1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Thiviyanathan, V.
Guliaev, A.B.
Leontis, N.B.
Gorenstein, D.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
300
1143
1154
10.1006/jmbi.2000.3931
10903860
Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement.
2000
10.2210/pdb1k8s/pdb
pdb_00001k8s
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
Bulged base RNA duplex E Coli 5S rRNA
4211.582
5'-R(*GP*GP*CP*AP*GP*AP*GP*UP*GP*CP*CP*GP*C)-3'
1
syn
polymer
3802.328
5'-R(*GP*CP*GP*GP*CP*AP*CP*CP*UP*GP*CP*C)-3'
1
syn
polymer
no
no
GGCAGAGUGCCGC
GGCAGAGUGCCGC
A
polyribonucleotide
no
no
GCGGCACCUGCC
GCGGCACCUGCC
B
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
-7.155
1
19
A
1
B
25
-0.662
A_G1:C25_B
1
3.286
-0.439
-0.222
-0.234
2.275
1
19
A
2
B
24
0.373
A_G2:C24_B
2
-6.351
-0.267
0.126
-0.155
2.881
1
19
A
3
B
23
0.310
A_C3:G23_B
3
-15.578
0.548
-0.103
-0.272
-15.588
1
20
A
4
B
22
0.583
A_A4:U22_B
4
-13.630
-0.112
-0.108
-0.089
-10.459
1
19
A
5
B
21
-1.259
A_G5:C21_B
5
-19.144
-0.318
-0.157
-0.189
-17.716
1
19
A
7
B
20
0.348
A_G7:C20_B
6
-19.435
-0.321
0.098
-0.162
-11.636
1
20
A
8
B
19
4.834
A_U8:A19_B
7
-0.894
0.004
0.873
-0.143
5.892
1
19
A
9
B
18
-0.340
A_G9:C18_B
8
-19.264
-0.475
0.250
-0.261
-3.253
1
19
A
10
B
17
-0.539
A_C10:G17_B
9
-15.494
0.370
0.353
-0.213
-0.738
1
19
A
11
B
16
-0.446
A_C11:G16_B
10
-24.110
0.316
0.070
-0.231
-24.806
1
19
A
12
B
15
7.363
A_G12:C15_B
11
-29.070
-0.632
-0.937
-0.239
-24.615
1
19
A
13
B
14
2.101
A_C13:G14_B
12
12.521
0.489
0.469
-0.125
2.662
30.279
A
A
1
2
11.188
B
B
25
24
3.034
5.808
0.730
-1.574
AA_G1G2:C24C25_BB
1
-0.897
1.729
29.716
-4.045
-1.558
3.183
38.911
A
A
2
3
1.850
B
B
24
23
3.254
1.231
-0.261
-1.468
AA_G2C3:G23C24_BB
2
2.771
-4.164
38.797
-2.350
0.723
2.732
36.608
A
A
3
4
23.667
B
B
23
22
3.484
14.476
0.584
-1.335
AA_C3A4:U22G23_BB
3
2.208
-3.610
33.644
-4.103
-0.628
2.619
31.933
A
A
4
5
17.684
B
B
22
21
3.127
9.586
-0.498
-1.299
AA_A4G5:C21U22_BB
4
-0.707
1.304
30.488
-3.927
0.790
3.908
58.187
A
A
5
7
17.260
B
B
21
20
5.388
16.254
-1.867
-1.279
AA_G5G7:C20C21_BB
5
21.207
-22.519
52.172
-2.618
3.621
2.996
34.430
A
A
7
8
0.529
B
B
20
19
3.142
0.310
0.183
-0.989
AA_G7U8:A19C20_BB
6
-8.535
14.562
33.385
-1.716
-1.576
2.261
28.785
A
A
8
9
8.420
B
B
19
18
2.566
4.167
-0.756
-1.497
AA_U8G9:C18A19_BB
7
2.285
-4.617
28.398
-3.705
1.901
3.265
37.675
A
A
9
10
5.347
B
B
18
17
3.414
3.440
-0.231
-1.566
AA_G9C10:G17C18_BB
8
-4.766
7.408
37.230
-2.883
-0.277
2.932
29.826
A
A
10
11
8.387
B
B
17
16
3.134
4.286
0.762
-1.779
AA_C10C11:G16G17_BB
9
4.623
-9.048
29.166
-4.294
-0.576
1.289
41.499
A
A
11
12
55.647
B
B
16
15
3.794
33.575
0.315
-1.124
AA_C11G12:C15G16_BB
10
9.608
-15.924
22.778
-5.264
0.607
3.047
32.789
A
A
12
13
5.296
B
B
15
14
3.470
2.907
0.182
-0.758
AA_G12C13:G14C15_BB
11
-13.045
23.766
30.010
-1.864
-2.663
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-11-14
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
RCSB
Y
RCSB
2001-10-25
REL
Enzymatically synthesized using T7 RNA Polymerase.
sample
Enzymatically synthesized using T7 RNA Polymerase.
sample
1
2D NOESY
110 mM
6.8
ambient
298
K
matrix relaxation,
molecular dynamics,
torsion angle dynamics
100 mM NaCl, 10 mM sodium phosphate, 0.02 mM EDTA
D2O/H2O
MSI
data analysis
Felix
95
Meadows, Gorenstein et al.
iterative matrix relaxation
MORASS
2.1
UCSF
refinement
Amber
5.0
500
Varian
VXRS
RG5
1
n
1
G
1
A
RG
2
n
2
G
2
A
RC
3
n
3
C
3
A
RA
4
n
4
A
4
A
RG
5
n
5
G
5
A
RA
6
n
6
A
6
A
RG
7
n
7
G
7
A
RU
8
n
8
U
8
A
RG
9
n
9
G
9
A
RC
10
n
10
C
10
A
RC
11
n
11
C
11
A
RG
12
n
12
G
12
A
RC3
13
n
13
C
13
A
RG5
14
n
1
G
14
B
RC
15
n
2
C
15
B
RG
16
n
3
G
16
B
RG
17
n
4
G
17
B
RC
18
n
5
C
18
B
RA
19
n
6
A
19
B
RC
20
n
7
C
20
B
RC
21
n
8
C
21
B
RU
22
n
9
U
22
B
RG
23
n
10
G
23
B
RC
24
n
11
C
24
B
RC3
25
n
12
C
25
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
4
0.071
SIDE CHAIN
1
A
G
7
0.051
SIDE CHAIN
1
A
G
9
0.092
SIDE CHAIN
1
A
C
11
0.089
SIDE CHAIN
1
A
G
12
0.079
SIDE CHAIN
1
A
C
13
0.087
SIDE CHAIN
1
B
C
20
0.061
SIDE CHAIN
1
B
C
21
0.096
SIDE CHAIN
1
4.97
0.70
108.50
113.47
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
1
4.74
0.70
108.50
113.24
A
A
A
O4'
C1'
N1
C
C
C
3
3
3
N
1
4.41
0.70
108.50
112.91
A
A
A
O4'
C1'
N9
A
A
A
4
4
4
N
1
3.29
0.50
117.70
120.99
A
A
A
C5
C6
N1
A
A
A
6
6
6
N
1
-4.11
0.60
118.60
114.49
A
A
A
N1
C6
N6
A
A
A
6
6
6
N
1
6.59
0.70
108.50
115.09
A
A
A
O4'
C1'
N1
U
U
U
8
8
8
N
1
6.37
0.70
108.50
114.87
A
A
A
O4'
C1'
N1
C
C
C
11
11
11
N
1
-4.31
0.70
121.90
117.59
A
A
A
N3
C2
O2
C
C
C
11
11
11
N
1
4.47
0.70
108.50
112.97
A
A
A
O4'
C1'
N9
G
G
G
12
12
12
N
1
4.80
0.70
108.50
113.30
A
A
A
O4'
C1'
N1
C
C
C
13
13
13
N
1
5.92
0.80
101.50
107.42
B
B
B
C3'
C2'
C1'
C
C
C
15
15
15
N
1
4.84
0.70
108.50
113.34
B
B
B
O4'
C1'
N1
C
C
C
15
15
15
N
1
4.62
0.70
108.50
113.12
B
B
B
O4'
C1'
N9
G
G
G
16
16
16
N
1
4.81
0.70
108.50
113.31
B
B
B
O4'
C1'
N1
C
C
C
18
18
18
N
1
4.22
0.70
108.50
112.72
B
B
B
O4'
C1'
N9
A
A
A
19
19
19
N
1
-4.15
0.60
118.60
114.45
B
B
B
N1
C6
N6
A
A
A
19
19
19
N
1
4.46
0.70
108.50
112.96
B
B
B
O4'
C1'
N1
C
C
C
20
20
20
N
1
5.15
0.80
101.50
106.65
B
B
B
C3'
C2'
C1'
C
C
C
21
21
21
N
1
5.26
0.80
101.50
106.76
B
B
B
C3'
C2'
C1'
U
U
U
22
22
22
N
1
5.15
0.70
108.50
113.65
B
B
B
O4'
C1'
N1
U
U
U
22
22
22
N
BULGED ADENOSINE IN AN RNA DUPLEX
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
25
B
N3
C
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
25
B
O2
C
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
25
B
N4
C
12
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
24
B
N3
C
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
24
B
O2
C
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
24
B
N4
C
11
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
B
G
23
B
N1
G
10
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
B
G
23
B
O6
G
10
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
B
G
23
B
N2
G
10
1_555
hydrog
WATSON-CRICK
A
A
4
A
N1
A
4
1_555
B
U
22
B
N3
U
9
1_555
hydrog
WATSON-CRICK
A
A
4
A
N6
A
4
1_555
B
U
22
B
O4
U
9
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
B
C
21
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
B
C
21
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
B
C
21
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
B
C
20
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
B
C
20
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
B
C
20
B
N4
C
7
1_555
hydrog
WATSON-CRICK
A
U
8
A
N3
U
8
1_555
B
A
19
B
N1
A
6
1_555
hydrog
WATSON-CRICK
A
U
8
A
O4
U
8
1_555
B
A
19
B
N6
A
6
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
B
C
18
B
N3
C
5
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
B
C
18
B
O2
C
5
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
B
C
18
B
N4
C
5
1_555
hydrog
WATSON-CRICK
A
C
10
A
N3
C
10
1_555
B
G
17
B
N1
G
4
1_555
hydrog
WATSON-CRICK
A
C
10
A
N4
C
10
1_555
B
G
17
B
O6
G
4
1_555
hydrog
WATSON-CRICK
A
C
10
A
O2
C
10
1_555
B
G
17
B
N2
G
4
1_555
hydrog
WATSON-CRICK
A
C
11
A
N3
C
11
1_555
B
G
16
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
11
A
N4
C
11
1_555
B
G
16
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
11
A
O2
C
11
1_555
B
G
16
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
G
12
A
N1
G
12
1_555
B
C
15
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
12
A
N2
G
12
1_555
B
C
15
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
12
A
O6
G
12
1_555
B
C
15
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
C
13
A
N3
C
13
1_555
B
G
14
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
13
A
N4
C
13
1_555
B
G
14
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
13
A
O2
C
13
1_555
B
G
14
B
N2
G
1
1_555
RNA
Bulged base, bulged adenosine, bulged RNA, RNA bulges, RNA
1K8S
PDB
1
1K8S
1K8S
PDB
2
1K8S
1
13
1K8S
1
13
1K8S
A
1
1
13
14
25
1K8S
14
25
1K8S
B
2
1
12