1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Katahira, M.
Mashima, T.
Matsugami, A.
Nishikawa, F.
Nishikawa, S.
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 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA 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
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
Y
51
N
N
Y
52
N
C
Y
53
N
N
Y
54
N
C
N
55
N
C
N
56
N
O
N
57
N
N
N
58
N
C
N
59
N
N
N
60
N
N
Y
61
N
C
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
H
N
75
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
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
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
Y
64
N
sing
Y
65
N
sing
Y
66
N
doub
N
67
N
sing
Y
68
N
sing
N
69
N
sing
Y
70
N
doub
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
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
37
6249
6258
10.1093/nar/gkp647
19666719
Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein
2009
10.2210/pdb2rqj/pdb
pdb_00002rqj
4033.512
RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
2
syn
polymer
no
no
GGAGGAGGAGGA
GGAGGAGGAGGA
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
refined structure
0.376
3
6
A
2
A
11
97.799
A_G2:G11_A
1
-0.973
-0.643
0.170
-3.514
3.148
3
6
A
5
A
8
-88.943
A_G5:G8_A
2
0.249
0.339
-0.349
3.799
0.765
3
6
A
1
A
4
-86.907
A_G1:G4_A
3
-1.248
0.528
0.007
3.864
5.387
6
A
7
A
10
-98.276
A_G7:G10_A
4
5.868
1.300
-0.207
3.493
2.138
3
6
B
23
B
20
90.662
B_G23:G20_B
5
-0.033
-0.510
-0.014
-3.857
5.077
6
B
19
B
22
-98.053
B_G19:G22_B
6
8.231
1.116
-0.291
3.607
-1.580
3
6
B
16
B
13
88.183
B_G16:G13_B
7
0.798
-0.423
-0.009
-3.841
-0.088
176.433
A
A
2
5
1.443
A
A
11
8
-0.084
2.885
-1.158
-3.923
AA_G2G5:G8G11_AA
1
3.346
-1.674
176.431
-1.962
0.579
-3.216
-126.549
A
A
5
1
-1.817
A
A
8
4
-3.162
3.245
-0.096
3.744
AA_G5G1:G4G8_AA
2
-2.703
-1.513
-126.510
-2.070
-0.032
-3.179
-31.513
B
B
23
19
4.046
B
B
20
22
-3.201
-2.185
0.760
1.435
BB_G23G19:G22G20_BB
3
5.513
10.210
-30.963
-3.043
0.388
-0.054
174.977
B
B
19
16
1.381
B
B
22
13
-0.050
2.759
-0.832
-3.833
BB_G19G16:G13G22_BB
4
-0.668
0.334
174.976
-1.918
0.417
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2009-11-17
1
1
2011-07-13
1
2
2022-03-16
1
3
2024-05-29
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
BMRB
Y
PDBJ
2009-07-18
REL
REL
structures with the lowest energy
200
9
1
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-1H TOCSY
2D 1H-1H TOCSY
2D DQF-COSY
2D 1H-13C HSQC
JRHMBC
1
mM
10
mM
100
mM
0.01
mM
3
mM
1
mM
10
mM
100
mM
0.01
mM
3
mM
0.1
6.2
ambient
atm
278
K
0.1
6.2
ambient
atm
303
K
simulated annealing
1
lowest energy
1mM RNA-1, 10mM potassium phosphate-2, 100mM potassium chloride-3, 0.01mM DSS-4, 3mM sodium azide-5, 95% H2O/5% D2O
95% H2O/5% D2O
1mM RNA-6, 10mM potassium phosphate-7, 100mM potassium chloride-8, 0.01mM DSS-9, 3mM sodium azide-10, 95% H2O/5% D2O
100% D2O
Schwieters, Kuszewski, Tjandra and Clore
structure solution
X-PLOR NIH
2.20
Bruker Biospin
collection
XwinNMR
Bruker Biospin
collection
TopSpin
Goddard
chemical shift assignment
Sparky
Goddard
peak picking
Sparky
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Garrett
chemical shift assignment
PIPP
Garrett
peak picking
PIPP
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
2.20
800
Bruker
DRX
Bruker DRX
600
Bruker
DRX
Bruker DRX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
G
4
n
4
G
4
A
G
5
n
5
G
5
A
A
6
n
6
A
6
A
G
7
n
7
G
7
A
G
8
n
8
G
8
A
A
9
n
9
A
9
A
G
10
n
10
G
10
A
G
11
n
11
G
11
A
A
12
n
12
A
12
A
G
13
n
1
G
13
B
G
14
n
2
G
14
B
A
15
n
3
A
15
B
G
16
n
4
G
16
B
G
17
n
5
G
17
B
A
18
n
6
A
18
B
G
19
n
7
G
19
B
G
20
n
8
G
20
B
A
21
n
9
A
21
B
G
22
n
10
G
22
B
G
23
n
11
G
23
B
A
24
n
12
A
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
HO2'
O5'
G
G
1
2
1.54
1
A
A
N7
H21
G
G
1
10
1.59
1
B
B
N7
H21
G
G
13
22
1.60
2
A
A
HO2'
OP2
G
G
1
2
1.49
2
A
A
N7
H21
G
G
1
10
1.60
3
A
B
HO2'
O2'
G
A
10
18
1.39
3
A
A
HO2'
OP2
G
G
1
2
1.50
3
A
A
HO2'
N1
G
A
4
6
1.51
3
B
B
N7
H21
G
G
13
22
1.58
3
A
A
HO2'
O5'
G
G
7
8
1.58
3
A
A
N7
H21
G
G
1
10
1.59
4
A
B
O2'
HO2'
A
G
6
22
1.41
4
A
A
N7
H21
G
G
1
10
1.58
4
B
B
N7
H21
G
G
13
22
1.59
5
B
B
HO2'
N1
G
A
16
18
1.41
5
A
A
N7
H21
G
G
1
10
1.59
6
B
B
HO2'
OP2
G
G
13
14
1.48
6
B
B
HO2'
O5'
G
A
23
24
1.52
6
B
B
O2'
H5'
G
G
16
17
1.56
6
A
B
O2'
HO2'
G
A
10
18
1.58
6
A
A
N7
H21
G
G
1
10
1.59
6
A
B
O2'
O2'
A
G
6
22
2.14
7
A
A
HO2'
N1
G
A
4
6
1.39
7
A
A
HO2'
OP2
G
G
1
2
1.39
7
B
B
N7
H21
G
G
13
22
1.59
7
A
A
N7
H21
G
G
1
10
1.60
8
A
A
OP1
H61
G
A
2
3
1.49
8
B
B
N7
H21
G
G
13
22
1.58
9
A
B
HO2'
O2'
A
G
6
22
1.36
9
B
B
HO2'
O5'
G
G
19
20
1.50
9
A
A
HO2'
OP2
G
G
7
8
1.57
9
A
B
O2'
O2'
A
G
6
22
2.12
lowest energy, model 1
Quadruplex structure of an RNA aptamer against bovine prion protein
1
N
N
1
N
N
hydrog
TYPE_11_PAIR
A
G
1
A
N2
G
1
1_555
A
A
3
A
N7
A
3
1_555
hydrog
TYPE_11_PAIR
A
G
1
A
N3
G
1
1_555
A
A
3
A
N6
A
3
1_555
hydrog
TYPE_6_PAIR
A
G
1
A
N1
G
1
1_555
A
G
4
A
O6
G
4
1_555
hydrog
TYPE_6_PAIR
A
G
1
A
N2
G
1
1_555
A
G
4
A
N7
G
4
1_555
hydrog
TYPE_6_PAIR
A
G
1
A
N7
G
1
1_555
A
G
10
A
N2
G
10
1_555
hydrog
TYPE_6_PAIR
A
G
1
A
O6
G
1
1_555
A
G
10
A
N1
G
10
1_555
hydrog
TYPE_6_PAIR
A
G
2
A
N1
G
2
1_555
A
G
5
A
O6
G
5
1_555
hydrog
TYPE_6_PAIR
A
G
2
A
N2
G
2
1_555
A
G
5
A
N7
G
5
1_555
hydrog
TYPE_6_PAIR
A
G
2
A
N7
G
2
1_555
A
G
11
A
N2
G
11
1_555
hydrog
TYPE_6_PAIR
A
G
2
A
O6
G
2
1_555
A
G
11
A
N1
G
11
1_555
hydrog
TYPE_6_PAIR
A
G
4
A
N1
G
4
1_555
A
G
7
A
O6
G
7
1_555
hydrog
TYPE_6_PAIR
A
G
4
A
N2
G
4
1_555
A
G
7
A
N7
G
7
1_555
hydrog
TYPE_6_PAIR
A
G
5
A
N1
G
5
1_555
A
G
8
A
O6
G
8
1_555
hydrog
TYPE_6_PAIR
A
G
5
A
N2
G
5
1_555
A
G
8
A
N7
G
8
1_555
hydrog
TYPE_11_PAIR
A
G
7
A
N2
G
7
1_555
A
A
9
A
N7
A
9
1_555
hydrog
TYPE_11_PAIR
A
G
7
A
N3
G
7
1_555
A
A
9
A
N6
A
9
1_555
hydrog
TYPE_6_PAIR
A
G
7
A
N1
G
7
1_555
A
G
10
A
O6
G
10
1_555
hydrog
TYPE_6_PAIR
A
G
7
A
N2
G
7
1_555
A
G
10
A
N7
G
10
1_555
hydrog
TYPE_6_PAIR
A
G
8
A
N1
G
8
1_555
A
G
11
A
O6
G
11
1_555
hydrog
TYPE_6_PAIR
A
G
8
A
N2
G
8
1_555
A
G
11
A
N7
G
11
1_555
hydrog
TYPE_11_PAIR
B
G
13
B
N2
G
1
1_555
B
A
15
B
N7
A
3
1_555
hydrog
TYPE_11_PAIR
B
G
13
B
N3
G
1
1_555
B
A
15
B
N6
A
3
1_555
hydrog
TYPE_6_PAIR
B
G
13
B
N1
G
1
1_555
B
G
16
B
O6
G
4
1_555
hydrog
TYPE_6_PAIR
B
G
13
B
N2
G
1
1_555
B
G
16
B
N7
G
4
1_555
hydrog
TYPE_6_PAIR
B
G
13
B
N7
G
1
1_555
B
G
22
B
N2
G
10
1_555
hydrog
TYPE_6_PAIR
B
G
13
B
O6
G
1
1_555
B
G
22
B
N1
G
10
1_555
hydrog
TYPE_6_PAIR
B
G
14
B
N1
G
2
1_555
B
G
17
B
O6
G
5
1_555
hydrog
TYPE_6_PAIR
B
G
14
B
N2
G
2
1_555
B
G
17
B
N7
G
5
1_555
hydrog
TYPE_6_PAIR
B
G
14
B
N7
G
2
1_555
B
G
23
B
N2
G
11
1_555
hydrog
TYPE_6_PAIR
B
G
14
B
O6
G
2
1_555
B
G
23
B
N1
G
11
1_555
hydrog
TYPE_6_PAIR
B
G
16
B
N1
G
4
1_555
B
G
19
B
O6
G
7
1_555
hydrog
TYPE_6_PAIR
B
G
16
B
N2
G
4
1_555
B
G
19
B
N7
G
7
1_555
hydrog
TYPE_6_PAIR
B
G
17
B
N1
G
5
1_555
B
G
20
B
O6
G
8
1_555
hydrog
TYPE_6_PAIR
B
G
17
B
N2
G
5
1_555
B
G
20
B
N7
G
8
1_555
hydrog
TYPE_11_PAIR
B
G
19
B
N2
G
7
1_555
B
A
21
B
N7
A
9
1_555
hydrog
TYPE_11_PAIR
B
G
19
B
N3
G
7
1_555
B
A
21
B
N6
A
9
1_555
hydrog
TYPE_6_PAIR
B
G
19
B
N1
G
7
1_555
B
G
22
B
O6
G
10
1_555
hydrog
TYPE_6_PAIR
B
G
19
B
N2
G
7
1_555
B
G
22
B
N7
G
10
1_555
hydrog
TYPE_6_PAIR
B
G
20
B
N1
G
8
1_555
B
G
23
B
O6
G
11
1_555
hydrog
TYPE_6_PAIR
B
G
20
B
N2
G
8
1_555
B
G
23
B
N7
G
11
1_555
RNA
Aptamer, Prion, Quadruplex, RNA
2RQJ
PDB
1
2RQJ
1
12
2RQJ
1
12
2RQJ
A
1
1
12
13
24
2RQJ
13
24
2RQJ
B
1
1
12
1
P 1