0.021432
0.000000
0.000000
0.000000
0.021004
0.000000
0.000000
0.000000
0.018505
0.00000
0.00000
0.00000
Sudarsanakumar, C.
Xiong, Y.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.0
90.0
90.0
46.66
47.61
54.04
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
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
N
C
N
49
R
C
N
50
N
N
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
C
N
57
N
C
N
58
N
H
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
O
N
73
N
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
N
C
N
83
R
C
N
84
N
N
N
85
N
C
N
86
N
O
N
87
N
N
N
88
N
C
N
89
N
O
N
90
N
C
N
91
N
C
N
92
N
C
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
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
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
R
C
N
119
N
O
N
120
R
C
Y
121
N
N
Y
122
N
C
Y
123
N
N
Y
124
N
C
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
N
Y
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
145
N
H
N
146
N
O
N
147
N
H
N
148
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
doub
N
66
N
sing
N
67
N
doub
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
doub
N
78
N
sing
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
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
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
Y
136
N
sing
Y
137
N
sing
Y
138
N
doub
N
139
N
sing
Y
140
N
sing
N
141
N
sing
Y
142
N
doub
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
299
103
112
10.1006/jmbi.2000.3730
10860725
Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag).
2000
10.2210/pdb1efo/pdb
pdb_00001efo
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
297
1
IMAGE PLATE
1999-07-22
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
2617.723
DNA (5'-D(*CP*TP*CP*CP*TP*CP*TP*TP*C)-3')
1
syn
polymer
3327.100
RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')
1
syn
polymer
18.015
water
23
nat
water
no
no
(DC)(DT)(DC)(DC)(DT)(DC)(DT)(DT)(DC)
CTCCTCTTC
A
polydeoxyribonucleotide
no
no
GAAGAGAGAG
GAAGAGAGAG
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.49
50.62
VAPOR DIFFUSION, HANGING DROP
6.0
MPD, LITHIUM CHLORIDE, SPERMINE TETRACHLORIDE, CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
SPERMINE TETRACHLORIDE
1
CACODYLATE
1
LICL
1
MPD
1
LICL
2
MPD
2
-9.099
1
19
A
1
B
19
0.561
A_DC1:G19_B
1
0.527
0.463
0.245
-0.357
10.510
1
20
A
2
B
18
2.003
A_DT2:A18_B
2
-5.910
0.248
-0.035
-0.240
11.155
1
19
A
3
B
17
7.133
A_DC3:G17_B
3
-9.044
1.077
-0.201
-0.279
3.697
1
19
A
4
B
15
5.100
A_DC4:G15_B
4
-7.725
0.071
-0.052
0.010
12.821
1
20
A
5
B
14
7.429
A_DT5:A14_B
5
-11.543
-0.397
-0.060
-0.027
10.339
1
19
A
6
B
13
0.974
A_DC6:G13_B
6
-10.329
0.903
-0.060
-0.400
6.136
1
20
A
7
B
12
10.038
A_DT7:A12_B
7
-17.095
0.198
-0.052
-0.362
6.486
1
20
A
8
B
11
3.365
A_DT8:A11_B
8
-11.057
0.287
0.186
-0.285
5.302
1
19
A
9
B
10
7.221
A_DC9:G10_B
9
-13.089
0.382
0.098
-0.146
2.937
25.062
A
A
1
2
-2.410
B
B
19
18
2.870
-1.046
-0.393
-1.882
AA_DC1DT2:A18G19_BB
1
0.465
-1.071
25.036
-4.061
1.027
3.368
35.280
A
A
2
3
1.500
B
B
18
17
3.422
0.909
0.443
-1.736
AA_DT2DC3:G17A18_BB
2
-0.739
1.219
35.261
-3.005
-0.845
3.256
27.757
A
A
3
4
7.474
B
B
17
15
3.512
3.575
-0.451
-1.953
AA_DC3DC4:G15G17_BB
3
-1.448
3.028
27.493
-4.966
0.577
2.944
28.292
A
A
4
5
9.272
B
B
15
14
3.233
4.504
-0.173
-1.585
AA_DC4DT5:A14G15_BB
4
-3.242
6.675
27.754
-4.238
-0.363
2.882
35.453
A
A
5
6
17.484
B
B
14
13
3.413
10.475
-0.888
-1.615
AA_DT5DC6:G13A14_BB
5
-3.984
6.650
33.689
-4.172
0.881
2.809
32.343
A
A
6
7
16.745
B
B
13
12
3.304
9.182
1.025
-1.673
AA_DC6DT7:A12G13_BB
6
3.975
-7.250
30.795
-4.561
-1.167
2.662
29.133
A
A
7
8
18.275
B
B
12
11
3.351
9.043
-0.962
-1.888
AA_DT7DT8:A11A12_BB
7
-1.546
3.124
27.681
-5.619
1.594
3.280
35.245
A
A
8
9
0.413
B
B
11
10
3.300
0.250
0.086
-1.337
AA_DT8DC9:G10A11_BB
8
-2.053
3.392
35.186
-2.245
-0.450
software
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
1
0
2000-05-29
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2000-02-09
REL
REL
HOH
water
WAT
103
3
HOH
HOH
103
A
WAT
106
3
HOH
HOH
106
A
WAT
113
3
HOH
HOH
113
A
WAT
117
3
HOH
HOH
117
A
WAT
118
3
HOH
HOH
118
A
WAT
120
3
HOH
HOH
120
A
WAT
121
3
HOH
HOH
121
A
WAT
101
3
HOH
HOH
101
B
WAT
102
3
HOH
HOH
102
B
WAT
104
3
HOH
HOH
104
B
WAT
105
3
HOH
HOH
105
B
WAT
107
3
HOH
HOH
107
B
WAT
108
3
HOH
HOH
108
B
WAT
109
3
HOH
HOH
109
B
WAT
110
3
HOH
HOH
110
B
WAT
111
3
HOH
HOH
111
B
WAT
112
3
HOH
HOH
112
B
WAT
114
3
HOH
HOH
114
B
WAT
115
3
HOH
HOH
115
B
WAT
116
3
HOH
HOH
116
B
WAT
119
3
HOH
HOH
119
B
WAT
122
3
HOH
HOH
122
B
WAT
123
3
HOH
HOH
123
B
C
1
n
1
DC
1
A
T
2
n
2
DT
2
A
C
3
n
3
DC
3
A
C
4
n
4
DC
4
A
T
5
n
5
DT
5
A
C
6
n
6
DC
6
A
T
7
n
7
DT
7
A
T
8
n
8
DT
8
A
C
9
n
9
DC
9
A
G
10
n
1
G
10
B
A
11
n
2
A
11
B
A
12
n
3
A
12
B
G
13
n
4
G
13
B
A
14
n
5
A
14
B
G
15
n
6
G
15
B
A
16
n
7
A
16
B
G
17
n
8
G
17
B
A
18
n
9
A
18
B
G
19
n
10
G
19
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
0.2220000
0.1990000
0.1990000
2.30
10.0
237
2578
2486
9
91.4
RANDOM
1
THROUGHOUT
2.0
1.0
2.30
10.0
23
417
0
394
0
0.007
1.2
2.3
10.0
1EFO
2880
2486
2.0
1.0
0.0700000
1
5.6
91.4
0.0800000
2.30
2.38
4.0
71.3
phasing
AMoRE
refinement
CNS
data scaling
SCALEPACK
CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)
1
N
N
2
N
N
3
N
N
3
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
G
19
B
N1
G
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
G
19
B
O6
G
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
G
19
B
N2
G
10
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
A
18
B
N1
A
9
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
A
18
B
N6
A
9
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
G
17
B
N1
G
8
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
G
17
B
O6
G
8
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
G
17
B
N2
G
8
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
G
15
B
N1
G
6
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
G
15
B
O6
G
6
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
G
15
B
N2
G
6
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
A
14
B
N1
A
5
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
A
14
B
N6
A
5
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
G
13
B
N1
G
4
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
G
13
B
O6
G
4
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
G
13
B
N2
G
4
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
A
12
B
N1
A
3
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
A
12
B
N6
A
3
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
A
11
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
A
11
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
G
10
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
G
10
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
G
10
B
N2
G
1
1_555
DNA-RNA HYBRID
A-FORM CONFORMATION, HYBRID, ADENINE BULGE, LOOPED OUT, DNA-RNA COMPLEX, DNA-RNA HYBRID
1EFO
PDB
1
1EFO
1EFO
PDB
2
1EFO
1
9
1EFO
1
9
1EFO
A
1
1
9
10
19
1EFO
10
19
1EFO
B
2
1
10
23
orthorhombic
I 2 2 2