1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kumar, S.
Reed, M.W.
Gamper Junior, H.B.
Gorn, V.V.
Lukhtanov, E.A.
Foti, M.
West, J.
Meyer Junior, R.B.
Schweitzer, B.I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
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
C50 H53 N10 O12 P
1016.989
PHOSPHONIC ACID 6-({6-[6-(6-CARBAMOYL-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONYL)-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDOCENE-2-CA RBONYL]-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONL}-AMINO)-HEXYL ESTER 5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL ESTER
CDPI3
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
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
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
H
N
142
N
H
N
143
N
H
N
144
R
C
N
145
N
C
N
146
N
C
N
147
N
C
N
148
N
C
Y
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
Y
153
N
C
Y
154
N
C
N
155
N
C
N
156
N
C
Y
157
N
C
Y
158
N
C
N
159
N
C
N
160
N
C
N
161
N
C
Y
162
N
C
Y
163
N
C
Y
164
N
C
Y
165
N
C
Y
166
N
C
N
167
S
C
Y
168
N
C
Y
169
N
C
Y
170
N
C
N
171
N
C
N
172
N
C
N
173
N
C
Y
174
N
C
Y
175
N
C
Y
176
N
C
Y
177
N
C
N
178
N
C
N
179
R
C
Y
180
N
C
Y
181
N
C
Y
182
N
C
Y
183
N
C
N
184
N
C
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
C
N
193
N
C
N
194
N
N
N
195
N
N
N
196
N
N
N
197
N
N
N
198
N
N
Y
199
N
N
N
200
N
N
Y
201
N
N
N
202
N
N
Y
203
N
N
N
204
N
O
N
205
N
O
N
206
N
O
N
207
N
O
N
208
N
O
N
209
N
O
N
210
N
O
N
211
N
O
N
212
N
O
N
213
N
O
N
214
N
O
N
215
N
O
N
216
S
P
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
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
doub
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
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
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
doub
Y
167
N
doub
Y
168
N
sing
Y
169
N
sing
N
170
N
sing
Y
171
N
sing
Y
172
N
doub
Y
173
N
doub
Y
174
N
sing
Y
175
N
sing
N
176
N
sing
Y
177
N
doub
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
Y
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
doub
Y
197
N
doub
Y
198
N
sing
Y
199
N
sing
N
200
N
sing
Y
201
N
sing
Y
202
N
doub
Y
203
N
doub
Y
204
N
sing
Y
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
Y
210
N
doub
N
211
N
sing
Y
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
doub
Y
224
N
doub
Y
225
N
sing
Y
226
N
sing
N
227
N
sing
Y
228
N
sing
Y
229
N
doub
Y
230
N
doub
Y
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
doub
N
235
N
sing
N
236
N
sing
N
237
N
sing
Y
238
N
sing
N
239
N
sing
Y
240
N
doub
N
241
N
sing
Y
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
doub
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
doub
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
26
831
838
10.1093/nar/26.3.831
9443977
Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.
1998
10.2210/pdb1aul/pdb
pdb_00001aul
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA RESIDUE WITH A HEXAMETHYLENE LINKER
3744.794
DNA (5'-D(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3')
1
syn
polymer
TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA RESIDUE WITH A HEXAMETHYLENE LINKER
3037.032
DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3')
1
syn
polymer
no
yes
(THX)(DG)(DA)(DT)(DT)(DA)(DT)(DC)(DT)(DG)
NGATTATCTG
A
polydeoxyribonucleotide
no
no
(DC)(DA)(DG)(DA)(DT)(DA)(DA)(DT)(DC)(DA)
CAGATAATCA
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
0.709
1
A
2
B
19
26.294
A_DG2:DC19_B
1
7.219
0.840
0.941
0.149
3.244
1
20
A
3
B
18
14.693
A_DA3:DT18_B
2
-20.653
-1.088
0.744
-0.539
-24.666
1
20
A
4
B
17
14.899
A_DT4:DA17_B
3
-11.516
0.144
1.258
-0.460
-9.415
1
20
A
5
B
16
4.457
A_DT5:DA16_B
4
-1.416
-0.283
0.534
-0.212
-1.083
1
20
A
6
B
15
-6.322
A_DA6:DT15_B
5
-6.569
0.467
-0.465
-0.077
16.877
1
20
A
7
B
14
1.194
A_DT7:DA14_B
6
-14.113
-0.175
-0.590
-0.122
7.590
1
19
A
8
B
13
3.882
A_DC8:DG13_B
7
-8.338
0.684
-0.424
-0.242
9.588
1
20
A
9
B
12
-5.710
A_DT9:DA12_B
8
-7.991
0.400
0.176
-0.259
6.923
1
19
A
10
B
11
-3.536
A_DG10:DC11_B
9
1.045
-0.616
0.206
-0.342
2.674
28.852
A
A
2
3
14.748
B
B
19
18
3.171
7.125
0.023
-0.895
AA_DG2DA3:DT18DC19_BB
1
9.932
-20.557
26.185
-3.287
2.032
4.196
42.791
A
A
3
4
13.320
B
B
18
17
4.347
9.642
0.458
-0.197
AA_DA3DT4:DA17DT18_BB
2
-0.655
0.905
41.736
-1.545
-0.715
2.913
29.589
A
A
4
5
7.458
B
B
17
16
3.031
3.791
-0.064
-0.560
AA_DT4DT5:DA16DA17_BB
3
3.245
-6.383
29.174
-1.830
0.755
2.273
35.981
A
A
5
6
9.916
B
B
16
15
2.762
6.010
-0.531
-1.104
AA_DT5DA6:DT15DA16_BB
4
10.725
-17.696
33.881
-2.467
2.074
2.672
34.716
A
A
6
7
10.360
B
B
15
14
2.782
6.151
0.506
-0.384
AA_DA6DT7:DA14DT15_BB
5
-0.186
0.313
34.183
-1.435
-0.871
3.115
38.710
A
A
7
8
17.651
B
B
14
13
3.388
11.535
-0.478
-0.453
AA_DT7DC8:DG13DA14_BB
6
0.019
-0.029
37.015
-2.124
0.723
3.586
37.505
A
A
8
9
-9.038
B
B
13
12
3.505
-5.778
-0.102
-0.869
AA_DC8DT9:DA12DG13_BB
7
-4.169
6.521
36.846
-0.524
-0.439
2.824
30.325
A
A
9
10
4.864
B
B
12
11
2.927
2.490
-0.705
-1.955
AA_DT9DG10:DC11DA12_BB
8
-10.600
20.704
28.346
-4.194
-0.595
chem_comp
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Structure summary
Data collection
1
0
1997-12-24
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
1
4
2024-05-22
_chem_comp.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_conn.pdbx_leaving_atom_flag
Y
BNL
1997-08-29
REL
CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER
sample
CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER
sample
LEAST RESTRAINT VIOLATION
6
1
NOESY
DQF-COSY
HETEROTOCSY
TOCSY
6.0
293.15
K
CANONICAL B-TYPE STRUCTURE USED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS GENERATING SIX STRUCTURES FROM DIFFERENT RANDOM NUMBER SEEDS. THE SIX STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX REFINEMENT TO GENERATE THE SIX FINAL STRUCTURES. THESE SIX STRUCTURES WERE AVERAGED AND MINIMIZED TO GIVE THE FINAL STRUCTURE PRESENTED HERE.
RESTRAINED MOLECULAR DYNAMICS/RELAXATION MATRIX REFINEMENT
BRUNGER
refinement
X-PLOR
structure solution
X-PLOR
3.1
600
Varian
UNITYPLUS
THX
1
n
1
THX
1
A
G
2
n
2
DG
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
T
5
n
5
DT
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
C
8
n
8
DC
8
A
T
9
n
9
DT
9
A
G
10
n
10
DG
10
A
C
11
n
1
DC
11
B
A
12
n
2
DA
12
B
G
13
n
3
DG
13
B
A
14
n
4
DA
14
B
T
15
n
5
DT
15
B
A
16
n
6
DA
16
B
A
17
n
7
DA
17
B
T
18
n
8
DT
18
B
C
19
n
9
DC
19
B
A
20
n
10
DA
20
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
B
O4
H61
THX
DA
1
20
1.39
1
A
B
H3
N1
THX
DA
1
20
1.57
1
B
DC
19
0.072
SIDE CHAIN
1
B
DA
20
0.059
SIDE CHAIN
1
B
B
O3'
P
DT
DC
18
19
1.75
1
-3.72
0.60
128.60
124.88
A
A
A
C5
C6
O6
DG
DG
DG
10
10
10
N
1
-3.72
0.60
128.60
124.88
B
B
B
C5
C6
O6
DG
DG
DG
13
13
13
N
1
A
A
O3'
P
THX
DG
1
2
0.127
0.012
1.607
1.734
Y
1
A
A
P
O5'
DG
DG
2
2
0.149
0.010
1.593
1.742
N
1
A
A
O3'
P
DG
DA
2
3
0.123
0.012
1.607
1.730
Y
1
A
A
P
O5'
DA
DA
3
3
0.133
0.010
1.593
1.726
N
1
A
A
N9
C4
DA
DA
3
3
-0.042
0.006
1.374
1.332
N
1
A
A
O3'
P
DA
DT
3
4
0.124
0.012
1.607
1.731
Y
1
A
A
P
O5'
DT
DT
4
4
0.140
0.010
1.593
1.733
N
1
A
A
O3'
P
DT
DT
4
5
0.118
0.012
1.607
1.725
Y
1
A
A
P
O5'
DT
DT
5
5
0.123
0.010
1.593
1.716
N
1
A
A
O3'
P
DT
DA
5
6
0.115
0.012
1.607
1.722
Y
1
A
A
P
O5'
DA
DA
6
6
0.134
0.010
1.593
1.727
N
1
A
A
C3'
C2'
DA
DA
6
6
0.134
0.012
1.518
1.652
N
1
A
A
O3'
P
DA
DT
6
7
0.122
0.012
1.607
1.729
Y
1
A
A
P
O5'
DT
DT
7
7
0.137
0.010
1.593
1.730
N
1
A
A
O3'
P
DT
DC
7
8
0.127
0.012
1.607
1.734
Y
1
A
A
P
O5'
DC
DC
8
8
0.140
0.010
1.593
1.733
N
1
A
A
O3'
P
DC
DT
8
9
0.123
0.012
1.607
1.730
Y
1
A
A
P
O5'
DT
DT
9
9
0.133
0.010
1.593
1.726
N
1
A
A
C2'
C1'
DT
DT
9
9
0.070
0.010
1.519
1.589
N
1
A
A
O3'
P
DT
DG
9
10
0.125
0.012
1.607
1.732
Y
1
A
A
P
O5'
DG
DG
10
10
0.139
0.010
1.593
1.732
N
1
B
B
C2'
C1'
DC
DC
11
11
0.065
0.010
1.519
1.584
N
1
B
B
O3'
P
DC
DA
11
12
0.130
0.012
1.607
1.737
Y
1
B
B
P
O5'
DA
DA
12
12
0.140
0.010
1.593
1.733
N
1
B
B
O3'
P
DA
DG
12
13
0.119
0.012
1.607
1.726
Y
1
B
B
P
O5'
DG
DG
13
13
0.134
0.010
1.593
1.727
N
1
B
B
O3'
P
DG
DA
13
14
0.121
0.012
1.607
1.728
Y
1
B
B
P
O5'
DA
DA
14
14
0.133
0.010
1.593
1.726
N
1
B
B
O3'
P
DA
DT
14
15
0.124
0.012
1.607
1.731
Y
1
B
B
P
O5'
DT
DT
15
15
0.143
0.010
1.593
1.736
N
1
B
B
O3'
P
DT
DA
15
16
0.121
0.012
1.607
1.728
Y
1
B
B
P
O5'
DA
DA
16
16
0.137
0.010
1.593
1.730
N
1
B
B
C2'
C1'
DA
DA
16
16
0.062
0.010
1.519
1.581
N
1
B
B
O3'
P
DA
DA
16
17
0.116
0.012
1.607
1.723
Y
1
B
B
P
O5'
DA
DA
17
17
0.125
0.010
1.593
1.718
N
1
B
B
O3'
P
DA
DT
17
18
0.117
0.012
1.607
1.724
Y
1
B
B
P
O5'
DT
DT
18
18
0.151
0.010
1.593
1.744
N
1
B
B
O3'
P
DT
DC
18
19
0.145
0.012
1.607
1.752
Y
1
B
B
P
O5'
DC
DC
19
19
0.145
0.010
1.593
1.738
N
1
B
B
C2'
C1'
DC
DC
19
19
0.082
0.010
1.519
1.601
N
1
B
B
O3'
P
DC
DA
19
20
0.129
0.012
1.607
1.736
Y
1
B
B
P
O5'
DA
DA
20
20
0.133
0.010
1.593
1.726
N
1
B
B
C3'
C2'
DA
DA
20
20
0.075
0.012
1.518
1.593
N
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
covale
1.734
one
A
THX
1
A
O3'
THX
1
1_555
A
DG
2
A
P
DG
2
1_555
hydrog
DG-DC PAIR
A
DG
2
A
N1
DG
2
1_555
B
DC
19
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
18
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
18
B
O4
DT
8
1_555
hydrog
DT-DA PAIR
A
DT
4
A
O4
DT
4
1_555
B
DA
16
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
17
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
17
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
16
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
16
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
15
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
15
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
14
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
14
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
13
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
13
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
12
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
12
B
N6
DA
2
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
11
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
11
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
11
B
N4
DC
1
1_555
DNA
DEOXYRIBONUCLEIC ACID, CDPI3, DNA
1AUL
PDB
1
1AUL
1AUL
PDB
2
1AUL
1
10
1AUL
1
10
1AUL
A
1
1
10
11
20
1AUL
11
20
1AUL
B
2
1
10
1
P 1