0.039246
0.000000
0.000000
0.000000
0.024237
0.000000
0.000000
0.000000
0.014952
0.00000
0.00000
0.00000
Coll, M.
Aymami, J.
Van Der Marel, G.A.
Van Boom, J.H.
Rich, A.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.480
41.260
66.880
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
H2 O
18.015
WATER
non-polymer
C18 H26 N10 O3
430.464
NETROPSIN
non-polymer
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
N
O
N
145
N
H
N
146
N
H
N
147
N
C
N
148
N
N
N
149
N
N
N
150
N
N
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
N
Y
155
N
C
Y
156
N
C
Y
157
N
C
Y
158
N
N
N
159
N
C
Y
160
N
C
N
161
N
C
N
162
N
O
N
163
N
N
Y
164
N
C
Y
165
N
C
Y
166
N
C
Y
167
N
N
N
168
N
C
Y
169
N
C
N
170
N
C
N
171
N
O
N
172
N
N
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
N
N
177
N
N
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
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
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
doub
N
164
N
sing
N
165
N
sing
N
166
N
sing
Y
167
N
sing
Y
168
N
doub
Y
169
N
doub
N
170
N
sing
Y
171
N
sing
N
172
N
sing
N
173
N
sing
Y
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
Y
183
N
sing
Y
184
N
doub
Y
185
N
doub
N
186
N
sing
Y
187
N
sing
N
188
N
sing
N
189
N
sing
Y
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
doub
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
doub
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
28
310
320
10.1021/bi00427a042
2539859
Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment.
1989
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
84
8385
8389
A Bifurcated Hydrogen-Bonded Conformation in the d(A.T) Base Pairs of the DNA Dodecamer d(CGCAAATTTGCG) and Its Complex with Distamycin
1987
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
82
1376
1380
The Molecular Origin of DNA-Drug Specificity in Netropsin and Distamycin
1985
10.2210/pdb1dne/pdb
pdb_00001dne
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
283.00
1
DIFFRACTOMETER
NICOLET P3
x-ray
1
1.0
3663.392
DNA (5'-D(*CP*GP*CP*GP*AP*TP*AP*TP*CP*GP*CP*G)-3')
2
syn
polymer
430.464
NETROPSIN
1
syn
non-polymer
18.015
water
60
nat
water
no
no
(DC)(DG)(DC)(DG)(DA)(DT)(DA)(DT)(DC)(DG)(DC)(DG)
CGCGATATCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2.40
48.73
VAPOR DIFFUSION
6.50
pH 6.50, VAPOR DIFFUSION, temperature 283.00K
283.00
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
SPERMINE
1
WATER
2
MPD
2
5.314
1
19
A
1
B
24
-3.558
A_DC1:DG24_B
1
-5.149
0.102
0.197
-0.122
1.377
1
19
A
2
B
23
-6.101
A_DG2:DC23_B
2
-14.686
-0.122
-0.044
-0.471
-11.269
1
19
A
3
B
22
-2.685
A_DC3:DG22_B
3
-6.554
-0.273
0.706
-0.245
13.600
1
19
A
4
B
21
-2.103
A_DG4:DC21_B
4
-9.302
0.506
0.177
-0.409
1.227
1
20
A
5
B
20
2.705
A_DA5:DT20_B
5
-1.432
0.055
-0.125
-0.055
10.130
1
20
A
6
B
19
-0.786
A_DT6:DA19_B
6
-11.874
-0.383
-0.327
-0.353
-4.723
1
20
A
7
B
18
-2.367
A_DA7:DT18_B
7
-17.006
0.245
-0.139
-0.278
2.647
1
20
A
8
B
17
-5.199
A_DT8:DA17_B
8
-6.747
0.024
0.245
-0.163
-8.861
1
19
A
9
B
16
-3.823
A_DC9:DG16_B
9
-11.658
0.312
0.421
-0.350
7.974
1
19
A
10
B
15
-3.660
A_DG10:DC15_B
10
-11.125
0.537
0.268
-0.172
-11.679
1
19
A
11
B
14
-6.025
A_DC11:DG14_B
11
-15.428
0.439
1.135
-0.607
-5.120
1
19
A
12
B
13
3.086
A_DG12:DC13_B
12
-1.501
0.363
0.176
-0.122
3.566
42.518
A
A
1
2
18.335
B
B
24
23
3.468
13.099
-1.220
0.881
AA_DC1DG2:DC23DG24_BB
1
0.277
-0.388
40.538
-0.249
1.713
3.728
32.189
A
A
2
3
-15.187
B
B
23
22
3.777
-8.226
0.169
-1.025
AA_DG2DC3:DG22DC23_BB
2
-8.768
16.188
29.915
-0.099
-2.171
2.847
37.082
A
A
3
4
9.745
B
B
22
21
2.878
6.158
-0.827
0.709
AA_DC3DG4:DC21DG22_BB
3
4.206
-6.656
36.350
0.385
1.799
3.670
32.408
A
A
4
5
3.285
B
B
21
20
3.729
1.832
0.677
-0.657
AA_DG4DA5:DT20DC21_BB
4
-0.794
1.423
32.348
-1.541
-1.372
3.009
30.572
A
A
5
6
-3.222
B
B
20
19
3.056
-1.698
-0.450
0.491
AA_DA5DT6:DA19DT20_BB
5
1.027
-1.949
30.509
1.244
1.042
3.611
45.796
A
A
6
7
-2.937
B
B
19
18
3.600
-2.284
0.311
-0.081
AA_DT6DA7:DT18DA19_BB
6
2.674
-3.439
45.668
0.115
-0.143
2.955
26.267
A
A
7
8
12.971
B
B
18
17
3.180
5.831
-0.276
-0.720
AA_DA7DT8:DA17DT18_BB
7
-3.325
7.397
25.409
-3.082
-0.247
3.560
43.053
A
A
8
9
-4.913
B
B
17
16
3.566
-3.601
0.022
-0.059
AA_DT8DC9:DG16DA17_BB
8
0.296
-0.404
42.908
0.308
0.001
3.123
38.865
A
A
9
10
1.813
B
B
16
15
3.086
1.206
0.247
1.059
AA_DC9DG10:DC15DG16_BB
9
1.272
-1.913
38.827
1.452
-0.224
3.941
30.778
A
A
10
11
-16.760
B
B
15
14
3.965
-8.667
-0.988
-0.056
AA_DG10DC11:DG14DC15_BB
10
-8.399
16.241
28.366
2.032
-0.208
3.257
47.773
A
A
11
12
-2.472
B
B
14
13
3.267
-2.000
0.425
0.789
AA_DC11DG12:DC13DG14_BB
11
4.045
-5.001
47.572
1.133
-0.203
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1989-01-09
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
BNL
1988-09-14
REL
NT
NETROPSIN
HOH
water
NT
25
2
NT
NT
25
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
33
3
HOH
HOH
33
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
40
3
HOH
HOH
40
A
HOH
42
3
HOH
HOH
42
A
HOH
45
3
HOH
HOH
45
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
48
3
HOH
HOH
48
A
HOH
49
3
HOH
HOH
49
A
HOH
50
3
HOH
HOH
50
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
57
3
HOH
HOH
57
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
62
3
HOH
HOH
62
A
HOH
63
3
HOH
HOH
63
A
HOH
65
3
HOH
HOH
65
A
HOH
66
3
HOH
HOH
66
A
HOH
69
3
HOH
HOH
69
A
HOH
77
3
HOH
HOH
77
A
HOH
82
3
HOH
HOH
82
A
HOH
83
3
HOH
HOH
83
A
HOH
85
3
HOH
HOH
85
A
HOH
26
3
HOH
HOH
26
B
HOH
27
3
HOH
HOH
27
B
HOH
28
3
HOH
HOH
28
B
HOH
31
3
HOH
HOH
31
B
HOH
32
3
HOH
HOH
32
B
HOH
34
3
HOH
HOH
34
B
HOH
35
3
HOH
HOH
35
B
HOH
38
3
HOH
HOH
38
B
HOH
39
3
HOH
HOH
39
B
HOH
41
3
HOH
HOH
41
B
HOH
43
3
HOH
HOH
43
B
HOH
44
3
HOH
HOH
44
B
HOH
51
3
HOH
HOH
51
B
HOH
54
3
HOH
HOH
54
B
HOH
55
3
HOH
HOH
55
B
HOH
56
3
HOH
HOH
56
B
HOH
58
3
HOH
HOH
58
B
HOH
59
3
HOH
HOH
59
B
HOH
64
3
HOH
HOH
64
B
HOH
67
3
HOH
HOH
67
B
HOH
68
3
HOH
HOH
68
B
HOH
70
3
HOH
HOH
70
B
HOH
71
3
HOH
HOH
71
B
HOH
72
3
HOH
HOH
72
B
HOH
73
3
HOH
HOH
73
B
HOH
74
3
HOH
HOH
74
B
HOH
75
3
HOH
HOH
75
B
HOH
76
3
HOH
HOH
76
B
HOH
78
3
HOH
HOH
78
B
HOH
79
3
HOH
HOH
79
B
HOH
80
3
HOH
HOH
80
B
HOH
81
3
HOH
HOH
81
B
HOH
84
3
HOH
HOH
84
B
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
A
5
n
5
DA
5
A
T
6
n
6
DT
6
A
A
7
n
7
DA
7
A
T
8
n
8
DT
8
A
C
9
n
9
DC
9
A
G
10
n
10
DG
10
A
C
11
n
11
DC
11
A
G
12
n
12
DG
12
A
C
13
n
1
DC
13
B
G
14
n
2
DG
14
B
C
15
n
3
DC
15
B
G
16
n
4
DG
16
B
A
17
n
5
DA
17
B
T
18
n
6
DT
18
B
A
19
n
7
DA
19
B
T
20
n
8
DT
20
B
C
21
n
9
DC
21
B
G
22
n
10
DG
22
B
C
23
n
11
DC
23
B
G
24
n
12
DG
24
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
DG
2
0.050
SIDE CHAIN
1
A
A
O3'
P
DC
DG
11
12
1.77
1
9.93
1.20
119.70
129.63
A
A
A
C3'
O3'
P
DC
DC
DG
1
1
2
Y
1
-14.70
1.50
119.60
104.90
A
A
A
OP1
P
OP2
DG
DG
DG
2
2
2
N
1
12.25
0.30
108.30
120.55
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
3.87
0.60
123.90
127.77
A
A
A
N1
C2
N3
DG
DG
DG
2
2
2
N
1
8.17
0.60
119.90
128.07
A
A
A
N1
C6
O6
DG
DG
DG
2
2
2
N
1
-9.78
0.60
128.60
118.82
A
A
A
C5
C6
O6
DG
DG
DG
2
2
2
N
1
8.13
1.20
119.70
127.83
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
12.14
1.90
104.00
116.14
A
A
A
O3'
P
O5'
DG
DC
DC
2
3
3
Y
1
-15.20
1.50
119.60
104.40
A
A
A
OP1
P
OP2
DC
DC
DC
3
3
3
N
1
-11.84
1.60
120.90
109.06
A
A
A
P
O5'
C5'
DC
DC
DC
3
3
3
N
1
-3.46
0.40
104.50
101.04
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
-8.05
1.00
110.10
102.05
A
A
A
C1'
O4'
C4'
DC
DC
DC
3
3
3
N
1
-7.83
0.70
108.00
100.17
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
4.40
0.70
121.90
126.30
A
A
A
N3
C2
O2
DC
DC
DC
3
3
3
N
1
-8.91
1.20
119.70
110.79
A
A
A
C3'
O3'
P
DC
DC
DG
3
3
4
Y
1
-16.06
1.50
119.60
103.54
A
A
A
OP1
P
OP2
DG
DG
DG
4
4
4
N
1
13.43
1.60
120.90
134.33
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
1
-6.77
0.40
104.50
97.73
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
-7.29
1.00
110.10
102.81
A
A
A
C1'
O4'
C4'
DG
DG
DG
4
4
4
N
1
7.12
0.30
108.30
115.42
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-3.99
0.60
128.60
124.61
A
A
A
C5
C6
O6
DG
DG
DG
4
4
4
N
1
8.05
0.30
108.30
116.35
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
18.80
1.20
119.70
138.50
A
A
A
C3'
O3'
P
DA
DA
DT
5
5
6
Y
1
12.77
1.10
110.50
123.27
A
A
A
O3'
P
OP1
DA
DT
DT
5
6
6
Y
1
-13.92
1.50
119.60
105.68
A
A
A
OP1
P
OP2
DT
DT
DT
6
6
6
N
1
-6.09
0.90
105.70
99.61
A
A
A
O5'
P
OP1
DT
DT
DT
6
6
6
N
1
-11.05
1.60
120.90
109.85
A
A
A
P
O5'
C5'
DT
DT
DT
6
6
6
N
1
-4.31
0.40
104.50
100.19
A
A
A
O4'
C4'
C3'
DT
DT
DT
6
6
6
N
1
-5.85
0.70
102.20
96.35
A
A
A
C4'
C3'
C2'
DT
DT
DT
6
6
6
N
1
-5.67
0.80
123.10
117.43
A
A
A
N1
C2
O2
DT
DT
DT
6
6
6
N
1
11.08
1.20
119.70
130.78
A
A
A
C3'
O3'
P
DT
DT
DA
6
6
7
Y
1
-13.03
1.50
119.60
106.57
A
A
A
OP1
P
OP2
DA
DA
DA
7
7
7
N
1
12.73
1.20
110.70
123.43
A
A
A
O5'
P
OP2
DA
DA
DA
7
7
7
N
1
-7.62
0.80
109.40
101.78
A
A
A
O5'
C5'
C4'
DA
DA
DA
7
7
7
N
1
-4.45
0.70
102.20
97.75
A
A
A
C4'
C3'
C2'
DA
DA
DA
7
7
7
N
1
-9.47
0.80
102.40
92.93
A
A
A
C3'
C2'
C1'
DA
DA
DA
7
7
7
N
1
-6.81
0.80
105.90
99.09
A
A
A
O4'
C1'
C2'
DA
DA
DA
7
7
7
N
1
9.01
0.30
108.30
117.31
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
4.28
0.60
118.60
122.88
A
A
A
N1
C6
N6
DA
DA
DA
7
7
7
N
1
-13.12
1.90
104.00
90.88
A
A
A
O3'
P
O5'
DA
DT
DT
7
8
8
Y
1
-5.10
0.80
109.40
104.30
A
A
A
O5'
C5'
C4'
DT
DT
DT
8
8
8
N
1
-14.87
1.60
120.90
106.03
A
A
A
P
O5'
C5'
DT
DT
DT
8
8
8
N
1
4.76
0.30
108.30
113.06
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
4.48
0.60
114.60
119.08
A
A
A
N1
C2
N3
DT
DT
DT
8
8
8
N
1
-5.87
0.60
127.20
121.33
A
A
A
C2
N3
C4
DT
DT
DT
8
8
8
N
1
3.84
0.60
115.20
119.04
A
A
A
N3
C4
C5
DT
DT
DT
8
8
8
N
1
14.32
1.20
119.70
134.02
A
A
A
C3'
O3'
P
DT
DT
DC
8
8
9
Y
1
8.47
1.20
110.70
119.17
A
A
A
O5'
P
OP2
DC
DC
DC
9
9
9
N
1
-13.81
1.60
120.90
107.09
A
A
A
P
O5'
C5'
DC
DC
DC
9
9
9
N
1
-3.67
0.40
104.50
100.83
A
A
A
O4'
C4'
C3'
DC
DC
DC
9
9
9
N
1
-5.23
0.70
102.20
96.97
A
A
A
C4'
C3'
C2'
DC
DC
DC
9
9
9
N
1
-9.72
0.80
102.40
92.68
A
A
A
C3'
C2'
C1'
DC
DC
DC
9
9
9
N
1
4.47
0.30
108.30
112.77
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
4.84
0.70
121.90
126.74
A
A
A
N3
C2
O2
DC
DC
DC
9
9
9
N
1
-6.69
1.10
118.80
112.11
A
A
A
C2
N1
C1'
DC
DC
DC
9
9
9
N
1
13.56
1.10
110.50
124.06
A
A
A
O3'
P
OP1
DC
DG
DG
9
10
10
Y
1
-7.14
0.80
109.40
102.26
A
A
A
O5'
C5'
C4'
DG
DG
DG
10
10
10
N
1
-16.26
1.60
120.90
104.64
A
A
A
P
O5'
C5'
DG
DG
DG
10
10
10
N
1
14.29
0.30
108.30
122.59
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
-3.66
0.60
125.10
121.44
A
A
A
C6
N1
C2
DG
DG
DG
10
10
10
N
1
5.07
0.50
111.50
116.57
A
A
A
C5
C6
N1
DG
DG
DG
10
10
10
N
1
-5.54
0.80
109.40
103.86
A
A
A
O5'
C5'
C4'
DC
DC
DC
11
11
11
N
1
-13.43
1.60
120.90
107.47
A
A
A
P
O5'
C5'
DC
DC
DC
11
11
11
N
1
-2.79
0.40
104.50
101.71
A
A
A
O4'
C4'
C3'
DC
DC
DC
11
11
11
N
1
-10.21
1.00
110.10
99.89
A
A
A
C1'
O4'
C4'
DC
DC
DC
11
11
11
N
1
3.81
0.40
120.30
124.11
A
A
A
C6
N1
C2
DC
DC
DC
11
11
11
N
1
-4.78
0.70
119.20
114.42
A
A
A
N1
C2
N3
DC
DC
DC
11
11
11
N
1
4.32
0.50
119.90
124.22
A
A
A
C2
N3
C4
DC
DC
DC
11
11
11
N
1
-4.13
0.60
118.90
114.77
A
A
A
N1
C2
O2
DC
DC
DC
11
11
11
N
1
8.80
0.70
121.90
130.70
A
A
A
N3
C2
O2
DC
DC
DC
11
11
11
N
1
4.31
0.70
118.00
122.31
A
A
A
N3
C4
N4
DC
DC
DC
11
11
11
N
1
-17.31
1.20
119.70
102.39
A
A
A
C3'
O3'
P
DC
DC
DG
11
11
12
Y
1
15.70
1.20
110.70
126.40
A
A
A
O5'
P
OP2
DG
DG
DG
12
12
12
N
1
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
-4.82
0.60
125.10
120.28
A
A
A
C6
N1
C2
DG
DG
DG
12
12
12
N
1
3.66
0.60
123.90
127.56
A
A
A
N1
C2
N3
DG
DG
DG
12
12
12
N
1
3.60
0.50
111.50
115.10
A
A
A
C5
C6
N1
DG
DG
DG
12
12
12
N
1
-4.90
0.70
119.90
115.00
A
A
A
N3
C2
N2
DG
DG
DG
12
12
12
N
1
-8.18
0.80
109.40
101.22
B
B
B
O5'
C5'
C4'
DC
DC
DC
13
13
13
N
1
3.80
0.60
118.90
122.70
B
B
B
N1
C2
O2
DC
DC
DC
13
13
13
N
1
-10.88
1.20
119.70
108.82
B
B
B
C3'
O3'
P
DC
DC
DG
13
13
14
Y
1
-4.32
0.60
125.10
120.78
B
B
B
C6
N1
C2
DG
DG
DG
14
14
14
N
1
4.49
0.60
119.90
124.39
B
B
B
N1
C6
O6
DG
DG
DG
14
14
14
N
1
-7.24
0.60
128.60
121.36
B
B
B
C5
C6
O6
DG
DG
DG
14
14
14
N
1
-10.61
1.20
119.70
109.09
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
1
-10.07
1.50
119.60
109.53
B
B
B
OP1
P
OP2
DC
DC
DC
15
15
15
N
1
9.38
1.20
110.70
120.08
B
B
B
O5'
P
OP2
DC
DC
DC
15
15
15
N
1
-7.11
1.00
110.10
102.99
B
B
B
C1'
O4'
C4'
DC
DC
DC
15
15
15
N
1
-7.29
0.80
105.90
98.61
B
B
B
O4'
C1'
C2'
DC
DC
DC
15
15
15
N
1
11.90
0.30
108.30
120.20
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
-19.11
1.50
119.60
100.49
B
B
B
OP1
P
OP2
DG
DG
DG
16
16
16
N
1
20.58
1.20
110.70
131.28
B
B
B
O5'
P
OP2
DG
DG
DG
16
16
16
N
1
-6.42
0.80
109.40
102.98
B
B
B
O5'
C5'
C4'
DG
DG
DG
16
16
16
N
1
4.59
0.60
119.90
124.49
B
B
B
N1
C6
O6
DG
DG
DG
16
16
16
N
1
-6.77
0.60
128.60
121.83
B
B
B
C5
C6
O6
DG
DG
DG
16
16
16
N
1
-7.60
1.20
119.70
112.10
B
B
B
C3'
O3'
P
DG
DG
DA
16
16
17
Y
1
7.01
1.10
110.50
117.51
B
B
B
O3'
P
OP1
DG
DA
DA
16
17
17
Y
1
-17.49
1.60
120.90
103.41
B
B
B
P
O5'
C5'
DA
DA
DA
17
17
17
N
1
3.84
0.30
108.30
112.14
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
3.74
0.60
118.60
122.34
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
1
-12.16
1.20
119.70
107.54
B
B
B
C3'
O3'
P
DA
DA
DT
17
17
18
Y
1
-11.61
1.90
104.00
92.39
B
B
B
O3'
P
O5'
DA
DT
DT
17
18
18
Y
1
11.16
1.20
110.70
121.86
B
B
B
O5'
P
OP2
DT
DT
DT
18
18
18
N
1
-6.60
0.40
104.50
97.90
B
B
B
O4'
C4'
C3'
DT
DT
DT
18
18
18
N
1
-4.67
0.70
102.20
97.53
B
B
B
C4'
C3'
C2'
DT
DT
DT
18
18
18
N
1
2.06
0.30
108.30
110.36
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
1
-3.02
0.50
121.30
118.28
B
B
B
C6
N1
C2
DT
DT
DT
18
18
18
N
1
5.43
0.60
114.60
120.03
B
B
B
N1
C2
N3
DT
DT
DT
18
18
18
N
1
-5.52
0.60
127.20
121.68
B
B
B
C2
N3
C4
DT
DT
DT
18
18
18
N
1
-4.33
0.60
119.00
114.67
B
B
B
C4
C5
C7
DT
DT
DT
18
18
18
N
1
9.05
1.10
110.50
119.55
B
B
B
O3'
P
OP1
DT
DA
DA
18
19
19
Y
1
-13.31
1.50
119.60
106.29
B
B
B
OP1
P
OP2
DA
DA
DA
19
19
19
N
1
12.22
1.20
110.70
122.92
B
B
B
O5'
P
OP2
DA
DA
DA
19
19
19
N
1
14.29
1.40
114.30
128.59
B
B
B
N9
C1'
C2'
DA
DA
DA
19
19
19
N
1
-12.52
0.70
108.00
95.48
B
B
B
O4'
C1'
N9
DA
DA
DA
19
19
19
N
1
3.81
0.60
118.60
122.41
B
B
B
N1
C6
N6
DA
DA
DA
19
19
19
N
1
9.15
1.20
110.70
119.85
B
B
B
O5'
P
OP1
DT
DT
DT
20
20
20
N
1
-5.88
0.40
104.50
98.62
B
B
B
O4'
C4'
C3'
DT
DT
DT
20
20
20
N
1
-5.91
0.80
102.40
96.49
B
B
B
C3'
C2'
C1'
DT
DT
DT
20
20
20
N
1
5.42
0.30
108.30
113.72
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
-3.70
0.60
127.20
123.50
B
B
B
C2
N3
C4
DT
DT
DT
20
20
20
N
1
-12.51
1.90
104.00
91.49
B
B
B
O3'
P
O5'
DT
DC
DC
20
21
21
Y
1
9.93
1.20
110.70
120.63
B
B
B
O5'
P
OP2
DC
DC
DC
21
21
21
N
1
-10.08
0.80
109.40
99.32
B
B
B
O5'
C5'
C4'
DC
DC
DC
21
21
21
N
1
-22.33
1.60
120.90
98.57
B
B
B
P
O5'
C5'
DC
DC
DC
21
21
21
N
1
7.66
0.30
108.30
115.96
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
4.55
0.70
118.00
122.55
B
B
B
N3
C4
N4
DC
DC
DC
21
21
21
N
1
6.67
1.10
110.50
117.17
B
B
B
O3'
P
OP2
DC
DG
DG
21
22
22
Y
1
-14.08
1.60
120.90
106.82
B
B
B
P
O5'
C5'
DG
DG
DG
22
22
22
N
1
-8.79
0.80
102.40
93.61
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
5.98
0.30
108.30
114.28
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-8.71
1.20
119.70
110.99
B
B
B
C3'
O3'
P
DG
DG
DC
22
22
23
Y
1
-7.68
0.40
104.50
96.82
B
B
B
O4'
C4'
C3'
DC
DC
DC
23
23
23
N
1
-11.98
1.00
110.10
98.12
B
B
B
C1'
O4'
C4'
DC
DC
DC
23
23
23
N
1
4.61
0.70
118.00
122.61
B
B
B
N3
C4
N4
DC
DC
DC
23
23
23
N
1
-9.64
1.50
119.60
109.96
B
B
B
OP1
P
OP2
DG
DG
DG
24
24
24
N
1
-2.41
0.40
104.50
102.09
B
B
B
O4'
C4'
C3'
DG
DG
DG
24
24
24
N
1
-9.72
1.00
110.10
100.38
B
B
B
C1'
O4'
C4'
DG
DG
DG
24
24
24
N
1
-4.04
0.60
128.60
124.56
B
B
B
C5
C6
O6
DG
DG
DG
24
24
24
N
1
A
A
N3
C4
DC
DC
1
1
0.063
0.007
1.335
1.398
N
1
A
A
P
OP2
DG
DG
2
2
0.110
0.017
1.485
1.595
N
1
A
A
P
O5'
DG
DG
2
2
-0.093
0.010
1.593
1.500
N
1
A
A
C2'
C1'
DG
DG
2
2
0.072
0.010
1.519
1.591
N
1
A
A
P
O5'
DC
DC
3
3
-0.070
0.010
1.593
1.523
N
1
A
A
C2'
C1'
DC
DC
3
3
-0.060
0.010
1.518
1.458
N
1
A
A
O4'
C1'
DC
DC
3
3
0.092
0.011
1.420
1.512
N
1
A
A
P
OP2
DG
DG
4
4
0.155
0.017
1.485
1.640
N
1
A
A
P
O5'
DG
DG
4
4
-0.091
0.010
1.593
1.502
N
1
A
A
O3'
P
DA
DT
5
6
-0.137
0.012
1.607
1.470
Y
1
A
A
P
O5'
DT
DT
6
6
0.099
0.010
1.593
1.692
N
1
A
A
P
O5'
DT
DT
8
8
0.128
0.010
1.593
1.721
N
1
A
A
P
OP1
DC
DC
9
9
0.121
0.017
1.485
1.606
N
1
A
A
P
OP2
DG
DG
10
10
0.112
0.017
1.485
1.597
N
1
A
A
P
O5'
DG
DG
10
10
0.106
0.010
1.593
1.699
N
1
A
A
O3'
P
DC
DG
11
12
0.160
0.012
1.607
1.767
Y
1
B
B
O3'
P
DC
DG
13
14
0.092
0.012
1.607
1.699
Y
1
B
B
P
OP1
DG
DG
16
16
0.145
0.017
1.485
1.630
N
1
B
B
P
O5'
DG
DG
16
16
-0.151
0.010
1.593
1.442
N
1
B
B
O4'
C1'
DG
DG
16
16
0.095
0.011
1.420
1.515
N
1
B
B
O3'
P
DA
DT
17
18
0.093
0.012
1.607
1.700
Y
1
B
B
C2'
C1'
DA
DA
19
19
-0.089
0.010
1.518
1.429
N
1
B
B
O4'
C1'
DA
DA
19
19
0.091
0.011
1.420
1.511
N
1
B
B
N9
C4
DA
DA
19
19
-0.048
0.006
1.374
1.326
N
1
B
B
P
O5'
DC
DC
21
21
0.091
0.010
1.593
1.684
N
1
B
B
O5'
C5'
DC
DC
21
21
0.125
0.016
1.440
1.565
N
1
B
B
P
OP1
DG
DG
22
22
0.136
0.017
1.485
1.621
N
1
B
B
P
OP2
DG
DG
22
22
-0.109
0.017
1.485
1.376
N
1
B
B
P
O5'
DG
DG
22
22
0.084
0.010
1.593
1.677
N
1
B
B
P
OP1
DG
DG
24
24
0.108
0.017
1.485
1.593
N
1
B
B
O4'
C1'
DG
DG
24
24
0.090
0.011
1.420
1.510
N
1
A
B
O3'
N2
DG
DG
12
22
1.77
1_555
2_664
0.2010000
2.400
20.000
1848
1
2.000
TR
isotropic
TR
isotropic
2.400
20.000
60
577
31
486
0
fix
fix
2.400
1DNE
5696
1848
1.000
1
refinement
NUCLSQ
MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
24
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
24
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
24
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
23
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
23
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
23
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
22
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
21
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
21
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
21
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
20
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
20
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
19
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
19
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
18
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
18
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
17
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
17
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
16
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
13
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
13
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
13
B
N4
DC
1
1_555
DNA
B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA
1DNE
PDB
1
1DNE
1
12
1DNE
1
12
1DNE
A
1
1
12
13
24
1DNE
13
24
1DNE
B
1
1
12
BINDING SITE FOR RESIDUE NT A 25
A
NT
25
Software
12
A
DG
4
A
DG
4
12
1_555
A
DA
5
A
DA
5
12
1_555
A
DT
6
A
DT
6
12
1_555
A
DA
7
A
DA
7
12
1_555
A
DT
8
A
DT
8
12
1_555
A
DC
9
A
DC
9
12
1_555
B
DA
17
B
DA
5
12
1_555
B
DT
18
B
DT
6
12
1_555
B
DA
19
B
DA
7
12
1_555
B
DT
20
B
DT
8
12
1_555
B
DC
21
B
DC
9
12
1_555
B
DG
22
B
DG
10
12
1_555
19
P 21 21 21