1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Yang, Y.S.
Kochoyan, M.
Burgstaller, P.
Westhof, E.
Famulok, M.
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
C6 H13 N3 O3
175.186
n
CITRULLINE
L-peptide 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
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
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
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
H
N
73
N
C
N
74
N
O
N
75
N
O
N
76
S
C
N
77
N
N
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
N
N
82
N
C
N
83
N
O
N
84
N
N
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
O
N
99
N
P
N
100
N
O
N
101
N
O
N
102
N
O
N
103
N
C
N
104
R
C
N
105
N
O
N
106
S
C
N
107
N
O
N
108
R
C
N
109
N
O
N
110
R
C
Y
111
N
N
Y
112
N
C
Y
113
N
N
Y
114
N
C
N
115
N
C
N
116
N
O
N
117
N
N
N
118
N
C
N
119
N
N
N
120
N
N
Y
121
N
C
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
O
N
137
N
P
N
138
N
O
N
139
N
O
N
140
N
O
N
141
N
C
N
142
R
C
N
143
N
O
N
144
S
C
N
145
N
O
N
146
R
C
N
147
N
O
N
148
R
C
N
149
N
N
N
150
N
C
N
151
N
O
N
152
N
N
N
153
N
C
N
154
N
O
N
155
N
C
N
156
N
C
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
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
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
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
doub
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
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
sing
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
Y
124
N
sing
Y
125
N
sing
Y
126
N
doub
N
127
N
sing
Y
128
N
sing
N
129
N
sing
Y
130
N
doub
N
131
N
doub
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
doub
N
171
N
sing
N
172
N
doub
N
173
N
sing
N
174
N
sing
US
Science
SCIEAS
0038
0036-8075
272
1343
1347
8650546
Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy.
1996
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
23
4769
Structural Probing and Damage Selection of Citrulline-and Arginine-Specific RNA Aptamers Identify Base Positions Required for Binding
1995
10.2210/pdb1kod/pdb
pdb_00001kod
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3610.226
RNA (5'-R(P*AP*GP*AP*AP*GP*GP*AP*GP*UP*GP*U)-3')
1
syn
polymer
4479.691
RNA (5'-R(P*AP*CP*GP*GP*UP*UP*AP*GP*GP*UP*CP*GP*CP*U)-3')
1
syn
polymer
175.186
CITRULLINE
1
syn
non-polymer
no
no
AGAAGGAGUGU
AGAAGGAGUGU
A
polyribonucleotide
no
no
ACGGUUAGGUCGCU
ACGGUUAGGUCGCU
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
-2.274
1
20
A
5
B
40
7.876
A_A5:U40_B
1
-8.721
-0.412
-2.167
-0.563
-9.481
1
A
7
B
39
21.580
A_A7:C39_B
2
12.823
-1.172
1.051
-0.577
-16.307
B
34
B
38
-141.160
B_G34:G38_B
3
30.454
-0.139
-1.222
3.948
26.579
1
A
10
B
37
10.281
A_G10:C37_B
4
0.032
-0.808
0.301
0.211
-22.278
A
11
B
30
160.737
A_A11:G30_B
5
49.070
-0.679
-0.058
-4.191
47.975
A
12
A
9
108.561
A_G12:G9_A
6
-19.965
1.457
-0.431
-4.929
-17.695
A
13
B
29
-75.134
A_U13:G29_B
7
-41.512
-3.568
-1.453
0.780
-16.697
1
19
A
14
B
28
-0.559
A_G14:C28_B
8
-5.923
-0.539
-1.499
-0.705
43.986
1
20
A
15
B
27
8.745
A_U15:A27_B
9
3.814
-0.643
-1.293
0.215
46.568
5
B
33
B
35
-122.402
B_A33:G35_B
10
0.416
-2.798
1.130
4.394
4.726
44.541
A
A
5
7
30.052
B
B
40
39
5.680
21.881
-0.805
-0.611
AA_A5A7:C39U40_BB
1
-0.365
0.501
39.035
-4.250
1.005
1.299
-173.147
A
B
7
34
60.694
B
B
39
38
0.380
-120.166
3.616
-0.555
AB_A7G34:G38C39_BB
2
-113.444
-57.299
-124.474
0.428
1.670
-2.306
-170.074
B
A
34
10
8.571
B
B
38
37
-3.573
-16.907
1.958
2.584
BA_G34G10:C37G38_BB
3
-155.756
-78.967
-129.333
-1.367
1.630
3.713
-58.941
A
A
10
11
44.321
B
B
37
30
4.208
-39.981
4.201
-0.180
AA_G10A11:G30C37_BB
4
-10.193
-11.299
-43.048
3.160
3.510
0.586
76.519
A
A
11
12
41.883
B
A
30
9
1.956
48.808
-1.084
-1.651
AA_A11G12:G9G30_AB
5
4.638
-3.980
60.688
-1.984
0.937
3.652
125.701
A
A
12
13
1.837
A
B
9
29
3.660
3.266
-0.264
-1.125
AA_G12U13:G29G9_BA
6
-17.726
9.972
124.966
-0.662
-0.016
3.742
22.682
A
A
13
14
15.206
B
B
29
28
3.687
5.905
0.850
0.457
AA_U13G14:C28G29_BB
7
2.081
-5.360
21.812
-1.314
-1.288
2.043
31.295
A
A
14
15
21.181
B
B
28
27
2.560
9.960
-1.076
-1.009
AA_G14U15:A27C28_BB
8
-22.683
48.238
19.274
-3.530
-1.786
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
atom_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Atomic model
Data collection
1
0
1996-11-08
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-23
2
0
2023-11-15
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_atom_site.auth_atom_id
_atom_site.label_atom_id
1 STRUCTURE
Y
BNL
1996-03-28
REL
CIR
CITRULLINE
1
WESTHOF,DUMAS,MORAS
refinement
NUCLSQ
CIR
1
3
CIR
CIR
1
B
A
5
n
1
A
5
A
G
6
n
2
G
6
A
A
7
n
3
A
7
A
A
8
n
4
A
8
A
G
9
n
5
G
9
A
G
10
n
6
G
10
A
A
11
n
7
A
11
A
G
12
n
8
G
12
A
U
13
n
9
U
13
A
G
14
n
10
G
14
A
U
15
n
11
U
15
A
A
27
n
1
A
27
B
C
28
n
2
C
28
B
G
29
n
3
G
29
B
G
30
n
4
G
30
B
U
31
n
5
U
31
B
U
32
n
6
U
32
B
A
33
n
7
A
33
B
G
34
n
8
G
34
B
G
35
n
9
G
35
B
U
36
n
10
U
36
B
C
37
n
11
C
37
B
G
38
n
12
G
38
B
C
39
n
13
C
39
B
U
40
n
14
U
40
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
-9.26
1.50
119.60
110.34
A
A
A
OP1
P
OP2
A
A
A
5
5
5
N
1
4.85
0.80
101.50
106.35
A
A
A
C3'
C2'
C1'
A
A
A
5
5
5
N
1
3.85
0.50
113.80
117.65
A
A
A
N7
C8
N9
A
A
A
5
5
5
N
1
4.97
0.80
101.50
106.47
A
A
A
C3'
C2'
C1'
G
G
G
6
6
6
N
1
4.63
0.50
113.10
117.73
A
A
A
N7
C8
N9
G
G
G
6
6
6
N
1
-2.73
0.40
106.40
103.67
A
A
A
C8
N9
C4
G
G
G
6
6
6
N
1
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
A
A
A
7
7
7
N
1
3.77
0.50
113.80
117.57
A
A
A
N7
C8
N9
A
A
A
8
8
8
N
1
4.67
0.50
113.10
117.77
A
A
A
N7
C8
N9
G
G
G
9
9
9
N
1
4.42
0.50
113.10
117.52
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
1
-2.86
0.40
106.40
103.54
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
1
3.99
0.50
113.80
117.79
A
A
A
N7
C8
N9
A
A
A
11
11
11
N
1
4.61
0.70
108.50
113.11
A
A
A
O4'
C1'
N9
G
G
G
12
12
12
N
1
4.45
0.50
113.10
117.55
A
A
A
N7
C8
N9
G
G
G
12
12
12
N
1
-2.73
0.40
106.40
103.67
A
A
A
C8
N9
C4
G
G
G
12
12
12
N
1
5.09
0.50
113.10
118.19
A
A
A
N7
C8
N9
G
G
G
14
14
14
N
1
-2.76
0.40
106.40
103.64
A
A
A
C8
N9
C4
G
G
G
14
14
14
N
1
4.91
0.80
101.50
106.41
A
A
A
C3'
C2'
C1'
U
U
U
15
15
15
N
1
-9.25
1.50
119.60
110.35
B
B
B
OP1
P
OP2
A
A
A
27
27
27
N
1
3.67
0.50
113.80
117.47
B
B
B
N7
C8
N9
A
A
A
27
27
27
N
1
4.53
0.50
113.10
117.63
B
B
B
N7
C8
N9
G
G
G
29
29
29
N
1
-2.79
0.40
106.40
103.61
B
B
B
C8
N9
C4
G
G
G
29
29
29
N
1
4.90
0.80
101.50
106.40
B
B
B
C3'
C2'
C1'
G
G
G
30
30
30
N
1
4.32
0.50
113.10
117.42
B
B
B
N7
C8
N9
G
G
G
30
30
30
N
1
-2.78
0.40
106.40
103.62
B
B
B
C8
N9
C4
G
G
G
30
30
30
N
1
4.92
0.80
101.50
106.42
B
B
B
C3'
C2'
C1'
U
U
U
31
31
31
N
1
4.87
0.80
101.50
106.37
B
B
B
C3'
C2'
C1'
U
U
U
32
32
32
N
1
3.80
0.50
113.80
117.60
B
B
B
N7
C8
N9
A
A
A
33
33
33
N
1
4.83
0.50
113.10
117.93
B
B
B
N7
C8
N9
G
G
G
34
34
34
N
1
-2.95
0.40
106.40
103.45
B
B
B
C8
N9
C4
G
G
G
34
34
34
N
1
6.08
0.70
108.50
114.58
B
B
B
O4'
C1'
N9
G
G
G
35
35
35
N
1
5.47
0.50
113.10
118.57
B
B
B
N7
C8
N9
G
G
G
35
35
35
N
1
-2.81
0.40
106.40
103.59
B
B
B
C8
N9
C4
G
G
G
35
35
35
N
1
4.53
0.70
108.50
113.03
B
B
B
O4'
C1'
N1
U
U
U
36
36
36
N
1
4.41
0.50
113.10
117.51
B
B
B
N7
C8
N9
G
G
G
38
38
38
N
1
-2.52
0.40
106.40
103.88
B
B
B
C8
N9
C4
G
G
G
38
38
38
N
1
5.42
0.80
101.50
106.92
B
B
B
C3'
C2'
C1'
C
C
C
39
39
39
N
1
4.40
0.70
108.50
112.90
B
B
B
O4'
C1'
N1
C
C
C
39
39
39
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
RNA APTAMER COMPLEXED WITH CITRULLINE, NMR
1
N
N
2
N
N
3
N
N
hydrog
WATSON-CRICK
A
A
5
A
N1
A
1
1_555
B
U
40
B
N3
U
14
1_555
hydrog
WATSON-CRICK
A
A
5
A
N6
A
1
1_555
B
U
40
B
O4
U
14
1_555
hydrog
WATSON-CRICK
A
G
6
A
N1
G
2
1_555
B
C
39
B
N3
C
13
1_555
hydrog
WATSON-CRICK
A
G
6
A
N2
G
2
1_555
B
C
39
B
O2
C
13
1_555
hydrog
WATSON-CRICK
A
G
6
A
O6
G
2
1_555
B
C
39
B
N4
C
13
1_555
hydrog
G-U MISPAIR
A
G
6
A
N1
G
2
1_555
B
U
40
B
O2
U
14
1_555
hydrog
TYPE_8_PAIR
A
A
7
A
N1
A
3
1_555
B
G
38
B
N1
G
12
1_555
hydrog
TYPE_8_PAIR
A
A
7
A
N6
A
3
1_555
B
G
38
B
O6
G
12
1_555
hydrog
A-C MISPAIR
A
A
7
A
N6
A
3
1_555
B
C
39
B
N3
C
13
1_555
hydrog
G-G MISPAIR
A
G
9
A
N1
G
5
1_555
A
G
12
A
N7
G
8
1_555
hydrog
G-C PAIR
A
G
10
A
N1
G
6
1_555
B
C
37
B
O2
C
11
1_555
hydrog
A-G MISPAIR
A
A
11
A
N6
A
7
1_555
B
G
30
B
O6
G
4
1_555
hydrog
A-U PAIR
A
A
11
A
N1
A
7
1_555
B
U
36
B
N3
U
10
1_555
hydrog
TYPE_6_PAIR
A
G
12
A
N1
G
8
1_555
B
G
35
B
O6
G
9
1_555
hydrog
TYPE_6_PAIR
A
G
12
A
N2
G
8
1_555
B
G
35
B
N7
G
9
1_555
hydrog
U-G MISPAIR
A
U
13
A
O4
U
9
1_555
B
G
29
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
G
14
A
N1
G
10
1_555
B
C
28
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
14
A
N2
G
10
1_555
B
C
28
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
14
A
O6
G
10
1_555
B
C
28
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
U
15
A
N3
U
11
1_555
B
A
27
B
N1
A
1
1_555
hydrog
WATSON-CRICK
A
U
15
A
O4
U
11
1_555
B
A
27
B
N6
A
1
1_555
hydrog
A-G MISPAIR
B
A
33
B
N3
A
7
1_555
B
G
35
B
N1
G
9
1_555
hydrog
G-C PAIR
B
G
34
B
O6
G
8
1_555
B
C
37
B
N4
C
11
1_555
hydrog
G-G MISPAIR
B
G
34
B
N1
G
8
1_555
B
G
38
B
O6
G
12
1_555
RNA
IN VITRO SELECTED RNA, RNA APTAMER, RNA
1KOD
PDB
1
1KOD
1KOD
PDB
2
1KOD
5
15
1KOD
5
15
1KOD
A
1
1
11
27
40
1KOD
27
40
1KOD
B
2
1
14
BINDING SITE FOR RESIDUE CIR B 1
B
CIR
1
Software
6
A
G
12
A
G
8
6
1_555
A
U
13
A
U
9
6
1_555
B
G
30
B
G
4
6
1_555
B
U
31
B
U
5
6
1_555
B
A
33
B
A
7
6
1_555
B
G
35
B
G
9
6
1_555
1
P 1