1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Chen, X.
McDowell, J.A.
Kierzek, R.
Krugh, T.R.
Turner, D.H.
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
US
Biochemistry
BICHAW
0033
0006-2960
39
8970
8982
10.1021/bi992938e
10913310
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).
2000
10.2210/pdb1eka/pdb
pdb_00001eka
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2542.561
RNA (5'-R(*GP*AP*GP*UP*GP*CP*UP*C)-3')
2
syn
polymer
no
no
GAGUGCUC
GAGUGCUC
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
-10.745
1
19
A
1
B
8
-0.733
A_G1:C8_B
1
-11.610
-0.542
-0.225
-0.123
-7.188
1
20
A
2
B
7
-0.135
A_A2:U7_B
2
-9.294
0.172
-0.164
0.029
-1.001
1
19
A
3
B
6
-0.690
A_G3:C6_B
3
-9.454
-0.328
-0.059
-0.072
3.017
1
28
A
4
B
5
5.973
A_U4:G5_B
4
-9.007
2.175
-0.198
-0.293
0.413
1
28
A
5
B
4
4.166
A_G5:U4_B
5
-7.854
-2.169
-0.018
-0.311
4.315
1
19
A
6
B
3
-0.521
A_C6:G3_B
6
-10.624
0.331
-0.052
-0.064
11.085
1
20
A
7
B
2
0.161
A_U7:A2_B
7
-9.210
-0.184
-0.228
0.039
18.450
1
19
A
8
B
1
-0.675
A_C8:G1_B
8
-13.024
0.545
-0.432
-0.096
2.834
33.452
A
A
1
2
11.709
B
B
8
7
3.175
6.693
0.263
-1.492
AA_G1A2:U7C8_BB
1
2.039
-3.568
32.733
-3.619
-0.144
2.730
29.620
A
A
2
3
11.021
B
B
7
6
3.108
5.602
0.193
-1.747
AA_A2G3:C6U7_BB
2
-0.155
0.305
29.097
-4.483
-0.408
3.280
38.617
A
A
3
4
-0.033
B
B
6
5
3.261
-0.022
0.598
-1.607
AA_G3U4:G5C6_BB
3
1.393
-2.107
38.593
-2.427
-0.733
3.115
16.049
A
A
4
5
10.227
B
B
5
4
3.561
2.835
-0.339
-2.313
AA_U4G5:U4G5_BB
4
-1.661
5.989
15.712
-10.407
-0.028
3.275
38.855
A
A
5
6
-0.279
B
B
4
3
3.260
-0.186
-0.518
-1.584
AA_G5C6:G3U4_BB
5
-0.673
1.012
38.849
-2.359
0.697
2.746
29.678
A
A
6
7
10.949
B
B
3
2
3.108
5.576
-0.272
-1.667
AA_C6U7:A2G3_BB
6
0.288
-0.565
29.160
-4.313
0.586
2.823
33.218
A
A
7
8
11.181
B
B
2
1
3.133
6.354
-0.182
-1.393
AA_U7C8:G1A2_BB
7
-0.908
1.598
32.610
-3.414
0.179
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2000-11-13
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2000-03-07
REL
REL
1
0.1M
7
ambient
32
K
Simulated annealing, Molecular dynamics, Energy minimization
minimized average structure
3.5 mM RNA Oligomer
10 mM phosphate, 80 mM NaCl, 100 D2O
1.5 mM RNA Oligomer
10 mM Phosphate, 80 mM NaCl, 10% D2O, 90 % H2O
500
Varian
UNITYPLUS
500
Varian
INOVA
G
1
n
1
G
1
A
A
2
n
2
A
2
A
G
3
n
3
G
3
A
U
4
n
4
U
4
A
G
5
n
5
G
5
A
C
6
n
6
C
6
A
U
7
n
7
U
7
A
C
8
n
8
C
8
A
G
1
n
1
G
1
B
A
2
n
2
A
2
B
G
3
n
3
G
3
B
U
4
n
4
U
4
B
G
5
n
5
G
5
B
C
6
n
6
C
6
B
U
7
n
7
U
7
B
C
8
n
8
C
8
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
U
7
0.064
SIDE CHAIN
1
B
U
7
0.067
SIDE CHAIN
1
5.46
0.70
108.50
113.96
A
A
A
O4'
C1'
N1
U
U
U
4
4
4
N
1
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N9
G
G
G
5
5
5
N
1
4.74
0.70
108.50
113.24
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
1
5.15
0.70
108.50
113.65
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
1
4.36
0.70
108.50
112.86
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
minimized average
NMR AND MOLECULAR MODELING REVEAL THAT DIFFERENT HYDROGEN BONDING PATTERNS ARE POSSIBLE FOR GU PAIRS: ONE HYDROGEN BOND FOR EACH GU PAIR IN R(GGCGUGCC)2 AND TWO FOR EACH GU PAIR IN R(GAGUGCUC)2
1
N
N
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
8
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
8
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
8
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
A
2
A
N1
A
2
1_555
B
U
7
B
N3
U
7
1_555
hydrog
WATSON-CRICK
A
A
2
A
N6
A
2
1_555
B
U
7
B
O4
U
7
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
B
C
6
B
N3
C
6
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
B
C
6
B
O2
C
6
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
B
C
6
B
N4
C
6
1_555
hydrog
TYPE_28_PAIR
A
U
4
A
N3
U
4
1_555
B
G
5
B
O6
G
5
1_555
hydrog
TYPE_28_PAIR
A
U
4
A
O2
U
4
1_555
B
G
5
B
N1
G
5
1_555
hydrog
TYPE_28_PAIR
A
G
5
A
N1
G
5
1_555
B
U
4
B
O2
U
4
1_555
hydrog
TYPE_28_PAIR
A
G
5
A
O6
G
5
1_555
B
U
4
B
N3
U
4
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
B
G
3
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
B
G
3
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
B
G
3
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
U
7
A
N3
U
7
1_555
B
A
2
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
U
7
A
O4
U
7
1_555
B
A
2
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
B
G
1
B
N2
G
1
1_555
RNA
RNA, GU Pair, Hydrogen Bonds, Duble Helix
1EKA
PDB
1
1EKA
1
8
1EKA
1
8
1EKA
A
1
1
8
1
8
1EKA
1
8
1EKA
B
1
1
8
1
P 1