1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Matsugami, A.
Ouhashi, K.
Kanagawa, M.
Liu, H.
Kanagawa, S.
Uesugi, S.
Katahira, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
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
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
313
255
269
10.1006/jmbi.2001.5047
11800555
An intramolecular quadruplex of (GGA)(4) triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction.
2001
10.2210/pdb1myq/pdb
pdb_00001myq
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
K+ Cation Stabilized
3841.516
5'-D(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'
2
syn
polymer
no
no
(DG)(DG)(DA)(DG)(DG)(DA)(DG)(DG)(DA)(DG)(DG)(DA)
GGAGGAGGAGGA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Data collection
1
0
2002-10-23
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2002-10-04
REL
structures with the lowest energy
1
2D NOESY
2D NOESY
2D TOCSY
DQF-COSY
100 mM KCl
6.5
ambient
274
K
100 mM KCl
6.5
ambient
298
K
simulated annealing
1
lowest energy
2 mM DNA; 10 mM sodium phosphate buffer (pH 6.5); 100 mM KCl;
95% H2O/5% D2O
2 mM DNA; 10 mM sodium phosphate buffer (pH 6.5);
100% D2O
Brunger
structure solution
X-PLOR
3.851
Brunger
refinement
X-PLOR
3.851
600
Bruker
DRX
G
1
n
1
DG
1
A
G
2
n
2
DG
2
A
A
3
n
3
DA
3
A
G
4
n
4
DG
4
A
G
5
n
5
DG
5
A
A
6
n
6
DA
6
A
G
7
n
7
DG
7
A
G
8
n
8
DG
8
A
A
9
n
9
DA
9
A
G
10
n
10
DG
10
A
G
11
n
11
DG
11
A
A
12
n
12
DA
12
A
G
13
n
1
DG
13
B
G
14
n
2
DG
14
B
A
15
n
3
DA
15
B
G
16
n
4
DG
16
B
G
17
n
5
DG
17
B
A
18
n
6
DA
18
B
G
19
n
7
DG
19
B
G
20
n
8
DG
20
B
A
21
n
9
DA
21
B
G
22
n
10
DG
22
B
G
23
n
11
DG
23
B
A
24
n
12
DA
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
A
O6
H61
DG
DA
8
12
1.47
1
B
B
H1
O6
DG
DG
19
22
1.47
1
B
B
H1
O6
DG
DG
16
19
1.50
1
A
A
H1
O6
DG
DG
4
7
1.52
1
A
A
N7
H21
DG
DG
2
11
1.54
1
A
A
H22
N7
DG
DA
1
3
1.59
1
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
DG
DG
DG
1
1
1
N
1
-2.56
0.40
106.40
103.84
A
A
A
C8
N9
C4
DG
DG
DG
1
1
1
N
1
3.57
0.30
108.30
111.87
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
DA
DA
DA
3
3
3
N
1
-2.66
0.40
105.80
103.14
A
A
A
C8
N9
C4
DA
DA
DA
3
3
3
N
1
4.71
0.50
113.10
117.81
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
4.40
0.50
113.10
117.50
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
1
-2.49
0.40
106.40
103.91
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
1
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
3.72
0.50
113.80
117.52
A
A
A
N7
C8
N9
DA
DA
DA
6
6
6
N
1
3.12
0.30
108.30
111.42
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
4.21
0.50
113.10
117.31
A
A
A
N7
C8
N9
DG
DG
DG
7
7
7
N
1
3.87
0.30
108.30
112.17
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.41
0.50
113.10
117.51
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
1
3.63
0.50
113.80
117.43
A
A
A
N7
C8
N9
DA
DA
DA
9
9
9
N
1
-2.79
0.40
105.80
103.01
A
A
A
C8
N9
C4
DA
DA
DA
9
9
9
N
1
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
DG
DG
DG
10
10
10
N
1
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
DG
DG
DG
10
10
10
N
1
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
1
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
DA
DA
DA
12
12
12
N
1
3.40
0.30
108.30
111.70
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
4.57
0.50
113.10
117.67
B
B
B
N7
C8
N9
DG
DG
DG
13
13
13
N
1
-2.49
0.40
106.40
103.91
B
B
B
C8
N9
C4
DG
DG
DG
13
13
13
N
1
3.71
0.30
108.30
112.01
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
4.63
0.50
113.10
117.73
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
1
-2.80
0.40
106.40
103.60
B
B
B
C8
N9
C4
DG
DG
DG
14
14
14
N
1
3.69
0.50
113.80
117.49
B
B
B
N7
C8
N9
DA
DA
DA
15
15
15
N
1
-2.55
0.40
105.80
103.25
B
B
B
C8
N9
C4
DA
DA
DA
15
15
15
N
1
4.79
0.50
113.10
117.89
B
B
B
N7
C8
N9
DG
DG
DG
16
16
16
N
1
-2.74
0.40
106.40
103.66
B
B
B
C8
N9
C4
DG
DG
DG
16
16
16
N
1
2.50
0.30
108.30
110.80
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
1
4.44
0.50
113.10
117.54
B
B
B
N7
C8
N9
DG
DG
DG
17
17
17
N
1
-2.52
0.40
106.40
103.88
B
B
B
C8
N9
C4
DG
DG
DG
17
17
17
N
1
2.24
0.30
108.30
110.54
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
3.72
0.50
113.80
117.52
B
B
B
N7
C8
N9
DA
DA
DA
18
18
18
N
1
-2.42
0.40
105.80
103.38
B
B
B
C8
N9
C4
DA
DA
DA
18
18
18
N
1
3.14
0.30
108.30
111.44
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
4.28
0.50
113.10
117.38
B
B
B
N7
C8
N9
DG
DG
DG
19
19
19
N
1
4.05
0.30
108.30
112.35
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
4.43
0.50
113.10
117.53
B
B
B
N7
C8
N9
DG
DG
DG
20
20
20
N
1
-2.55
0.40
106.40
103.85
B
B
B
C8
N9
C4
DG
DG
DG
20
20
20
N
1
3.77
0.50
113.80
117.57
B
B
B
N7
C8
N9
DA
DA
DA
21
21
21
N
1
-2.84
0.40
105.80
102.96
B
B
B
C8
N9
C4
DA
DA
DA
21
21
21
N
1
2.81
0.30
108.30
111.11
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.57
0.50
113.10
117.67
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
-2.58
0.40
106.40
103.82
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
N
1
2.47
0.30
108.30
110.77
B
B
B
O4'
C1'
N9
DG
DG
DG
23
23
23
N
1
4.43
0.50
113.10
117.53
B
B
B
N7
C8
N9
DG
DG
DG
23
23
23
N
1
-2.64
0.40
106.40
103.76
B
B
B
C8
N9
C4
DG
DG
DG
23
23
23
N
1
2.27
0.30
108.30
110.57
B
B
B
O4'
C1'
N9
DA
DA
DA
24
24
24
N
1
3.70
0.50
113.80
117.50
B
B
B
N7
C8
N9
DA
DA
DA
24
24
24
N
An intramolecular quadruplex of (GGA)(4) triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction
1
N
N
1
N
N
hydrog
TYPE_11_PAIR
A
DG
1
A
N2
DG
1
1_555
A
DA
3
A
N7
DA
3
1_555
hydrog
TYPE_11_PAIR
A
DG
1
A
N3
DG
1
1_555
A
DA
3
A
N6
DA
3
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
N1
DG
1
1_555
A
DG
4
A
O6
DG
4
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
N2
DG
1
1_555
A
DG
4
A
N7
DG
4
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
N7
DG
1
1_555
A
DG
10
A
N2
DG
10
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
O6
DG
1
1_555
A
DG
10
A
N1
DG
10
1_555
hydrog
DG-DG MISPAIR
A
DG
1
A
N7
DG
1
1_555
A
DG
11
A
N1
DG
11
1_555
hydrog
DG-DG MISPAIR
A
DG
2
A
N1
DG
2
1_555
A
DG
5
A
O6
DG
5
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N7
DG
2
1_555
A
DG
11
A
N2
DG
11
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
O6
DG
2
1_555
A
DG
11
A
N1
DG
11
1_555
hydrog
DA-DG MISPAIR
A
DA
3
A
N6
DA
3
1_555
B
DG
22
B
N7
DG
10
1_555
hydrog
TYPE_11_PAIR
A
DG
4
A
N2
DG
4
1_555
A
DA
6
A
N7
DA
6
1_555
hydrog
TYPE_11_PAIR
A
DG
4
A
N3
DG
4
1_555
A
DA
6
A
N6
DA
6
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N1
DG
4
1_555
A
DG
7
A
O6
DG
7
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N2
DG
4
1_555
A
DG
7
A
N7
DG
7
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
N1
DG
5
1_555
A
DG
8
A
O6
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
N2
DG
5
1_555
A
DG
8
A
N7
DG
8
1_555
hydrog
DA-DG MISPAIR
A
DA
6
A
N6
DA
6
1_555
B
DG
19
B
N7
DG
7
1_555
hydrog
TYPE_11_PAIR
A
DG
7
A
N2
DG
7
1_555
A
DA
9
A
N7
DA
9
1_555
hydrog
TYPE_11_PAIR
A
DG
7
A
N3
DG
7
1_555
A
DA
9
A
N6
DA
9
1_555
hydrog
TYPE_6_PAIR
A
DG
7
A
N1
DG
7
1_555
A
DG
10
A
O6
DG
10
1_555
hydrog
TYPE_6_PAIR
A
DG
7
A
N2
DG
7
1_555
A
DG
10
A
N7
DG
10
1_555
hydrog
DG-DA MISPAIR
A
DG
7
A
N7
DG
7
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N1
DG
8
1_555
A
DG
11
A
O6
DG
11
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N2
DG
8
1_555
A
DG
11
A
N7
DG
11
1_555
hydrog
DG-DA MISPAIR
A
DG
8
A
O6
DG
8
1_555
A
DA
12
A
N6
DA
12
1_555
hydrog
DG-DA MISPAIR
A
DG
10
A
N7
DG
10
1_555
B
DA
15
B
N6
DA
3
1_555
hydrog
TYPE_11_PAIR
B
DG
13
B
N2
DG
1
1_555
B
DA
15
B
N7
DA
3
1_555
hydrog
TYPE_11_PAIR
B
DG
13
B
N3
DG
1
1_555
B
DA
15
B
N6
DA
3
1_555
hydrog
TYPE_6_PAIR
B
DG
13
B
N1
DG
1
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
TYPE_6_PAIR
B
DG
13
B
N2
DG
1
1_555
B
DG
16
B
N7
DG
4
1_555
hydrog
TYPE_6_PAIR
B
DG
13
B
N7
DG
1
1_555
B
DG
22
B
N2
DG
10
1_555
hydrog
TYPE_6_PAIR
B
DG
13
B
O6
DG
1
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
TYPE_6_PAIR
B
DG
13
B
N7
DG
1
1_555
B
DG
23
B
N2
DG
11
1_555
hydrog
TYPE_6_PAIR
B
DG
13
B
O6
DG
1
1_555
B
DG
23
B
N1
DG
11
1_555
hydrog
DG-DG MISPAIR
B
DG
14
B
N1
DG
2
1_555
B
DG
17
B
O6
DG
5
1_555
hydrog
TYPE_6_PAIR
B
DG
14
B
N7
DG
2
1_555
B
DG
23
B
N2
DG
11
1_555
hydrog
TYPE_6_PAIR
B
DG
14
B
O6
DG
2
1_555
B
DG
23
B
N1
DG
11
1_555
hydrog
TYPE_11_PAIR
B
DG
16
B
N2
DG
4
1_555
B
DA
18
B
N7
DA
6
1_555
hydrog
TYPE_11_PAIR
B
DG
16
B
N3
DG
4
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
TYPE_6_PAIR
B
DG
16
B
N1
DG
4
1_555
B
DG
19
B
O6
DG
7
1_555
hydrog
TYPE_6_PAIR
B
DG
16
B
N2
DG
4
1_555
B
DG
19
B
N7
DG
7
1_555
hydrog
TYPE_6_PAIR
B
DG
17
B
N1
DG
5
1_555
B
DG
20
B
O6
DG
8
1_555
hydrog
TYPE_6_PAIR
B
DG
17
B
N2
DG
5
1_555
B
DG
20
B
N7
DG
8
1_555
hydrog
TYPE_11_PAIR
B
DG
19
B
N2
DG
7
1_555
B
DA
21
B
N7
DA
9
1_555
hydrog
TYPE_11_PAIR
B
DG
19
B
N3
DG
7
1_555
B
DA
21
B
N6
DA
9
1_555
hydrog
TYPE_6_PAIR
B
DG
19
B
N1
DG
7
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
TYPE_6_PAIR
B
DG
19
B
N2
DG
7
1_555
B
DG
22
B
N7
DG
10
1_555
hydrog
TYPE_6_PAIR
B
DG
20
B
N1
DG
8
1_555
B
DG
23
B
O6
DG
11
1_555
hydrog
TYPE_6_PAIR
B
DG
20
B
N2
DG
8
1_555
B
DG
23
B
N7
DG
11
1_555
hydrog
DG-DA MISPAIR
B
DG
20
B
O6
DG
8
1_555
B
DA
24
B
N6
DA
12
1_555
DNA
intramolecular parallel quadruplex structure, dimeric structure, DNA
1MYQ
PDB
1
1MYQ
1
12
1MYQ
1
12
1MYQ
A
1
1
12
13
24
1MYQ
13
24
1MYQ
B
1
1
12