1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Flinders, J.C.
Dieckmann, T.
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
308
665
679
10.1006/jmbi.2001.4627
11350168
A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA.
2001
10.2210/pdb1hwq/pdb
pdb_00001hwq
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9705.832
VS RIBOZYME SUBSTRATE RNA
1
syn
polymer
no
no
GGUGCGAAGGGCGUCGUCGCCCCGAGCGCC
GGUGCGAAGGGCGUCGUCGCCCCGAGCGCC
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
-3.603
1
19
A
1
A
30
-0.955
A_G1:C30_A
1
-2.478
0.931
0.171
-0.417
1.655
1
19
A
2
A
29
-0.569
A_G2:C29_A
2
1.358
0.924
-0.120
-0.399
-0.993
1
28
A
3
A
28
5.308
A_U3:G28_A
3
-2.897
1.763
0.037
-0.319
1.854
1
19
A
4
A
27
-0.174
A_G4:C27_A
4
-2.907
0.950
-0.185
-0.418
-1.049
1
19
A
5
A
26
-2.344
A_C5:G26_A
5
-1.542
-0.991
-0.337
-0.449
3.555
6
11
A
6
A
25
1.047
A_G6:A25_A
6
-7.882
6.568
-0.095
-4.591
1.164
9
11
A
7
A
24
2.015
A_A7:G24_A
7
0.770
-6.657
0.009
-4.215
-0.703
1
A
8
A
23
-8.616
A_A8:C23_A
8
1.155
-3.775
0.067
-1.348
-5.171
1
19
A
9
A
22
-1.644
A_G9:C22_A
9
-3.057
0.875
-0.079
-0.410
3.300
1
19
A
10
A
21
-1.279
A_G10:C21_A
10
0.485
0.908
-0.110
-0.404
2.930
1
19
A
11
A
20
0.484
A_G11:C20_A
11
-0.808
0.938
-0.373
-0.481
-1.073
1
19
A
12
A
19
-1.808
A_C12:G19_A
12
4.352
-1.280
-0.925
-0.646
3.022
31.818
A
A
1
2
33.631
A
A
30
29
3.887
17.464
0.504
-0.478
AA_G1G2:C29C30_AA
1
0.344
-0.662
26.699
-4.558
-0.847
2.778
44.228
A
A
2
3
35.076
A
A
29
28
3.475
24.922
1.033
-0.423
AA_G2U3:G28C29_AA
2
5.366
-7.553
36.447
-3.030
-0.840
1.877
32.253
A
A
3
4
38.262
A
A
28
27
3.121
19.714
-0.249
-0.884
AA_U3G4:C27G28_AA
3
5.061
-9.822
25.153
-4.624
1.227
2.154
31.344
A
A
4
5
29.948
A
A
27
26
3.157
15.462
1.155
-1.483
AA_G4C5:G26C27_AA
4
3.667
-7.103
27.105
-5.293
-1.534
3.567
70.174
A
A
5
6
-9.238
A
A
26
25
3.647
-10.590
0.577
0.313
AA_C5G6:A25G26_AA
5
-1.006
0.877
69.466
0.688
-0.541
2.556
-20.210
A
A
6
7
0.296
A
A
25
24
3.215
-0.102
1.600
-1.386
AA_G6A7:G24A25_AA
6
6.307
18.271
-19.211
3.993
7.164
4.175
46.068
A
A
7
8
-11.534
A
A
24
23
4.014
-8.973
0.034
-1.248
AA_A7A8:C23G24_AA
7
1.311
-1.686
45.214
-0.621
0.099
3.896
51.872
A
A
8
9
-10.676
A
A
23
22
3.782
-9.295
-0.491
-0.986
AA_A8G9:C22C23_AA
8
-0.182
0.208
51.089
-0.388
0.547
3.167
30.832
A
A
9
10
-3.717
A
A
22
21
3.142
-1.973
0.431
-1.195
AA_G9G10:C21C22_AA
9
-2.448
4.612
30.675
-1.876
-1.271
2.592
33.443
A
A
10
11
11.633
A
A
21
20
3.038
6.648
-0.489
-1.844
AA_G10G11:C20C21_AA
10
1.946
-3.405
32.738
-4.161
1.129
3.400
30.019
A
A
11
12
-4.107
A
A
20
19
3.252
-2.122
0.335
-2.000
AA_G11C12:G19C20_AA
11
3.169
-6.133
29.781
-3.416
0.019
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
2001-05-16
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
2001-01-09
REL
REL
RNA samples were transcribed from synthetic DNA templates using T7 RNA polymerase.
sample
structures with the lowest energy
200
20
2D NOESY
2D NOESY
3D_13C-separated_NOESY
DQF-COSY
5 mM NaCl
6.0
ambient
274
K
5 mM NaCl
6.0
ambient
298
K
5 mM NaCl
6.0
ambient
298
K
These structures were calculated using a total of 568 restraints; including 335 NOE-derived distance constraints, 158 dihedral angle restraints, 12 planarity restraints, and 63 H-bond distance restraints.
simulated annealing
1
lowest energy
1.5 mM VS RNA
90% H2O/10% D2O
1.5 mM VS RNA
100% D2O
1.5 mM VS RNA, 13C, 15N labeled
100% D2O
Bruker
collection
XwinNMR
2.6
Bruker
processing
XwinNMR
2.6
Bartels, C.
data analysis
XEASY
1.3.13
Brunger, A.
structure solution
CNS
1.0
Brunger, A.
refinement
CNS
1.0
600
Bruker
DRX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
U
3
n
3
U
3
A
G
4
n
4
G
4
A
C
5
n
5
C
5
A
G
6
n
6
G
6
A
A
7
n
7
A
7
A
A
8
n
8
A
8
A
G
9
n
9
G
9
A
G
10
n
10
G
10
A
G
11
n
11
G
11
A
C
12
n
12
C
12
A
G
13
n
13
G
13
A
U
14
n
14
U
14
A
C
15
n
15
C
15
A
G
16
n
16
G
16
A
U
17
n
17
U
17
A
C
18
n
18
C
18
A
G
19
n
19
G
19
A
C
20
n
20
C
20
A
C
21
n
21
C
21
A
C
22
n
22
C
22
A
C
23
n
23
C
23
A
G
24
n
24
G
24
A
A
25
n
25
A
25
A
G
26
n
26
G
26
A
C
27
n
27
C
27
A
G
28
n
28
G
28
A
C
29
n
29
C
29
A
C
30
n
30
C
30
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
A
A
H61
O2
A
C
8
23
1.34
1
A
A
HO2'
O5'
C
C
22
23
1.43
1
A
A
HO2'
O5'
G
U
13
14
1.44
1
A
A
O2'
H5'
C
G
18
19
1.47
1
A
A
HO2'
O5'
U
C
14
15
1.50
1
A
A
N3
H21
C
G
12
19
1.53
2
A
A
HO2'
O5'
G
G
9
10
1.35
2
A
A
H61
O2
A
C
8
23
1.36
2
A
A
HO2'
O5'
G
C
26
27
1.48
2
A
A
O2'
H61
G
A
6
25
1.53
2
A
A
H2'
O4'
C
U
15
17
1.56
2
A
A
H21
N3
G
C
4
27
1.58
2
A
A
H2'
O4'
C
G
5
6
1.60
3
A
A
HO2'
O5'
U
C
17
18
1.36
3
A
A
H61
O2
A
C
8
23
1.38
3
A
A
HO2'
O2
U
C
14
15
1.51
3
A
A
N3
H21
C
G
12
19
1.51
3
A
A
O2'
H5'
C
G
18
19
1.52
4
A
A
H61
O2
A
C
8
23
1.32
4
A
A
O2'
H5'
C
G
18
19
1.46
4
A
A
O2
H2'
U
C
17
18
1.48
4
A
A
HO2'
O5'
C
G
23
24
1.52
4
A
A
O3'
H8
C
G
15
16
1.58
5
A
A
H61
O2
A
C
8
23
1.34
5
A
A
HO2'
O2
U
C
14
15
1.43
5
A
A
O2'
H5'
C
G
18
19
1.49
5
A
A
N3
H21
C
G
12
19
1.52
5
A
A
O2'
H5'
G
G
9
10
1.54
5
A
A
HO2'
O5'
C
G
23
24
1.56
6
A
A
H61
O2
A
C
8
23
1.31
6
A
A
HO2'
O5'
G
A
6
7
1.43
6
A
A
O2'
H5'
C
G
18
19
1.50
6
A
A
O2'
H8
U
G
17
19
1.53
6
A
A
HO2'
O5'
G
U
13
14
1.54
6
A
A
HO2'
O5'
G
C
26
27
1.57
6
A
A
HO2'
O5'
C
G
5
6
1.57
6
A
A
N3
H21
C
G
12
19
1.58
6
A
A
O2'
H3'
U
C
17
18
1.59
6
A
A
H21
N3
G
C
4
27
1.59
7
A
A
H61
O2
A
C
8
23
1.37
7
A
A
O2'
H5'
C
G
18
19
1.55
7
A
A
N3
H21
C
G
12
19
1.58
8
A
A
H61
O2
A
C
8
23
1.38
8
A
A
HO2'
O5'
C
G
15
16
1.39
8
A
A
O2'
H3'
C
G
15
16
1.44
8
A
A
O2'
H8
C
G
18
19
1.57
9
A
A
HO2'
O5'
G
A
6
7
1.31
9
A
A
H61
O2
A
C
8
23
1.34
9
A
A
HO2'
O5'
U
C
17
18
1.39
9
A
A
HO2'
O2
U
C
14
15
1.40
9
A
A
N3
H21
C
G
12
19
1.51
9
A
A
HO2'
O5'
G
C
26
27
1.58
9
A
A
H21
N3
G
C
4
27
1.59
10
A
A
H61
O2
A
C
8
23
1.33
10
A
A
H2'
O4'
A
A
7
8
1.57
10
A
A
H21
N3
G
C
4
27
1.57
10
A
A
N3
H21
C
G
12
19
1.60
11
A
A
H61
O2
A
C
8
23
1.30
11
A
A
H1'
O5'
U
C
17
18
1.56
11
A
A
HO2'
O5'
G
C
26
27
1.59
12
A
A
H61
O2
A
C
8
23
1.32
12
A
A
HO2'
O2
U
C
14
15
1.36
12
A
A
O2'
H5'
C
G
18
19
1.48
12
A
A
N3
H21
C
G
12
19
1.51
13
A
A
H61
O2
A
C
8
23
1.29
13
A
A
O2
H2'
U
C
17
18
1.39
13
A
A
O2'
H5'
C
G
18
19
1.55
13
A
A
N3
H21
C
G
12
19
1.58
14
A
A
HO2'
O5'
U
C
17
18
1.33
14
A
A
H61
O2
A
C
8
23
1.36
14
A
A
O2'
H5'
C
G
18
19
1.52
14
A
A
N3
H21
C
G
12
19
1.52
15
A
A
HO2'
N3
U
C
14
15
1.32
15
A
A
H61
O2
A
C
8
23
1.33
15
A
A
O2'
H5'
C
G
18
19
1.50
15
A
A
N3
H21
C
G
12
19
1.59
16
A
A
H61
O2
A
C
8
23
1.34
16
A
A
HO2'
O5'
C
U
15
17
1.54
16
A
A
O2'
H8
C
G
15
16
1.54
16
A
A
O2'
H8
C
G
18
19
1.56
17
A
A
H61
O2
A
C
8
23
1.34
17
A
A
HO2'
O5'
U
C
17
18
1.39
17
A
A
O2'
H61
G
A
6
25
1.48
17
A
A
N3
H21
C
G
12
19
1.50
17
A
A
HO2'
O5'
C
G
23
24
1.51
17
A
A
HO2'
O5'
G
U
13
14
1.58
18
A
A
H61
O2
A
C
8
23
1.36
18
A
A
HO2'
O5'
C
U
15
17
1.41
18
A
A
O2'
H8
C
G
18
19
1.44
18
A
A
O2'
H8
C
G
15
16
1.52
18
A
A
H21
N3
G
C
4
27
1.58
19
A
A
H61
O2
A
C
8
23
1.32
19
A
A
O2'
H5'
C
G
18
19
1.51
20
A
A
H61
O2
A
C
8
23
1.34
20
A
A
HO2'
O5'
G
G
9
10
1.48
20
A
A
O2'
H2'
U
C
17
18
1.52
SOLUTION STRUCTURE OF THE VS RIBOZYME SUBSTRATE STEM-LOOP
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
30
A
N3
C
30
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
30
A
O2
C
30
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
30
A
N4
C
30
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
29
A
N3
C
29
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
29
A
O2
C
29
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
29
A
N4
C
29
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
N3
U
3
1_555
A
G
28
A
O6
G
28
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
O2
U
3
1_555
A
G
28
A
N1
G
28
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
27
A
N3
C
27
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
27
A
O2
C
27
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
27
A
N4
C
27
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
A
G
26
A
N1
G
26
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
A
G
26
A
O6
G
26
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
A
G
26
A
N2
G
26
1_555
hydrog
TYPE_11_PAIR
A
G
6
A
N2
G
6
1_555
A
A
25
A
N7
A
25
1_555
hydrog
TYPE_11_PAIR
A
G
6
A
N3
G
6
1_555
A
A
25
A
N6
A
25
1_555
hydrog
TYPE_11_PAIR
A
A
7
A
N6
A
7
1_555
A
G
24
A
N3
G
24
1_555
hydrog
TYPE_11_PAIR
A
A
7
A
N7
A
7
1_555
A
G
24
A
N2
G
24
1_555
hydrog
A-C MISPAIR
A
A
8
A
N6
A
8
1_555
A
C
23
A
O2
C
23
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
A
C
22
A
N3
C
22
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
A
C
22
A
O2
C
22
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
A
C
22
A
N4
C
22
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
A
C
21
A
N3
C
21
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
A
C
21
A
O2
C
21
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
A
C
21
A
N4
C
21
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
RNA
VS RIBOZYME, STEM-LOOP, TANDEM GA, PROTONATED ADENINE, A+C BASE PAIR, RNA
1HWQ
PDB
1
1HWQ
1
30
1HWQ
1
30
1HWQ
A
1
1
30
1
P 1