1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Luebke, K.J.
Landry, S.M.
Tinoco Junior, I.
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
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
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
R
C
N
122
N
O
N
123
R
C
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
C
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
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
doub
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
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
Berkeley : University of California, Berkeley (Thesis)
US
Biochemistry
BICHAW
0033
0006-2960
36
10246
10255
10.1021/bi9701540
9254623
Solution conformation of a five-nucleotide RNA bulge loop from a group I intron.
1997
10.2210/pdb1ajt/pdb
pdb_00001ajt
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3836.344
RNA (5'-R(*GP*GP*UP*AP*AP*UP*AP*AP*GP*CP*UP*C)-3')
1
syn
polymer
2220.395
RNA (5'-R(*GP*AP*GP*UP*AP*CP*C)-3')
1
syn
polymer
no
no
GGUAAUAAGCUC
GGUAAUAAGCUC
A
polyribonucleotide
no
no
GAGUACC
GAGUACC
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
25.736
1
19
A
2
B
24
8.013
A_G2:C24_B
1
-22.649
-0.578
-0.097
-0.463
-2.209
1
19
A
3
B
23
6.016
A_G3:C23_B
2
-26.603
-0.635
-0.635
-0.505
5.285
A
4
B
22
0.263
A_U4:A22_B
3
-16.998
4.459
0.025
-0.995
36.199
1
28
A
10
B
21
6.087
A_G10:U21_B
4
8.297
-2.407
-0.449
-0.426
42.663
1
19
A
11
B
20
-4.727
A_C11:G20_B
5
-23.155
0.234
-0.536
-0.172
20.394
1
20
A
12
B
19
-9.375
A_U12:A19_B
6
-10.528
-0.021
-0.443
-0.049
22.605
1
19
A
13
B
18
-2.922
A_C13:G18_B
7
-20.115
0.513
-0.444
-0.329
3.273
45.877
A
A
2
3
44.409
B
B
24
23
4.107
31.653
-1.329
0.310
AA_G2G3:C23C24_BB
1
-0.569
0.799
33.639
-3.241
1.640
2.915
54.172
A
A
3
4
8.337
B
B
23
22
2.964
7.569
0.991
0.072
AA_G3U4:A22C23_BB
2
-1.913
2.107
53.649
-0.341
-1.194
2.897
43.472
A
A
10
11
26.279
B
B
21
20
3.420
18.861
-1.877
-0.204
AA_G10C11:G20U21_BB
3
2.859
-3.983
39.247
-2.140
2.817
2.364
42.256
A
A
11
12
40.925
B
B
20
19
3.920
27.311
-1.243
-1.138
AA_C11U12:A19G20_BB
4
-1.175
1.760
32.535
-4.663
1.591
2.792
40.954
A
A
12
13
18.948
B
B
19
18
3.046
13.027
1.414
-0.722
AA_U12C13:G18A19_BB
5
3.790
-5.513
38.733
-2.342
-1.639
database_2
pdbx_database_status
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
Other
Data collection
1
0
1997-08-20
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
1 STRUCTURE
Y
BNL
1997-05-08
REL
REL
LEAST RESTRAINT VIOLATION
20
1
NOESY
DQF-COSY
HMQC
TOCSY
TOCSY-NOESY
H-P CORRELATED
6.7
298
K
RESTRAINED MOLECULAR DYNAMICS
BRUNGER
refinement
X-PLOR
2.2
structure solution
FELIX230
structure solution
X-PLOR2.2
300
Bruker
AMX300
500
Bruker
AMX600
500
GE
GN500
G
2
n
1
G
2
A
G
3
n
2
G
3
A
U
4
n
3
U
4
A
A
5
n
4
A
5
A
A
6
n
5
A
6
A
U
7
n
6
U
7
A
A
8
n
7
A
8
A
A
9
n
8
A
9
A
G
10
n
9
G
10
A
C
11
n
10
C
11
A
U
12
n
11
U
12
A
C
13
n
12
C
13
A
G
18
n
1
G
18
B
A
19
n
2
A
19
B
G
20
n
3
G
20
B
U
21
n
4
U
21
B
A
22
n
5
A
22
B
C
23
n
6
C
23
B
C
24
n
7
C
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
B
O2
H61
U
A
4
22
1.54
1
A
A
HO2'
OP2
A
G
9
10
1.56
1
A
B
H41
O6
C
G
11
20
1.59
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
FIVE-NUCLEOTIDE BULGE LOOP FROM TETRAHYMENA THERMOPHILA GROUP I INTRON, NMR, 1 STRUCTURE
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
2
A
N1
G
1
1_555
B
C
24
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
1
1_555
B
C
24
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
1
1_555
B
C
24
B
N4
C
7
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
2
1_555
B
C
23
B
N3
C
6
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
2
1_555
B
C
23
B
O2
C
6
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
2
1_555
B
C
23
B
N4
C
6
1_555
hydrog
U-A PAIR
A
U
4
A
O2
U
3
1_555
B
A
22
B
N6
A
5
1_555
hydrog
TYPE_28_PAIR
A
G
10
A
N1
G
9
1_555
B
U
21
B
O2
U
4
1_555
hydrog
TYPE_28_PAIR
A
G
10
A
O6
G
9
1_555
B
U
21
B
N3
U
4
1_555
hydrog
WATSON-CRICK
A
C
11
A
N3
C
10
1_555
B
G
20
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
11
A
N4
C
10
1_555
B
G
20
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
11
A
O2
C
10
1_555
B
G
20
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
U
12
A
N3
U
11
1_555
B
A
19
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
U
12
A
O4
U
11
1_555
B
A
19
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
C
13
A
N3
C
12
1_555
B
G
18
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
13
A
N4
C
12
1_555
B
G
18
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
13
A
O2
C
12
1_555
B
G
18
B
N2
G
1
1_555
RNA
RNA BULGE LOOP, GROUP I INTRON, RIBONUCLEIC ACID, RNA
1AJT
PDB
1
1AJT
1AJT
PDB
2
1AJT
2
13
1AJT
2
13
1AJT
A
1
1
12
18
24
1AJT
18
24
1AJT
B
2
1
7
1
P 1