONG HAND
4
A
C12
DDI
21
WRONG HAND
4
A
C11
DDI
21
WRONG HAND
4
A
C9
DDI
21
WRONG HAND
5
A
C27
DDI
21
WRONG HAND
5
A
C28
DDI
21
WRONG HAND
5
A
C29
DDI
21
WRONG HAND
5
A
C30
DDI
21
WRONG HAND
5
A
C26
DDI
21
WRONG HAND
5
A
C25
DDI
21
WRONG HAND
5
A
C12
DDI
21
WRONG HAND
5
A
C11
DDI
21
WRONG HAND
5
A
C9
DDI
21
WRONG HAND
6
A
C27
DDI
21
WRONG HAND
6
A
C28
DDI
21
WRONG HAND
6
A
C29
DDI
21
WRONG HAND
6
A
C30
DDI
21
WRONG HAND
6
A
C26
DDI
21
WRONG HAND
6
A
C25
DDI
21
WRONG HAND
6
A
C12
DDI
21
WRONG HAND
6
A
C11
DDI
21
WRONG HAND
6
A
C9
DDI
21
WRONG HAND
7
A
C27
DDI
21
WRONG HAND
7
A
C28
DDI
21
WRONG HAND
7
A
C29
DDI
21
WRONG HAND
7
A
C30
DDI
21
WRONG HAND
7
A
C26
DDI
21
WRONG HAND
7
A
C25
DDI
21
WRONG HAND
7
A
C12
DDI
21
WRONG HAND
7
A
C11
DDI
21
WRONG HAND
7
A
C9
DDI
21
WRONG HAND
8
A
C27
DDI
21
WRONG HAND
8
A
C28
DDI
21
WRONG HAND
8
A
C29
DDI
21
WRONG HAND
8
A
C30
DDI
21
WRONG HAND
8
A
C26
DDI
21
WRONG HAND
8
A
C25
DDI
21
WRONG HAND
8
A
C12
DDI
21
WRONG HAND
8
A
C11
DDI
21
WRONG HAND
8
A
C9
DDI
21
WRONG HAND
9
A
C27
DDI
21
WRONG HAND
9
A
C28
DDI
21
WRONG HAND
9
A
C29
DDI
21
WRONG HAND
9
A
C30
DDI
21
WRONG HAND
9
A
C26
DDI
21
WRONG HAND
9
A
C25
DDI
21
WRONG HAND
9
A
C12
DDI
21
WRONG HAND
9
A
C11
DDI
21
WRONG HAND
9
A
C9
DDI
21
WRONG HAND
10
A
C27
DDI
21
WRONG HAND
10
A
C28
DDI
21
WRONG HAND
10
A
C29
DDI
21
WRONG HAND
10
A
C30
DDI
21
WRONG HAND
10
A
C26
DDI
21
WRONG HAND
10
A
C25
DDI
21
WRONG HAND
10
A
C12
DDI
21
WRONG HAND
10
A
C11
DDI
21
WRONG HAND
10
A
C9
DDI
21
WRONG HAND
Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA
1
N
N
2
N
N
3
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
12
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
12
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
12
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
DT
11
B
N3
DT
11
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
DT
11
B
O4
DT
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
10
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
10
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
10
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
8
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
8
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
8
B
N2
DG
8
1_555
hydrog
DA-DT PAIR
A
DA
6
A
N6
DA
6
1_555
B
DT
7
B
O4
DT
7
1_555
hydrog
DT-DA PAIR
A
DT
9
A
N3
DT
9
1_555
B
DA
6
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
5
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
5
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
5
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
DC
4
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
DC
4
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
DC
4
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
3
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
3
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
3
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N1
DA
13
1_555
B
DT
2
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N6
DA
13
1_555
B
DT
2
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DC
14
A
N3
DC
14
1_555
B
DG
1
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
14
A
N4
DC
14
1_555
B
DG
1
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
14
A
O2
DC
14
1_555
B
DG
1
B
N2
DG
1
1_555
DNA
Wedge-shaped synthetic drug-bulged DNA complex, DNA
1P96
PDB
1
1P96
1P96
PDB
2
1P96
1
14
1P96
1
14
1P96
A
1
1
14
1
12
1P96
1
12
1P96
B
2
1
12
BINDING SITE FOR RESIDUE DDI A 21
A
DDI
21
Software
4
A
DA
6
A
DA
6
4
1_555
A
DG
7
A
DG
7
4
1_555
A
DT
9
A
DT
9
4
1_555
B
DT
7
B
DT
7
4
1_555