1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Clore, G.M.
Kuszewski, J.
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
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C7 H8 N4 O2
180.164
THEOPHYLLINE
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-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
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
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
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
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
H
N
111
N
C
Y
112
N
N
Y
113
N
C
N
114
N
O
Y
115
N
N
N
116
N
C
Y
117
N
C
Y
118
N
C
Y
119
N
C
N
120
N
O
Y
121
N
N
Y
122
N
C
Y
123
N
N
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
O
N
133
N
P
N
134
N
O
N
135
N
O
N
136
N
O
N
137
N
C
N
138
R
C
N
139
N
O
N
140
S
C
N
141
N
O
N
142
R
C
N
143
N
O
N
144
R
C
N
145
N
N
N
146
N
C
N
147
N
O
N
148
N
N
N
149
N
C
N
150
N
O
N
151
N
C
N
152
N
C
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
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
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
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
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
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
Y
120
N
sing
Y
121
N
sing
N
122
N
doub
Y
123
N
sing
N
124
N
sing
Y
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
Y
129
N
doub
Y
130
N
sing
Y
131
N
sing
Y
132
N
sing
N
133
N
doub
Y
134
N
sing
N
135
N
sing
Y
136
N
doub
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
N
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
doub
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
doub
N
169
N
sing
N
170
N
doub
N
171
N
sing
N
172
N
sing
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
125
1518
1525
10.1021/ja028383j
12568611
Improving the Accuracy of NMR Structures of RNA by Means of Conformational Database Potentials of Mean Force as Assessed by Complete Dipolar Coupling Cross-Validation
2003
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
4
644
649
Interlocking Structural Motifs Mediate Molecular Discrimination by a Theophylline-Binding RNA
1997
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
123
12135
12146
10.1021/ja011646+
Refinement of Local and Long Range Structural Order in Theophylline-Binding RNA Using Using 13C-1H Residual Dipolar Couplings and Restrained Molecular Dynamics.
2001
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
123
3903
3918
10.1021/ja010033u
Improving the Accuracy of NMR Structures of DNA by Means of a Database Potential of Mean Force Describing Base-Base Positional Interactions.
2001
10.2210/pdb1o15/pdb
pdb_00001o15
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
CONSENSUS SEQUENCE OF THE THEOPHYLLINE BINDING RNA APTAMER FLANKED BY A FOUR BASE-PAIR STEM, A THREE BASE-PAIR STEM, AND CAPPED BY A GAAA TETRALOOP
10638.409
THEOPHYLLINE-BINDING RNA
1
syn
polymer
180.164
THEOPHYLLINE
1
syn
non-polymer
no
no
GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGUC
GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGUC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
10.760
1
19
A
1
A
33
-2.593
A_G1:C33_A
1
6.865
-0.135
-0.046
-0.195
7.514
1
28
A
2
A
32
0.339
A_G2:U32_A
2
-23.022
-1.875
0.006
-0.375
8.696
1
19
A
3
A
31
0.300
A_C3:G31_A
3
-14.125
0.126
-0.255
-0.162
-5.936
1
19
A
4
A
30
0.541
A_G4:C30_A
4
-15.944
-0.137
-0.436
-0.182
-10.550
1
8
A
5
A
29
4.429
A_A5:G29_A
5
-17.722
0.256
-1.092
0.947
0.949
3
23
A
23
A
28
-74.340
A_U23:A28_A
6
-3.356
-0.326
-0.553
2.758
-5.644
1
19
A
8
A
26
-2.756
A_C8:G26_A
7
-1.843
0.011
0.014
-0.181
6.894
1
19
A
9
A
25
2.299
A_C9:G25_A
8
-21.686
0.244
-0.254
-0.219
9.162
1
19
A
11
A
20
-3.925
A_G11:C20_A
9
-21.229
-0.045
0.608
-0.238
2.951
1
19
A
12
A
19
1.049
A_C12:G19_A
10
-23.476
0.193
-0.088
-0.223
-1.623
1
19
A
13
A
18
-0.937
A_C13:G18_A
11
-4.383
0.172
-0.098
-0.196
18.272
A
14
A
17
-42.508
A_G14:A17_A
12
22.677
7.004
0.678
-5.448
3.001
23.322
A
A
1
2
15.097
A
A
33
32
3.621
6.034
0.132
-1.967
AA_G1G2:U32C33_AA
1
0.892
-2.232
22.521
-6.993
-0.011
2.850
40.486
A
A
2
3
10.647
A
A
32
31
3.114
7.328
-0.012
-1.232
AA_G2C3:G31U32_AA
2
-1.971
2.864
39.798
-2.535
-0.185
2.364
33.186
A
A
3
4
28.042
A
A
31
30
3.594
15.423
-0.118
-1.816
AA_C3G4:C30G31_AA
3
1.733
-3.152
29.424
-5.689
0.489
2.836
31.402
A
A
4
5
17.755
A
A
30
29
3.438
9.442
0.288
-1.560
AA_G4A5:G29C30_AA
4
3.989
-7.501
29.722
-4.632
0.206
1.767
-178.999
A
A
5
23
-54.914
A
A
29
28
1.955
109.794
-0.914
3.711
AA_A5U23:A28G29_AA
5
130.354
65.197
-167.971
-1.918
-0.383
1.244
39.592
A
A
8
9
36.967
A
A
26
25
2.674
23.501
0.376
-1.612
AA_C8C9:G25G26_AA
6
-0.612
0.962
32.085
-4.221
-0.602
3.188
35.941
A
A
11
12
7.080
A
A
20
19
3.394
4.354
0.173
-1.580
AA_G11C12:G19C20_AA
7
3.142
-5.110
35.550
-3.189
0.174
2.205
32.360
A
A
12
13
25.144
A
A
19
18
3.227
13.598
-0.178
-1.802
AA_C12C13:G18G19_AA
8
-0.936
1.730
29.420
-5.329
0.174
2.682
59.574
A
A
13
14
8.579
A
A
18
17
2.857
8.500
-2.867
-1.227
AA_C13G14:A17G18_AA
9
-0.194
0.195
59.019
-1.599
2.877
database_2
pdbx_database_remark
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Advisory
Data collection
Database references
Derived calculations
Data collection
1
0
2003-02-18
1
1
2008-04-26
1
2
2011-07-13
1
3
2022-02-23
1
4
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_remark.text
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
THE RESTRAINTS USED FOR DETERMINATION OF THIS STRUCTURE
ARE SUMMARIZED AS FOLLOWS:
DISTANCE RESTRAINTS
30 INTRARESIDUE NOES
86 SEQUENTIAL NOES
17 MEDIUM RANGE (1 < |i-j|<5) NOES
90 LONG RANGE (|i-j|>=5) NOES
52 DISTANCES FOR 8 W-C BASE PAIRS and 1 G-U
WOBBLE PAIR
TOTAL: 223
LOOSE TORSION ANGLE RESTRAINTS
31 DELTA
33 CHI
9 ALPHA, 9 BETA, 10 GAMMA, 9 EPSILON
AND 9 ZETA
TOTAL: 110.
13C-1H DIPOLAR COUPLINGS
55 SUGAR
46 BASE
TOTAL 101
RCSB
Y
RCSB
2002-10-21
REL
TEP
THEOPHYLLINE
THE DIPOLAR COUPLINGS WERE DIVIDED INTO 10 PAIRS
OF WORKING AND TEST DATA SETS CHOSEN AT RANDOM AND
PARTITIONED IN A RATIO OF 70% (WORKING) AND
30% (TEST). 25 SIMULATED ANNEALING STRUCTURES
WERE CALCULATED FOR EACH PAIR, RESULTING IN A TOTAL
OF 250 STRUCTURES. THE STRUCTURE REPORTED HERE IS
OBTAINED BY RESTRAINED REGULARIZED OF THE MEAN
COORDINATES OF THE ENSEMBLE OF 250 INDIVIDUAL
SIMULATED ANNEALING STRUCTURES CALCULATED WITH
COMPLETE DIPOLAR COUPLING CROSS-VALIDATION.
FOR THE ENSEMBLE OF 250 STRUCTURES THE WORKING
DIPOLAR COUPLING R-FACTOR IS 8.6+/-0.5% AND
THE FREE DIPOLAR COUPLING R-FACTOR IS 26.8+/-2.8%.
RESTRAINED REGULARIZED MEAN STRUCTURE
250
1
THE STRUCTURE IS BASED ON A TOTAL OF 223 NOE, 52 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 110 TORSION ANGLE RESTRAINTS, 101 CH DIPOLAR COUPLING RESTRAINTS. THE EXPERIMENTAL RESTRAINTS ARE ESSENTIALLY THE SAME AS THOSE LISTED IN N.SIBILLE,A.PARDI,J.P.SIMORRE,M.BLACKLEDGE J.AM.CHEM.SOC. V 123, 12135 2001. THE NON-BONDED CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, A BASE-BASE POSITIONING DATABASE POTENTIAL OF MEAN FORCE, AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE.
CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA
refinement
X-PLOR NIH
(HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH)
THE
34
2
TEP
TEP
34
A
GUA
1
n
1
G
1
A
GUA
2
n
2
G
2
A
CYT
3
n
3
C
3
A
GUA
4
n
4
G
4
A
ADE
5
n
5
A
5
A
URI
6
n
6
U
6
A
ADE
7
n
7
A
7
A
CYT
8
n
8
C
8
A
CYT
9
n
9
C
9
A
ADE
10
n
10
A
10
A
GUA
11
n
11
G
11
A
CYT
12
n
12
C
12
A
CYT
13
n
13
C
13
A
GUA
14
n
14
G
14
A
ADE
15
n
15
A
15
A
ADE
16
n
16
A
16
A
ADE
17
n
17
A
17
A
GUA
18
n
18
G
18
A
GUA
19
n
19
G
19
A
CYT
20
n
20
C
20
A
CYT
21
n
21
C
21
A
CYT
22
n
22
C
22
A
URI
23
n
23
U
23
A
URI
24
n
24
U
24
A
GUA
25
n
25
G
25
A
GUA
26
n
26
G
26
A
CYT
27
n
27
C
27
A
ADE
28
n
28
A
28
A
GUA
29
n
29
G
29
A
CYT
30
n
30
C
30
A
GUA
31
n
31
G
31
A
URI
32
n
32
U
32
A
CYT
33
n
33
C
33
A
author_defined_assembly
1
monomeric
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
4.11
0.40
120.30
124.41
A
A
A
C6
N1
C2
C
C
C
27
27
27
N
THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
33
A
N3
C
33
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
33
A
O2
C
33
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
33
A
N4
C
33
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
N1
G
2
1_555
A
U
32
A
O2
U
32
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
O6
G
2
1_555
A
U
32
A
N3
U
32
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
31
A
N1
G
31
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
31
A
O6
G
31
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
31
A
N2
G
31
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
30
A
N3
C
30
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
30
A
O2
C
30
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
30
A
N4
C
30
1_555
hydrog
TYPE_8_PAIR
A
A
5
A
N1
A
5
1_555
A
G
29
A
N1
G
29
1_555
hydrog
TYPE_8_PAIR
A
A
5
A
N6
A
5
1_555
A
G
29
A
O6
G
29
1_555
hydrog
U-U MISPAIR
A
U
6
A
N3
U
6
1_555
A
U
23
A
O4
U
23
1_555
hydrog
U-A PAIR
A
U
6
A
O2
U
6
1_555
A
A
28
A
N6
A
28
1_555
hydrog
A-C MISPAIR
A
A
7
A
N3
A
7
1_555
A
C
8
A
N4
C
8
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
A
G
26
A
N1
G
26
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
A
G
26
A
O6
G
26
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
A
G
26
A
N2
G
26
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
A
G
25
A
N1
G
25
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
A
G
25
A
O6
G
25
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
A
G
25
A
N2
G
25
1_555
hydrog
WATSON-CRICK
A
G
11
A
N1
G
11
1_555
A
C
20
A
N3
C
20
1_555
hydrog
WATSON-CRICK
A
G
11
A
N2
G
11
1_555
A
C
20
A
O2
C
20
1_555
hydrog
WATSON-CRICK
A
G
11
A
O6
G
11
1_555
A
C
20
A
N4
C
20
1_555
hydrog
WATSON-CRICK
A
C
12
A
N3
C
12
1_555
A
G
19
A
N1
G
19
1_555
hydrog
WATSON-CRICK
A
C
12
A
N4
C
12
1_555
A
G
19
A
O6
G
19
1_555
hydrog
WATSON-CRICK
A
C
12
A
O2
C
12
1_555
A
G
19
A
N2
G
19
1_555
hydrog
WATSON-CRICK
A
C
13
A
N3
C
13
1_555
A
G
18
A
N1
G
18
1_555
hydrog
WATSON-CRICK
A
C
13
A
N4
C
13
1_555
A
G
18
A
O6
G
18
1_555
hydrog
WATSON-CRICK
A
C
13
A
O2
C
13
1_555
A
G
18
A
N2
G
18
1_555
hydrog
G-A MISPAIR
A
G
14
A
N2
G
14
1_555
A
A
17
A
N7
A
17
1_555
hydrog
HOOGSTEEN
A
U
23
A
N3
U
23
1_555
A
A
28
A
N7
A
28
1_555
hydrog
HOOGSTEEN
A
U
23
A
O4
U
23
1_555
A
A
28
A
N6
A
28
1_555
RNA
RIBONUCLEIC ACID, RNA
1O15
PDB
1
1O15
1
33
1O15
1
33
1O15
A
1
1
33
BINDING SITE FOR RESIDUE TEP A 34
A
TEP
34
Software
3
A
A
7
A
A
7
3
1_555
A
C
22
A
C
22
3
1_555
A
U
24
A
U
24
3
1_555
1
P 1