0.019658
0.011350
0.000000
0.000000
0.022699
0.000000
0.000000
0.000000
0.019062
0.00000
0.00000
0.00000
Collie, G.W.
Promontorio, R.
Parkinson, G.N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
50.870
50.870
52.460
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-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
K 1
39.098
POTASSIUM ION
non-polymer
C46 H72 N12 O4
857.142
2,7-bis[3-(4-methylpiperazin-1-yl)propyl]-4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
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
Y
49
N
N
Y
50
N
C
Y
51
N
N
Y
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
C
N
57
N
N
N
58
N
N
Y
59
N
C
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
H
N
72
N
H
N
73
N
H
N
74
N
O
N
75
N
P
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
O
N
82
S
C
N
83
N
O
N
84
N
C
N
85
R
C
N
86
N
N
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
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
H
N
109
N
H
N
110
N
O
N
111
N
H
N
112
N
H
N
113
N
K
N
114
N
C
N
115
N
C
N
116
N
C
N
117
N
C
N
118
N
O
N
119
N
O
N
120
N
O
N
121
N
O
Y
122
N
C
Y
123
N
C
N
124
N
C
N
125
N
C
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
C
N
130
N
C
N
131
N
C
N
132
N
C
N
133
N
C
N
134
N
C
N
135
N
C
N
136
N
C
N
137
N
C
N
138
N
C
N
139
N
C
N
140
N
C
N
141
N
C
N
142
N
C
N
143
N
C
N
144
N
C
N
145
N
C
N
146
N
C
N
147
N
C
N
148
N
C
N
149
N
C
N
150
N
C
N
151
N
C
N
152
N
N
N
153
N
N
Y
154
N
C
Y
155
N
C
N
156
N
C
N
157
N
C
N
158
N
C
N
159
N
C
Y
160
N
C
Y
161
N
C
Y
162
N
C
Y
163
N
C
Y
164
N
C
Y
165
N
C
N
166
N
N
N
167
N
N
N
168
N
N
N
169
N
N
N
170
N
N
N
171
N
N
N
172
N
N
N
173
N
N
N
174
N
N
N
175
N
N
N
176
N
H
N
177
N
H
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
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
214
N
H
N
215
N
H
N
216
N
H
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
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
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
sing
N
67
N
sing
Y
68
N
doub
N
69
N
doub
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
doub
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
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
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
doub
Y
135
N
doub
Y
136
N
sing
Y
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
doub
N
142
N
sing
N
143
N
sing
Y
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
Y
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
Y
152
N
sing
Y
153
N
sing
Y
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
doub
Y
161
N
doub
N
162
N
sing
Y
163
N
doub
N
164
N
doub
Y
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
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
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
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
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
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
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
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
134
2723
2731
10.1021/ja2102423
22280460
Structural basis for telomeric g-quadruplex targeting by naphthalene diimide ligands.
2012
10.2210/pdb3sc8/pdb
pdb_00003sc8
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
PIXEL
2011-04-16
PSI PILATUS 6M
Si 111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
0.91730
1.0
I04-1
Diamond
0.91730
SYNCHROTRON
DIAMOND BEAMLINE I04-1
6983.497
Human telomeric repeat sequence
1
syn
polymer
39.098
POTASSIUM ION
3
syn
non-polymer
857.142
2,7-bis[3-(4-methylpiperazin-1-yl)propyl]-4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
1
syn
non-polymer
18.015
water
29
nat
water
no
no
(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)
(DG)(DG)
AGGGTTAGGGTTAGGGTTAGGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.81
56.16
VAPOR DIFFUSION, HANGING DROP
6.5
20 % PEG400, 50 mM potassium chloride, 20 mM potassium cacodylate, 50 mM sodium cacodylate, 100 mM lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
285
3.185
3
6
A
14
A
20
-93.084
A_DG14:DG20_A
1
-2.284
1.748
-0.404
3.631
2.054
3
6
A
15
A
21
-87.694
A_DG15:DG21_A
2
-8.739
1.768
0.230
3.312
15.759
3
6
A
16
A
22
-91.839
A_DG16:DG22_A
3
-9.105
1.441
-0.872
3.502
-10.498
3
6
A
10
A
4
88.751
A_DG10:DG4_A
4
7.703
-1.478
-0.045
-3.384
-1.154
3
6
A
9
A
3
88.560
A_DG9:DG3_A
5
5.256
-1.622
0.074
-3.552
1.202
3
6
A
8
A
2
88.578
A_DG8:DG2_A
6
3.543
-1.227
0.029
-3.613
3.226
34.422
A
A
14
15
5.845
A
A
20
21
3.330
3.444
-0.122
-0.775
AA_DG14DG15:DG21DG20_AA
1
-4.654
7.899
33.946
-1.850
-0.525
2.616
25.914
A
A
15
16
10.684
A
A
21
22
3.178
4.688
-0.821
-0.604
AA_DG15DG16:DG22DG21_AA
2
8.010
-18.255
24.221
-2.537
3.864
0.101
-179.291
A
A
16
10
6.476
A
A
22
4
0.100
-12.951
1.808
3.593
AA_DG16DG10:DG4DG22_AA
3
11.018
5.509
-179.283
-1.796
0.904
-3.013
-29.209
A
A
10
9
13.404
A
A
4
3
-3.224
-6.702
0.494
0.551
AA_DG10DG9:DG3DG4_AA
4
-0.282
-0.563
-28.444
-2.499
1.040
-3.190
-30.124
A
A
9
8
3.306
A
A
3
2
-3.275
-1.717
0.389
1.021
AA_DG9DG8:DG2DG3_AA
5
-1.513
-2.914
-30.039
-2.310
1.055
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-02-15
1
1
2012-02-22
1
2
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2011-06-07
REL
REL
K
POTASSIUM ION
R8G
2,7-bis[3-(4-methylpiperazin-1-yl)propyl]-4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
HOH
water
DNA sequence synthesized by standard by phosphoramidite chemistry
sample
1KF1
PDB ENTRY 1KF1
PDB
experimental model
K
24
2
K
K
24
A
K
25
2
K
K
25
A
K
26
2
K
K
26
A
R8G
1
3
R8G
R8G
23
A
HOH
27
4
HOH
HOH
27
A
HOH
28
4
HOH
HOH
28
A
HOH
29
4
HOH
HOH
29
A
HOH
1
4
HOH
HOH
30
A
HOH
2
4
HOH
HOH
31
A
HOH
3
4
HOH
HOH
32
A
HOH
4
4
HOH
HOH
33
A
HOH
5
4
HOH
HOH
34
A
HOH
6
4
HOH
HOH
35
A
HOH
7
4
HOH
HOH
36
A
HOH
8
4
HOH
HOH
37
A
HOH
9
4
HOH
HOH
38
A
HOH
10
4
HOH
HOH
39
A
HOH
11
4
HOH
HOH
40
A
HOH
12
4
HOH
HOH
41
A
HOH
13
4
HOH
HOH
42
A
HOH
14
4
HOH
HOH
43
A
HOH
15
4
HOH
HOH
44
A
HOH
16
4
HOH
HOH
45
A
HOH
17
4
HOH
HOH
46
A
HOH
18
4
HOH
HOH
47
A
HOH
19
4
HOH
HOH
48
A
HOH
20
4
HOH
HOH
49
A
HOH
21
4
HOH
HOH
50
A
HOH
22
4
HOH
HOH
51
A
HOH
23
4
HOH
HOH
52
A
HOH
24
4
HOH
HOH
53
A
HOH
25
4
HOH
HOH
54
A
HOH
26
4
HOH
HOH
55
A
n
1
1
A
G
2
n
2
DG
2
A
G
3
n
3
DG
3
A
G
4
n
4
DG
4
A
T
5
n
5
DT
5
A
T
6
n
6
DT
6
A
A
7
n
7
DA
7
A
G
8
n
8
DG
8
A
G
9
n
9
DG
9
A
G
10
n
10
DG
10
A
T
11
n
11
DT
11
A
T
12
n
12
DT
12
A
A
13
n
13
DA
13
A
G
14
n
14
DG
14
A
G
15
n
15
DG
15
A
G
16
n
16
DG
16
A
T
17
n
17
DT
17
A
T
18
n
18
DT
18
A
A
19
n
19
DA
19
A
G
20
n
20
DG
20
A
G
21
n
21
DG
21
A
G
22
n
22
DG
22
A
8.9591
0.5922
1.6308
6.3217
1.3446
5.7714
-0.2620
0.2123
0.9019
-0.8007
-0.0997
0.4667
-0.4757
-0.4314
0.3617
0.1706
0.1202
-0.0841
0.3520
-0.1192
0.2173
refined
-19.0280
-14.7400
-0.9020
X-RAY DIFFRACTION
14.0617
1.2752
9.7221
2.2653
1.8100
8.3360
-0.0325
-0.3200
-0.6067
-0.1961
0.0252
0.0023
0.0784
-0.3380
0.0073
0.0700
0.0229
0.0455
0.1199
-0.0543
0.1663
refined
-19.3900
-21.8120
-0.6520
X-RAY DIFFRACTION
0.0432
-0.4507
0.5448
4.9221
-6.0814
10.9385
-0.1025
0.0122
0.0245
0.9255
-0.3739
-0.2077
0.0551
0.5806
0.4765
0.6613
0.1035
0.0649
0.2994
0.0161
0.1999
refined
-10.0900
-23.3570
11.8630
X-RAY DIFFRACTION
7.6711
-0.6815
3.9997
10.2499
10.4854
13.7216
-0.5242
0.6259
0.1871
0.1725
0.7920
-0.3823
-0.3538
1.3182
-0.2678
0.4831
-0.2113
-0.0257
0.3550
-0.0304
0.2120
refined
-5.6780
-7.8810
10.3380
X-RAY DIFFRACTION
20.3792
5.2859
10.5318
3.8441
4.1860
8.9480
0.0168
-0.2229
0.8582
0.5714
-0.1345
-0.2014
-0.5280
0.3972
0.1177
0.4706
-0.1351
-0.0276
0.2512
-0.0124
0.2004
refined
-7.7740
-7.9220
3.4800
X-RAY DIFFRACTION
A
2
A
5
X-RAY DIFFRACTION
1
A
6
A
9
X-RAY DIFFRACTION
2
A
10
A
14
X-RAY DIFFRACTION
3
A
15
A
18
X-RAY DIFFRACTION
4
A
19
A
22
X-RAY DIFFRACTION
5
author_and_software_defined_assembly
PISA
1
monomeric
A
DG
2
A
O6
DG
2
1_555
A
K
25
C
K
K
1_555
A
DG
3
A
O6
DG
3
1_555
73.3
A
DG
2
A
O6
DG
2
1_555
A
K
25
C
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
62.7
A
DG
3
A
O6
DG
3
1_555
A
K
25
C
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
89.3
A
DG
2
A
O6
DG
2
1_555
A
K
25
C
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
126.8
A
DG
3
A
O6
DG
3
1_555
A
K
25
C
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
74.6
A
DG
8
A
O6
DG
8
1_555
A
K
25
C
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
75.7
A
DG
2
A
O6
DG
2
1_555
A
K
25
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
102.1
A
DG
3
A
O6
DG
3
1_555
A
K
25
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
155.4
A
DG
8
A
O6
DG
8
1_555
A
K
25
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
67.8
A
DG
9
A
O6
DG
9
1_555
A
K
25
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
90.4
A
DG
2
A
O6
DG
2
1_555
A
K
25
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
163.2
A
DG
3
A
O6
DG
3
1_555
A
K
25
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
114.5
A
DG
8
A
O6
DG
8
1_555
A
K
25
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
129.8
A
DG
9
A
O6
DG
9
1_555
A
K
25
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
69.9
A
DG
14
A
O6
DG
14
1_555
A
K
25
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
76.9
A
DG
2
A
O6
DG
2
1_555
A
K
25
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
73.3
A
DG
3
A
O6
DG
3
1_555
A
K
25
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
128.7
A
DG
8
A
O6
DG
8
1_555
A
K
25
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
108.2
A
DG
9
A
O6
DG
9
1_555
A
K
25
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
155.6
A
DG
14
A
O6
DG
14
1_555
A
K
25
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
70.0
A
DG
15
A
O6
DG
15
1_555
A
K
25
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
90.9
A
DG
2
A
O6
DG
2
1_555
A
K
25
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
94.0
A
DG
3
A
O6
DG
3
1_555
A
K
25
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
78.4
A
DG
8
A
O6
DG
8
1_555
A
K
25
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
156.2
A
DG
9
A
O6
DG
9
1_555
A
K
25
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
119.4
A
DG
14
A
O6
DG
14
1_555
A
K
25
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
126.2
A
DG
15
A
O6
DG
15
1_555
A
K
25
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
74.0
A
DG
20
A
O6
DG
20
1_555
A
K
25
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
66.3
A
DG
2
A
O6
DG
2
1_555
A
K
26
D
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
65.2
A
DG
2
A
O6
DG
2
1_555
A
K
26
D
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
109.5
A
DG
8
A
O6
DG
8
1_555
A
K
26
D
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
72.2
A
DG
2
A
O6
DG
2
1_555
A
K
26
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
73.9
A
DG
8
A
O6
DG
8
1_555
A
K
26
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
110.6
A
DG
14
A
O6
DG
14
1_555
A
K
26
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
72.0
A
DG
3
A
O6
DG
3
1_555
A
K
24
B
K
K
1_555
A
DG
4
A
O6
DG
4
1_555
75.0
A
DG
3
A
O6
DG
3
1_555
A
K
24
B
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
68.7
A
DG
4
A
O6
DG
4
1_555
A
K
24
B
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
89.6
A
DG
3
A
O6
DG
3
1_555
A
K
24
B
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
123.7
A
DG
4
A
O6
DG
4
1_555
A
K
24
B
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
72.6
A
DG
9
A
O6
DG
9
1_555
A
K
24
B
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
66.3
A
DG
3
A
O6
DG
3
1_555
A
K
24
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
104.8
A
DG
4
A
O6
DG
4
1_555
A
K
24
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
150.8
A
DG
9
A
O6
DG
9
1_555
A
K
24
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
64.3
A
DG
10
A
O6
DG
10
1_555
A
K
24
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
84.4
A
DG
3
A
O6
DG
3
1_555
A
K
24
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
147.8
A
DG
4
A
O6
DG
4
1_555
A
K
24
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
131.2
A
DG
9
A
O6
DG
9
1_555
A
K
24
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
121.5
A
DG
10
A
O6
DG
10
1_555
A
K
24
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
86.1
A
DG
15
A
O6
DG
15
1_555
A
K
24
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
62.5
A
DG
3
A
O6
DG
3
1_555
A
K
24
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
68.3
A
DG
4
A
O6
DG
4
1_555
A
K
24
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
136.2
A
DG
9
A
O6
DG
9
1_555
A
K
24
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
98.3
A
DG
10
A
O6
DG
10
1_555
A
K
24
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
149.2
A
DG
15
A
O6
DG
15
1_555
A
K
24
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
64.8
A
DG
16
A
O6
DG
16
1_555
A
K
24
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
79.8
A
DG
3
A
O6
DG
3
1_555
A
K
24
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
96.4
A
DG
4
A
O6
DG
4
1_555
A
K
24
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
80.8
A
DG
9
A
O6
DG
9
1_555
A
K
24
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
164.1
A
DG
10
A
O6
DG
10
1_555
A
K
24
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
121.8
A
DG
15
A
O6
DG
15
1_555
A
K
24
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
127.5
A
DG
16
A
O6
DG
16
1_555
A
K
24
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
74.0
A
DG
21
A
O6
DG
21
1_555
A
K
24
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
80.4
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
K
26
D
K
1
A
DA
1
A
DA
1
1
Y
1
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
-7.90
1.00
110.10
102.20
A
A
A
C1'
O4'
C4'
DA
DA
DA
13
13
13
N
1
4.47
0.30
108.30
112.77
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
45.257
0.01
0.00
0.00
0.01
0.00
-0.01
0.931
0.916
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.28828
0.25839
0.25989
0.25989
2.302
10.30
161
3467
3467
4.4
100.00
16.573
0.223
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.389
0.266
0.80
0.80
1.40
PDB ENTRY 1KF1
MAXIMUM LIKELIHOOD
MASK
2.302
10.30
29
541
65
447
0
0.007
0.021
572
1.048
3.000
877
0.060
0.200
84
0.011
0.020
261
1.831
3.000
572
2.884
4.500
877
0.481
0.404
2.359
11
240
20
100.00
58.898
2.17
26.23
3SC8
4385
4385
2.0
2.0
0.033
1
32.1
9.5
99.5
0.59
2.17
2.23
3.5
324
1
9.7
100
data collection
GDA
phasing
PHASER
refinement
REFMAC
5.5.0072
data reduction
XDS
data scaling
SCALA
Crystal structure of an intramolecular human telomeric DNA G-quadruplex bound by the naphthalene diimide BMSG-SH-3
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
metalc
2.876
A
DG
2
A
O6
DG
2
1_555
A
K
25
C
K
K
1_555
metalc
2.792
A
DG
2
A
O6
DG
2
1_555
A
K
26
D
K
K
1_555
metalc
2.858
A
DG
3
A
O6
DG
3
1_555
A
K
24
B
K
K
1_555
metalc
2.709
A
DG
3
A
O6
DG
3
1_555
A
K
25
C
K
K
1_555
metalc
2.592
A
DG
4
A
O6
DG
4
1_555
A
K
24
B
K
K
1_555
metalc
2.903
A
DG
8
A
O6
DG
8
1_555
A
K
25
C
K
K
1_555
metalc
2.784
A
DG
8
A
O6
DG
8
1_555
A
K
26
D
K
K
1_555
metalc
3.049
A
DG
9
A
O6
DG
9
1_555
A
K
24
B
K
K
1_555
metalc
2.797
A
DG
9
A
O6
DG
9
1_555
A
K
25
C
K
K
1_555
metalc
2.638
A
DG
10
A
O6
DG
10
1_555
A
K
24
B
K
K
1_555
metalc
2.968
A
DG
14
A
O6
DG
14
1_555
A
K
25
C
K
K
1_555
metalc
2.775
A
DG
14
A
O6
DG
14
1_555
A
K
26
D
K
K
1_555
metalc
3.157
A
DG
15
A
O6
DG
15
1_555
A
K
24
B
K
K
1_555
metalc
2.961
A
DG
15
A
O6
DG
15
1_555
A
K
25
C
K
K
1_555
metalc
2.583
A
DG
16
A
O6
DG
16
1_555
A
K
24
B
K
K
1_555
metalc
3.109
A
DG
20
A
O6
DG
20
1_555
A
K
25
C
K
K
1_555
metalc
3.137
A
DG
20
A
O6
DG
20
1_555
A
K
26
D
K
K
1_555
metalc
3.109
A
DG
21
A
O6
DG
21
1_555
A
K
24
B
K
K
1_555
metalc
2.597
A
DG
21
A
O6
DG
21
1_555
A
K
25
C
K
K
1_555
metalc
2.666
A
DG
22
A
O6
DG
22
1_555
A
K
24
B
K
K
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N1
DG
2
1_555
A
DG
8
A
O6
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N2
DG
2
1_555
A
DG
8
A
N7
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N7
DG
2
1_555
A
DG
20
A
N2
DG
20
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
O6
DG
2
1_555
A
DG
20
A
N1
DG
20
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N1
DG
3
1_555
A
DG
9
A
O6
DG
9
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N2
DG
3
1_555
A
DG
9
A
N7
DG
9
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N7
DG
3
1_555
A
DG
21
A
N2
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
O6
DG
3
1_555
A
DG
21
A
N1
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N1
DG
4
1_555
A
DG
10
A
O6
DG
10
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N2
DG
4
1_555
A
DG
10
A
N7
DG
10
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N7
DG
4
1_555
A
DG
22
A
N2
DG
22
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
O6
DG
4
1_555
A
DG
22
A
N1
DG
22
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N1
DG
8
1_555
A
DG
14
A
O6
DG
14
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N2
DG
8
1_555
A
DG
14
A
N7
DG
14
1_555
hydrog
TYPE_6_PAIR
A
DG
9
A
N1
DG
9
1_555
A
DG
15
A
O6
DG
15
1_555
hydrog
TYPE_6_PAIR
A
DG
9
A
N2
DG
9
1_555
A
DG
15
A
N7
DG
15
1_555
hydrog
TYPE_6_PAIR
A
DG
10
A
N1
DG
10
1_555
A
DG
16
A
O6
DG
16
1_555
hydrog
TYPE_6_PAIR
A
DG
10
A
N2
DG
10
1_555
A
DG
16
A
N7
DG
16
1_555
hydrog
TYPE_6_PAIR
A
DG
14
A
N1
DG
14
1_555
A
DG
20
A
O6
DG
20
1_555
hydrog
TYPE_6_PAIR
A
DG
14
A
N2
DG
14
1_555
A
DG
20
A
N7
DG
20
1_555
hydrog
TYPE_6_PAIR
A
DG
15
A
N1
DG
15
1_555
A
DG
21
A
O6
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
15
A
N2
DG
15
1_555
A
DG
21
A
N7
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
16
A
N1
DG
16
1_555
A
DG
22
A
O6
DG
22
1_555
hydrog
TYPE_6_PAIR
A
DG
16
A
N2
DG
16
1_555
A
DG
22
A
N7
DG
22
1_555
DNA
G-quadruplex, intramolecular, ligand-complex, telomeric, DNA
3SC8
PDB
1
1
3SC8
AGGGTTAGGGTTAGGGTTAGGG
1
22
3SC8
1
22
3SC8
A
1
1
22
BINDING SITE FOR RESIDUE K A 24
A
K
24
Software
9
BINDING SITE FOR RESIDUE K A 25
A
K
25
Software
11
BINDING SITE FOR RESIDUE K A 26
A
K
26
Software
10
BINDING SITE FOR RESIDUE R8G A 23
A
R8G
23
Software
9
A
DG
3
A
DG
3
9
1_555
A
DG
4
A
DG
4
9
1_555
A
DG
9
A
DG
9
9
1_555
A
DG
10
A
DG
10
9
1_555
A
DG
15
A
DG
15
9
1_555
A
DG
16
A
DG
16
9
1_555
A
DG
21
A
DG
21
9
1_555
A
DG
22
A
DG
22
9
1_555
A
K
25
C
K
9
1_555
A
DG
2
A
DG
2
11
1_555
A
DG
3
A
DG
3
11
1_555
A
DG
8
A
DG
8
11
1_555
A
DG
9
A
DG
9
11
1_555
A
DG
14
A
DG
14
11
1_555
A
DG
15
A
DG
15
11
1_555
A
DG
20
A
DG
20
11
1_555
A
DG
21
A
DG
21
11
1_555
A
K
24
B
K
11
1_555
A
K
26
D
K
11
4_555
A
K
26
D
K
11
1_555
A
DG
2
A
DG
2
10
1_555
A
DG
2
A
DG
2
10
4_555
A
DG
8
A
DG
8
10
1_555
A
DG
8
A
DG
8
10
4_555
A
DG
14
A
DG
14
10
1_555
A
DG
14
A
DG
14
10
4_555
A
DG
20
A
DG
20
10
4_555
A
DG
20
A
DG
20
10
1_555
A
K
25
C
K
10
4_555
A
K
25
C
K
10
1_555
A
DG
4
A
DG
4
9
1_555
A
DT
5
A
DT
5
9
1_555
A
DT
6
A
DT
6
9
2_455
A
DG
10
A
DG
10
9
1_555
A
DT
11
A
DT
11
9
1_555
A
DT
12
A
DT
12
9
6_455
A
DA
13
A
DA
13
9
6_455
A
DG
16
A
DG
16
9
1_555
A
DG
22
A
DG
22
9
1_555
152
P 31 2 1