1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Denisov, A.Y.
Hannoush, R.N.
Gehring, K.
Damha, M.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O8 P
363.221
GUANOSINE-5'-MONOPHOSPHATE
non-polymer
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
C9 H14 N3 O8 P
323.197
CYTIDINE-5'-MONOPHOSPHATE
non-polymer
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
C9 H13 N2 O9 P
324.181
URIDINE-5'-MONOPHOSPHATE
non-polymer
US
J.AM.CHEM.SOC.
JACSAT
0004
0002-7863
125
11525
11531
10.1021/ja036207k
13129354
A Novel RNA Motif Based on the Structure of Unusually Stable 2',5'-Linked r(UUCG) Loops
2003
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
x-ray
1
1.0
3804.296
5'-R(*GP*GP*AP*CP*(U25)P*(U25)P*(C25)P*(5GP)P*GP*UP*CP*C)-3'
1
syn
polymer
no
yes
GGAC(U5P)(U5P)(C5P)(5GP)GUCC
GGACXXXXGUCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
-13.203
1
19
A
1
A
12
1.107
A_G1:C12_A
1
-3.782
-0.379
-0.340
-0.326
0.316
1
19
A
2
A
11
4.841
A_G2:C11_A
2
-4.781
-1.287
-0.196
-0.500
9.817
1
20
A
3
A
10
-2.526
A_A3:U10_A
3
-7.317
-0.162
-0.162
-0.402
1.433
1
19
A
4
A
9
5.464
A_C4:G9_A
4
-3.632
0.769
-0.284
-0.191
2.844
31.491
A
A
1
2
0.561
A
A
12
11
2.858
0.304
-0.104
-1.276
AA_G1G2:C11C12_AA
1
-2.735
5.045
31.374
-2.401
-0.253
2.855
44.156
A
A
2
3
14.540
A
A
11
10
2.744
10.813
-1.670
0.168
AA_G2A3:U10C11_AA
2
-4.450
5.984
42.655
-0.660
1.858
2.348
38.774
A
A
3
4
21.792
A
A
10
9
3.111
14.150
1.545
-1.810
AA_A3C4:G9U10_AA
3
2.094
-3.225
36.134
-4.226
-2.106
repository
Initial release
Version format compliance
Version format compliance
Non-polymer description
1
0
2003-08-19
1
1
2008-04-28
1
2
2011-07-13
1
3
2011-08-24
CHIMERIC HAIRPIN WITH 2',5'-LINKED RNA LOOP AND DNA STEM
COMPOUND
NUCLOTIDES 5(U25), 6(U25), 7(C25), 8(5GP)
HAS A NON-STANDARD 2'-5' LINKAGE.
RCSB
Y
RCSB
2002-08-07
REL
REL
Solid phase synthesis, phosphoramidite chemistry
sample
Structure was determined using standard 2D homo- and heteronuclear techniques: 2D-NOESY, DQF-COSY, TOCSY, H,C-HMQC, H,P-HetCOSY
STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
20
10
2D NOESY
DQF-COSY
7.0
1
atm
288
K
Structures were refined by NMR-restrained molecular dynamics (12 ps, 300-1000 K) with final energy minimization
simulated annealing
1
closest to the average, lowest energy
1.5 mM hairpin
D2O, H2O/D2O
Brunger
refinement
X-PLOR
3.851
Brunger
data analysis
X-PLOR
500
Bruker
DRX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
C
4
n
4
C
4
A
U5P
5
n
5
U5P
5
A
U5P
6
n
6
U5P
6
A
C5P
7
n
7
C5P
7
A
5GP
8
n
8
5GP
8
A
G
9
n
9
G
9
A
U
10
n
10
U
10
A
C
11
n
11
C
11
A
C
12
n
12
C
12
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
H21
O2
G
C
1
12
1.56
2
A
A
H21
O2
G
C
1
12
1.57
2
A
A
O2
H21
C
G
4
9
1.60
3
A
A
H21
O2
G
C
2
11
1.59
3
A
A
O2
H21
C
G
4
9
1.60
4
A
A
O2
H21
C
G
4
9
1.57
4
A
A
O2
HN1
U5P
5GP
5
8
1.60
5
A
A
H21
O2
G
C
1
12
1.58
5
A
A
HO2'
O4'
C
C
11
12
1.59
5
A
A
O2
H21
C
G
4
9
1.59
5
A
A
O2
HN1
U5P
5GP
5
8
1.60
6
A
A
H21
O2
G
C
2
11
1.56
6
A
A
HN3
O6
U5P
5GP
5
8
1.57
6
A
A
HO3'
O2P
C5P
5GP
7
8
1.59
6
A
A
H61
O4
A
U
3
10
1.59
7
A
A
O2
H21
C
G
4
9
1.56
7
A
A
H21
O2
G
C
2
11
1.57
7
A
A
H21
O2
G
C
1
12
1.58
8
A
A
HO2'
O5'
G
A
2
3
1.54
8
A
A
O2
H21
C
G
4
9
1.56
8
A
A
HO2'
O4'
G
G
1
2
1.57
8
A
A
O2
HN1
U5P
5GP
5
8
1.59
8
A
A
H21
O2
G
C
1
12
1.60
9
A
A
O2
H21
C
G
4
9
1.58
9
A
A
O2
HN1
U5P
5GP
5
8
1.60
10
A
A
HO3'
O2P
C5P
5GP
7
8
1.54
10
A
A
HO2'
O4'
U
C
10
11
1.57
10
A
A
HO2'
O4'
C
C
11
12
1.57
10
A
A
HN3
O6
U5P
5GP
5
8
1.60
1
A
A
O3'
P
U5P
U5P
5
6
3.08
1
A
A
O3'
P
U5P
C5P
6
7
4.18
1
A
A
O3'
P
C5P
5GP
7
8
4.15
1
A
A
O3'
P
5GP
G
8
9
3.55
2
A
A
O3'
P
U5P
U5P
5
6
3.23
2
A
A
O3'
P
U5P
C5P
6
7
4.20
2
A
A
O3'
P
C5P
5GP
7
8
4.14
2
A
A
O3'
P
5GP
G
8
9
3.52
3
A
A
O3'
P
U5P
U5P
5
6
3.20
3
A
A
O3'
P
U5P
C5P
6
7
4.17
3
A
A
O3'
P
C5P
5GP
7
8
4.11
3
A
A
O3'
P
5GP
G
8
9
3.52
4
A
A
O3'
P
U5P
U5P
5
6
3.04
4
A
A
O3'
P
U5P
C5P
6
7
4.18
4
A
A
O3'
P
C5P
5GP
7
8
4.15
4
A
A
O3'
P
5GP
G
8
9
3.50
5
A
A
O3'
P
U5P
U5P
5
6
3.21
5
A
A
O3'
P
U5P
C5P
6
7
4.20
5
A
A
O3'
P
C5P
5GP
7
8
4.15
5
A
A
O3'
P
5GP
G
8
9
3.52
6
A
A
O3'
P
U5P
U5P
5
6
3.27
6
A
A
O3'
P
U5P
C5P
6
7
4.18
6
A
A
O3'
P
C5P
5GP
7
8
3.07
6
A
A
O3'
P
5GP
G
8
9
3.52
7
A
A
O3'
P
U5P
U5P
5
6
3.06
7
A
A
O3'
P
U5P
C5P
6
7
4.19
7
A
A
O3'
P
C5P
5GP
7
8
4.15
7
A
A
O3'
P
5GP
G
8
9
3.53
8
A
A
O3'
P
U5P
U5P
5
6
3.05
8
A
A
O3'
P
U5P
C5P
6
7
4.18
8
A
A
O3'
P
C5P
5GP
7
8
4.15
8
A
A
O3'
P
5GP
G
8
9
3.48
9
A
A
O3'
P
U5P
U5P
5
6
3.07
9
A
A
O3'
P
U5P
C5P
6
7
4.18
9
A
A
O3'
P
C5P
5GP
7
8
4.16
9
A
A
O3'
P
5GP
G
8
9
3.43
10
A
A
O3'
P
U5P
U5P
5
6
3.18
10
A
A
O3'
P
U5P
C5P
6
7
4.19
10
A
A
O3'
P
C5P
5GP
7
8
3.06
10
A
A
O3'
P
5GP
G
8
9
3.52
1
4.44
0.50
113.10
117.54
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
-2.40
0.40
106.40
104.00
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
1
4.84
0.50
113.10
117.94
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
1
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
1
4.30
0.50
113.80
118.10
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
1
4.40
0.50
113.10
117.50
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
1
-2.44
0.40
106.40
103.96
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
2
4.36
0.50
113.10
117.46
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
2
4.90
0.50
113.10
118.00
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
2
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
2
4.20
0.50
113.80
118.00
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
2
4.43
0.50
113.10
117.53
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
2
-2.54
0.40
106.40
103.86
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
3
4.77
0.50
113.10
117.87
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
3
-2.58
0.40
106.40
103.82
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
3
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
3
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
3
4.00
0.50
113.80
117.80
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
3
4.47
0.50
113.10
117.57
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
3
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
4
4.73
0.50
113.10
117.83
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
4
-2.59
0.40
106.40
103.81
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
4
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
4
-2.45
0.40
106.40
103.95
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
4
3.90
0.50
113.80
117.70
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
4
4.41
0.50
113.10
117.51
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
4
-2.45
0.40
106.40
103.95
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
5
4.35
0.50
113.10
117.45
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
5
4.87
0.50
113.10
117.97
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
5
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
5
4.37
0.50
113.80
118.17
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
5
4.46
0.50
113.10
117.56
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
5
-2.49
0.40
106.40
103.91
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
6
4.81
0.50
113.10
117.91
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
6
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
6
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
6
-2.56
0.40
106.40
103.84
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
6
3.93
0.50
113.80
117.73
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
6
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
6
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
7
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
7
4.78
0.50
113.10
117.88
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
7
-2.43
0.40
106.40
103.97
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
7
4.29
0.50
113.80
118.09
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
7
4.26
0.50
113.10
117.36
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
7
-2.40
0.40
106.40
104.00
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
8
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
8
-2.43
0.40
106.40
103.97
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
8
4.81
0.50
113.10
117.91
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
8
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
8
4.17
0.50
113.80
117.97
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
8
4.25
0.50
113.10
117.35
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
8
-2.51
0.40
106.40
103.89
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
9
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
9
-2.54
0.40
106.40
103.86
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
9
4.98
0.50
113.10
118.08
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
9
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
9
4.23
0.50
113.80
118.03
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
9
4.45
0.50
113.10
117.55
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
9
-2.52
0.40
106.40
103.88
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
10
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
10
4.82
0.50
113.10
117.92
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
10
4.28
0.50
113.80
118.08
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
10
4.27
0.50
113.10
117.37
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
10
-2.44
0.40
106.40
103.96
A
A
A
C8
N9
C4
G
G
G
9
9
9
N
5'-R(*GP*GP*AP*CP*(U25)P*(U25)P*(C25)P*(5GP)P*GP*UP*CP*C)-3'
Chimeric hairpin with 2',5'-linked RNA loop and RNA stem
1
N
N
covale
1.615
A
C
4
A
O3'
C
4
1_555
A
U5P
5
A
P
U5P
5
1_555
covale
1.610
A
U5P
5
A
O2'
U5P
5
1_555
A
U5P
6
A
P
U5P
6
1_555
covale
1.614
A
U5P
6
A
O2'
U5P
6
1_555
A
C5P
7
A
P
C5P
7
1_555
covale
1.619
A
C5P
7
A
O2'
C5P
7
1_555
A
5GP
8
A
P
5GP
8
1_555
covale
1.615
A
5GP
8
A
O2'
5GP
8
1_555
A
G
9
A
P
G
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
12
A
N3
C
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
12
A
O2
C
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
12
A
N4
C
12
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
11
A
N3
C
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
11
A
O2
C
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
11
A
N4
C
11
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
A
U
10
A
N3
U
10
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
A
U
10
A
O4
U
10
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
G
9
A
N1
G
9
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
G
9
A
O6
G
9
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
G
9
A
N2
G
9
1_555
RNA
Hairpin, (2', 5')-RNA, RNA
1ME1
PDB
1
1ME1
1
12
1ME1
1
12
1ME1
A
1
1
12