0.015864
0.009159
0.000000
0.000000
0.018319
0.000000
0.000000
0.000000
0.023591
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
63.034
63.034
42.389
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
C50 H80 N12 O4
913.248
2,7-bis[4-(4-methylpiperazin-1-yl)butyl]-4,9-bis{[4-(4-methylpiperazin-1-yl)butyl]amino}benzo[lmn][3,8]phenanthroline-1 ,3,6,8(2H,7H)-tetrone
BMSG-SH2
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
C
N
153
N
C
N
154
N
C
N
155
N
C
N
156
N
N
N
157
N
N
Y
158
N
C
Y
159
N
C
N
160
N
C
N
161
N
C
N
162
N
C
N
163
N
C
Y
164
N
C
Y
165
N
C
Y
166
N
C
Y
167
N
C
Y
168
N
C
Y
169
N
C
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
N
N
177
N
N
N
178
N
N
N
179
N
N
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
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
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
doub
N
134
N
doub
N
135
N
doub
N
136
N
doub
Y
137
N
doub
Y
138
N
sing
N
139
N
sing
Y
140
N
doub
Y
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
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
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
Y
255
N
sing
Y
256
N
doub
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
Y
265
N
sing
Y
266
N
doub
Y
267
N
doub
Y
268
N
sing
Y
269
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/pdb3t5e/pdb
pdb_00003t5e
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
CCD
2011-07-07
ADSC QUANTUM 315r
Si III channel
SINGLE WAVELENGTH
M
x-ray
1
0.97949
1.0
I02
Diamond
0.97949
SYNCHROTRON
DIAMOND BEAMLINE I02
6983.497
human telomeric DNA sequence
1
syn
polymer
913.248
2,7-bis[4-(4-methylpiperazin-1-yl)butyl]-4,9-bis{[4-(4-methylpiperazin-1-yl)butyl]amino}benzo[lmn][3,8]phenanthroline-1 ,3,6,8(2H,7H)-tetrone
1
syn
non-polymer
39.098
POTASSIUM ION
3
syn
non-polymer
18.015
water
38
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
3.48
64.67
VAPOR DIFFUSION, HANGING DROP
6.5
15% PEG400, 300 mM KBr, 50 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
283
chem_comp
chem_comp_atom
chem_comp_bond
database_2
entity
pdbx_entity_nonpoly
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
Structure summary
1
0
2012-02-15
1
1
2012-02-22
1
2
2023-09-13
_chem_comp.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_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
Same G-quadruplex bound by a related naphthalene diimide compound BMSG-SH1
Equivalent native G-quadruplex
RCSB
Y
RCSB
2011-07-27
REL
REL
T5E
2,7-bis[4-(4-methylpiperazin-1-yl)butyl]-4,9-bis{[4-(4-methylpiperazin-1-yl)butyl]amino}benzo[lmn][3,8]phenanthroline-1 ,3,6,8(2H,7H)-tetrone
K
POTASSIUM ION
HOH
water
DNA sequence synthesised by standard phosphoramidite chemistry
sample
1KF1
PDB entry 1KF1
PDB
experimental model
T5E
1
2
T5E
T5E
23
A
K
24
3
K
K
24
A
K
25
3
K
K
25
A
K
26
3
K
K
26
A
HOH
27
4
HOH
HOH
27
A
HOH
28
4
HOH
HOH
28
A
HOH
29
4
HOH
HOH
29
A
HOH
30
4
HOH
HOH
30
A
HOH
31
4
HOH
HOH
31
A
HOH
32
4
HOH
HOH
32
A
HOH
1
4
HOH
HOH
33
A
HOH
34
4
HOH
HOH
34
A
HOH
2
4
HOH
HOH
35
A
HOH
36
4
HOH
HOH
36
A
HOH
37
4
HOH
HOH
37
A
HOH
38
4
HOH
HOH
38
A
HOH
4
4
HOH
HOH
39
A
HOH
6
4
HOH
HOH
40
A
HOH
7
4
HOH
HOH
41
A
HOH
42
4
HOH
HOH
42
A
HOH
43
4
HOH
HOH
43
A
HOH
44
4
HOH
HOH
44
A
HOH
45
4
HOH
HOH
45
A
HOH
46
4
HOH
HOH
46
A
HOH
8
4
HOH
HOH
47
A
HOH
9
4
HOH
HOH
48
A
HOH
10
4
HOH
HOH
49
A
HOH
11
4
HOH
HOH
50
A
HOH
12
4
HOH
HOH
51
A
HOH
13
4
HOH
HOH
52
A
HOH
14
4
HOH
HOH
53
A
HOH
15
4
HOH
HOH
54
A
HOH
16
4
HOH
HOH
55
A
HOH
17
4
HOH
HOH
56
A
HOH
18
4
HOH
HOH
57
A
HOH
19
4
HOH
HOH
58
A
HOH
20
4
HOH
HOH
59
A
HOH
21
4
HOH
HOH
60
A
HOH
22
4
HOH
HOH
61
A
HOH
23
4
HOH
HOH
62
A
HOH
24
4
HOH
HOH
63
A
HOH
25
4
HOH
HOH
64
A
A
1
n
1
DA
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
0.0016
-0.0006
0.0001
0.0002
-0.0001
0.0000
-0.4401
-0.5931
0.9488
0.2709
0.2411
0.0693
-0.7166
-0.5570
0.1989
0.1236
0.0000
0.0000
0.1236
0.0000
0.1236
refined
-32.0340
7.3756
-4.6732
X-RAY DIFFRACTION
0.0383
-0.0870
-0.6211
0.1979
1.4122
10.0792
-0.0118
-0.3085
0.1188
0.3177
0.0804
-0.1556
0.0824
0.2819
-0.0685
0.1108
-0.0017
-0.0013
0.1122
0.0032
0.1354
refined
-26.0653
1.0155
1.5139
X-RAY DIFFRACTION
1.1106
-3.0983
0.0671
8.6439
-0.1872
0.0041
0.0152
0.2214
-0.2858
-0.2446
0.0211
-0.6145
0.3820
0.5307
-0.0364
0.1983
-0.0062
-0.0014
0.2132
-0.0009
0.1955
refined
-17.7297
-5.6219
-11.1316
X-RAY DIFFRACTION
2.2129
0.8673
0.4796
0.5016
-0.8601
6.8960
0.0808
0.3244
0.0534
-0.4719
-0.0705
-0.0607
-0.1696
0.0329
-0.0103
0.1063
-0.0068
-0.0004
0.1076
0.0017
0.1394
refined
-28.6497
4.6698
-17.9263
X-RAY DIFFRACTION
A
1
A
4
X-RAY DIFFRACTION
1
A
5
A
9
X-RAY DIFFRACTION
2
A
10
A
13
X-RAY DIFFRACTION
3
A
14
A
22
X-RAY DIFFRACTION
4
author_and_software_defined_assembly
PISA
1
monomeric
A
DG
2
A
O6
DG
2
1_555
A
K
25
D
K
K
1_555
A
DG
3
A
O6
DG
3
1_555
75.9
A
DG
2
A
O6
DG
2
1_555
A
K
25
D
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
68.0
A
DG
3
A
O6
DG
3
1_555
A
K
25
D
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
90.1
A
DG
2
A
O6
DG
2
1_555
A
K
25
D
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
132.9
A
DG
3
A
O6
DG
3
1_555
A
K
25
D
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
71.2
A
DG
8
A
O6
DG
8
1_555
A
K
25
D
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
79.2
A
DG
2
A
O6
DG
2
1_555
A
K
25
D
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
108.2
A
DG
3
A
O6
DG
3
1_555
A
K
25
D
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
154.5
A
DG
8
A
O6
DG
8
1_555
A
K
25
D
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
69.4
A
DG
9
A
O6
DG
9
1_555
A
K
25
D
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
89.7
A
DG
2
A
O6
DG
2
1_555
A
K
25
D
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
155.0
A
DG
3
A
O6
DG
3
1_555
A
K
25
D
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
112.2
A
DG
8
A
O6
DG
8
1_555
A
K
25
D
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
133.2
A
DG
9
A
O6
DG
9
1_555
A
K
25
D
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
70.8
A
DG
14
A
O6
DG
14
1_555
A
K
25
D
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
75.1
A
DG
2
A
O6
DG
2
1_555
A
K
25
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
71.7
A
DG
3
A
O6
DG
3
1_555
A
K
25
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
132.9
A
DG
8
A
O6
DG
8
1_555
A
K
25
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
107.8
A
DG
9
A
O6
DG
9
1_555
A
K
25
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
153.4
A
DG
14
A
O6
DG
14
1_555
A
K
25
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
70.1
A
DG
15
A
O6
DG
15
1_555
A
K
25
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
87.0
A
DG
2
A
O6
DG
2
1_555
A
K
25
D
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
89.9
A
DG
3
A
O6
DG
3
1_555
A
K
25
D
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
71.0
A
DG
8
A
O6
DG
8
1_555
A
K
25
D
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
154.1
A
DG
9
A
O6
DG
9
1_555
A
K
25
D
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
109.5
A
DG
14
A
O6
DG
14
1_555
A
K
25
D
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
133.0
A
DG
15
A
O6
DG
15
1_555
A
K
25
D
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
71.9
A
DG
20
A
O6
DG
20
1_555
A
K
25
D
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
75.7
A
DG
2
A
O6
DG
2
1_555
A
K
26
E
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
64.8
A
DG
2
A
O6
DG
2
1_555
A
K
26
E
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
103.1
A
DG
8
A
O6
DG
8
1_555
A
K
26
E
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
70.1
A
DG
2
A
O6
DG
2
1_555
A
K
26
E
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
67.2
A
DG
8
A
O6
DG
8
1_555
A
K
26
E
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
105.3
A
DG
14
A
O6
DG
14
1_555
A
K
26
E
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
69.4
A
DG
3
A
O6
DG
3
1_555
A
K
24
C
K
K
1_555
A
DG
4
A
O6
DG
4
1_555
73.3
A
DG
3
A
O6
DG
3
1_555
A
K
24
C
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
62.9
A
DG
4
A
O6
DG
4
1_555
A
K
24
C
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
93.2
A
DG
3
A
O6
DG
3
1_555
A
K
24
C
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
126.1
A
DG
4
A
O6
DG
4
1_555
A
K
24
C
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
77.7
A
DG
9
A
O6
DG
9
1_555
A
K
24
C
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
74.8
A
DG
3
A
O6
DG
3
1_555
A
K
24
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
97.0
A
DG
4
A
O6
DG
4
1_555
A
K
24
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
154.9
A
DG
9
A
O6
DG
9
1_555
A
K
24
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
62.1
A
DG
10
A
O6
DG
10
1_555
A
K
24
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
90.7
A
DG
3
A
O6
DG
3
1_555
A
K
24
C
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
155.6
A
DG
4
A
O6
DG
4
1_555
A
K
24
C
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
124.3
A
DG
9
A
O6
DG
9
1_555
A
K
24
C
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
125.9
A
DG
10
A
O6
DG
10
1_555
A
K
24
C
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
77.1
A
DG
15
A
O6
DG
15
1_555
A
K
24
C
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
73.2
A
DG
3
A
O6
DG
3
1_555
A
K
24
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
64.7
A
DG
4
A
O6
DG
4
1_555
A
K
24
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
126.3
A
DG
9
A
O6
DG
9
1_555
A
K
24
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
95.8
A
DG
10
A
O6
DG
10
1_555
A
K
24
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
155.3
A
DG
15
A
O6
DG
15
1_555
A
K
24
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
65.0
A
DG
16
A
O6
DG
16
1_555
A
K
24
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
91.0
A
DG
3
A
O6
DG
3
1_555
A
K
24
C
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
91.6
A
DG
4
A
O6
DG
4
1_555
A
K
24
C
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
76.9
A
DG
9
A
O6
DG
9
1_555
A
K
24
C
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
154.4
A
DG
10
A
O6
DG
10
1_555
A
K
24
C
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
124.5
A
DG
15
A
O6
DG
15
1_555
A
K
24
C
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
127.3
A
DG
16
A
O6
DG
16
1_555
A
K
24
C
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
78.0
A
DG
21
A
O6
DG
21
1_555
A
K
24
C
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
72.5
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
E
K
1
1.80
0.30
108.30
110.10
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-4.38
0.70
108.00
103.62
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
-5.68
0.80
109.40
103.72
A
A
A
O5'
C5'
C4'
DG
DG
DG
14
14
14
N
40.688
-0.12
-0.06
0.00
-0.12
0.00
0.19
0.945
0.935
HYDROGENS HAVE BEEN ADED IN THE RIDING POSITIONS
0.28158
0.24286
0.24474
0.24474
2.10
10.20
262
5372
5372
4.7
100.00
9.672
0.134
RANDOM
1
Isotropic plus TLS
THROUGHOUT
MOLECULAR REPLACEMENT
0.223
0.196
PDB entry 1KF1
MAXIMUM LIKELIHOOD
2.10
10.20
38
572
69
465
0
0.008
0.021
597
1.622
2.999
914
0.055
0.200
87
0.006
0.020
272
1.465
3.000
597
2.359
4.500
914
0.448
0.385
2.152
15
373
20
100.00
42.15
1.94
54.59
3T5E
7197
7197
2.0
2.0
0.06
1
15.2
8.9
99.6
0.66
1.94
1.99
2.0
531
1
7.0
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-4
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
4
N
N
metalc
2.642
A
DG
2
A
O6
DG
2
1_555
A
K
25
D
K
K
1_555
metalc
2.876
A
DG
2
A
O6
DG
2
1_555
A
K
26
E
K
K
1_555
metalc
2.971
A
DG
3
A
O6
DG
3
1_555
A
K
24
C
K
K
1_555
metalc
2.698
A
DG
3
A
O6
DG
3
1_555
A
K
25
D
K
K
1_555
metalc
2.683
A
DG
4
A
O6
DG
4
1_555
A
K
24
C
K
K
1_555
metalc
2.772
A
DG
8
A
O6
DG
8
1_555
A
K
25
D
K
K
1_555
metalc
2.772
A
DG
8
A
O6
DG
8
1_555
A
K
26
E
K
K
1_555
metalc
2.917
A
DG
9
A
O6
DG
9
1_555
A
K
24
C
K
K
1_555
metalc
2.574
A
DG
9
A
O6
DG
9
1_555
A
K
25
D
K
K
1_555
metalc
2.590
A
DG
10
A
O6
DG
10
1_555
A
K
24
C
K
K
1_555
metalc
2.802
A
DG
14
A
O6
DG
14
1_555
A
K
25
D
K
K
1_555
metalc
2.755
A
DG
14
A
O6
DG
14
1_555
A
K
26
E
K
K
1_555
metalc
3.051
A
DG
15
A
O6
DG
15
1_555
A
K
24
C
K
K
1_555
metalc
2.737
A
DG
15
A
O6
DG
15
1_555
A
K
25
D
K
K
1_555
metalc
2.626
A
DG
16
A
O6
DG
16
1_555
A
K
24
C
K
K
1_555
metalc
2.787
A
DG
20
A
O6
DG
20
1_555
A
K
25
D
K
K
1_555
metalc
2.876
A
DG
20
A
O6
DG
20
1_555
A
K
26
E
K
K
1_555
metalc
2.964
A
DG
21
A
O6
DG
21
1_555
A
K
24
C
K
K
1_555
metalc
2.770
A
DG
21
A
O6
DG
21
1_555
A
K
25
D
K
K
1_555
metalc
2.714
A
DG
22
A
O6
DG
22
1_555
A
K
24
C
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
3T5E
PDB
1
1
3T5E
AGGGTTAGGGTTAGGGTTAGGG
1
22
3T5E
1
22
3T5E
A
1
1
22
BINDING SITE FOR RESIDUE T5E A 23
A
T5E
23
Software
12
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
A
DA
1
A
DA
1
12
2_565
A
DG
4
A
DG
4
12
1_555
A
DG
8
A
DG
8
12
1_555
A
DG
9
A
DG
9
12
1_555
A
DG
10
A
DG
10
12
1_555
A
DT
11
A
DT
11
12
1_555
A
DT
12
A
DT
12
12
5_555
A
DA
13
A
DA
13
12
1_555
A
DG
16
A
DG
16
12
1_555
A
DT
17
A
DT
17
12
1_555
A
DG
21
A
DG
21
12
1_555
A
DG
22
A
DG
22
12
1_555
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
D
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
C
K
11
1_555
A
K
26
E
K
11
4_455
A
K
26
E
K
11
1_555
A
DG
2
A
DG
2
10
4_455
A
DG
2
A
DG
2
10
1_555
A
DG
8
A
DG
8
10
4_455
A
DG
8
A
DG
8
10
1_555
A
DG
14
A
DG
14
10
4_455
A
DG
14
A
DG
14
10
1_555
A
DG
20
A
DG
20
10
1_555
A
DG
20
A
DG
20
10
4_455
A
K
25
D
K
10
1_555
A
K
25
D
K
10
4_455
168
P 6