0.008192
0.000000
0.000497
0.000000
0.036603
0.000000
0.000000
0.000000
0.010878
0.00000
0.00000
0.00000
Ennifar, E.
Walter, P.
Ehresmann, B.
Ehresmann, C.
Dumas, P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
93.47
90.00
122.070
27.320
92.100
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
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
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
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
H
N
109
N
H
N
110
N
H
N
111
N
MG
N
112
N
O
N
113
N
P
N
114
N
O
N
115
N
O
N
116
N
O
N
117
N
C
N
118
R
C
N
119
N
O
N
120
S
C
N
121
N
O
N
122
R
C
N
123
N
O
N
124
R
C
N
125
N
N
N
126
N
C
N
127
N
O
N
128
N
N
N
129
N
C
N
130
N
O
N
131
N
C
N
132
N
C
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
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
sing
N
77
N
sing
N
78
N
doub
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
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
doub
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
N
136
N
sing
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
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
8
1064
1068
10.1038/nsb727
11702070
Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site.
2001
10.2210/pdb1k9w/pdb
pdb_00001k9w
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
MARRESEARCH
Crystal
SINGLE WAVELENGTH
M
x-ray
1
0.93
1.0
ID14-3
ESRF
0.93
SYNCHROTRON
ESRF BEAMLINE ID14-3
DIMERIZATION INITIATION SITE
7364.416
HIV-1 DIS(Mal)UU RNA
4
syn
polymer
24.305
MAGNESIUM ION
4
syn
non-polymer
no
no
UUUGCUGAGGUGCACACAGCAAU
UUUGCUGAGGUGCACACAGCAAU
A,B,C,D
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.60
52.73
VAPOR DIFFUSION, HANGING DROP
7.0
Isopropanol, magnesium chloride, spermine, cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
295
Isopropanol
1
MgCl2
1
spermine
1
cacodylate
1
-20.475
C
2
A
1
51.815
C_U2:U1_A
1
34.234
4.446
-0.803
-1.152
-18.286
C
3
C
21
15.689
C_U3:A21_C
2
-35.682
3.882
0.967
-0.590
15.414
1
C
4
C
20
22.088
C_G4:C20_C
3
-4.734
-2.140
0.919
-0.018
21.506
1
C
5
C
19
28.458
C_C5:G19_C
4
-36.550
-0.452
0.386
0.752
10.208
1
20
C
6
C
18
-13.948
C_U6:A18_C
5
-12.692
-1.740
0.024
-0.082
11.373
1
19
C
7
C
17
1.950
C_G7:C17_C
6
-8.219
-0.685
0.573
0.044
23.124
1
A
4
A
20
21.892
A_G4:C20_A
7
-30.503
0.083
0.512
0.123
12.076
1
A
5
A
19
-8.045
A_C5:G19_A
8
-10.712
-1.816
-0.830
-0.042
9.151
1
20
A
6
A
18
9.423
A_U6:A18_A
9
1.107
-1.201
-0.007
0.045
-0.563
1
19
A
7
A
17
9.301
A_G7:C17_A
10
-8.785
0.054
0.117
0.143
-19.511
1
19
A
10
B
15
-6.563
A_G10:C15_B
11
-6.065
0.309
-0.903
-0.350
-1.467
1
20
A
11
B
14
-1.228
A_U11:A14_B
12
-7.195
-0.149
-0.510
-0.504
-9.611
1
19
A
12
B
13
-3.916
A_G12:C13_B
13
-7.018
-0.092
-0.375
-0.396
0.199
1
19
A
13
B
12
-5.131
A_C13:G12_B
14
-3.134
-0.404
0.292
-0.351
2.909
1
20
A
14
B
11
2.207
A_A14:U11_B
15
-13.709
-0.357
-0.532
-0.370
12.200
1
19
A
15
B
10
4.449
A_C15:G10_B
16
-7.961
-0.096
-0.353
-0.255
9.744
B
1
B
23
-20.743
B_U1:U23_B
17
-18.967
-2.361
0.191
-1.242
-1.644
1
20
B
2
B
22
1.050
B_U2:A22_B
18
-9.545
0.603
0.270
-0.624
4.809
1
20
B
3
B
21
-1.291
B_U3:A21_B
19
-7.607
-0.244
0.116
-0.180
0.082
1
19
B
4
B
20
4.875
B_G4:C20_B
20
-10.498
-0.240
0.026
-0.094
12.621
1
19
B
5
B
19
9.125
B_C5:G19_B
21
-16.403
0.796
-0.311
-0.311
-3.529
1
20
B
6
B
18
-10.626
B_U6:A18_B
22
-0.536
-0.870
0.759
-0.454
8.144
1
19
B
7
B
17
0.542
B_G7:C17_B
23
2.607
-0.252
0.090
-0.221
-6.710
1
19
C
10
D
15
1.834
C_G10:C15_D
24
0.268
0.250
-0.554
0.240
-5.821
1
20
C
11
D
14
9.154
C_U11:A14_D
25
21.969
-1.038
0.399
-0.365
-16.930
1
C
12
D
13
-10.821
C_G12:C13_D
26
-8.879
2.006
-0.553
-0.138
-2.998
1
19
C
13
D
12
3.248
C_C13:G12_D
27
-7.660
-1.073
0.789
0.067
11.127
1
20
C
14
D
11
4.400
C_A14:U11_D
28
-6.809
-0.502
0.193
-0.239
4.073
1
19
C
15
D
10
1.632
C_C15:G10_D
29
-1.250
-0.463
0.134
0.239
-7.566
D
1
D
23
-30.797
D_U1:U23_D
30
-18.141
-3.306
-0.324
-1.866
-2.371
1
20
D
2
D
22
-3.947
D_U2:A22_D
31
-8.531
0.281
0.374
-0.139
5.366
1
20
D
3
D
21
-0.767
D_U3:A21_D
32
-15.092
-0.727
-0.286
-0.552
1.738
1
19
D
4
D
20
-5.593
D_G4:C20_D
33
-5.422
-0.312
-0.240
-0.603
-7.521
1
19
D
5
D
19
-3.708
D_C5:G19_D
34
-7.270
0.437
0.016
-0.554
-6.547
1
D
6
D
18
17.414
D_U6:A18_D
35
-8.987
0.689
-0.062
-0.112
17.947
1
19
D
7
D
17
-5.779
D_G7:C17_D
36
-5.020
-0.140
1.489
-0.330
2.651
90.774
C
C
2
3
36.986
A
C
1
21
3.700
50.676
4.250
-1.890
CC_U2U3:A21U1_CA
1
6.991
-5.102
77.731
-2.436
-2.832
-0.866
20.337
C
C
3
4
81.554
C
C
21
20
1.407
19.755
-0.049
-1.072
CC_U3G4:C20A21_CC
2
-4.217
17.408
2.365
-4.367
-0.145
3.177
36.234
C
C
4
5
6.211
C
C
20
19
3.283
3.819
0.175
-0.358
CC_G4C5:G19C20_CC
3
8.845
-14.384
34.971
-1.115
0.968
3.010
30.188
C
C
5
6
21.214
C
C
19
18
3.364
10.610
-1.433
-1.209
CC_C5U6:A18G19_CC
4
-9.910
19.814
26.539
-4.567
0.654
2.439
32.357
C
C
6
7
15.676
C
C
18
17
3.031
8.633
1.737
-1.597
CC_U6G7:C17A18_CC
5
-1.328
2.412
31.186
-4.165
-3.317
2.162
23.159
A
A
4
5
36.129
A
A
20
19
3.341
13.515
-1.964
-1.449
AA_G4C5:G19C20_AA
6
-4.003
10.701
18.422
-8.022
3.586
2.486
33.261
A
A
5
6
16.457
A
A
19
18
3.419
9.154
1.215
-1.041
AA_C5U6:A18G19_AA
7
-10.212
18.360
30.375
-3.267
-3.738
2.914
36.465
A
A
6
7
13.850
A
A
18
17
3.400
8.588
0.336
-1.669
AA_U6G7:C17A18_AA
8
-1.526
2.462
35.440
-3.833
-0.744
2.561
28.598
A
A
10
11
6.789
B
B
15
14
2.735
3.343
-0.198
-1.418
AA_G10U11:A14C15_BB
9
-2.304
4.679
28.314
-3.487
-0.025
2.475
32.900
A
A
11
12
28.059
B
B
14
13
3.436
15.306
-0.236
-1.298
AA_U11G12:C13A14_BB
10
-1.244
2.281
29.185
-4.806
0.212
3.035
30.006
A
A
12
13
7.484
B
B
13
12
3.217
3.835
-0.329
-1.220
AA_G12C13:G12C13_BB
11
-6.533
12.750
29.056
-3.123
-0.671
2.522
31.055
A
A
13
14
20.588
B
B
12
11
3.132
10.760
0.596
-1.405
AA_C13A14:U11G12_BB
12
4.795
-9.175
28.785
-4.482
-0.286
2.890
34.375
A
A
14
15
4.069
B
B
11
10
3.102
2.398
0.820
-1.350
AA_A14C15:G10U11_BB
13
-4.012
6.808
34.065
-2.629
-1.965
3.421
44.615
B
B
1
2
11.975
B
B
23
22
3.722
9.034
0.847
-1.208
BB_U1U2:A22U23_BB
14
0.046
-0.061
43.736
-2.506
-1.111
2.369
31.573
B
B
2
3
13.072
B
B
22
21
2.790
7.053
0.094
-1.629
BB_U2U3:A21A22_BB
15
1.266
-2.347
30.769
-4.041
0.015
2.989
28.242
B
B
3
4
9.231
B
B
21
20
3.350
4.486
0.689
-2.107
BB_U3G4:C20A21_BB
16
0.314
-0.647
27.889
-5.336
-1.340
2.760
40.128
B
B
4
5
7.601
B
B
20
19
2.886
5.182
0.127
-0.722
BB_G4C5:G19C20_BB
17
6.307
-9.251
39.323
-1.568
0.442
2.670
25.069
B
B
5
6
23.056
B
B
19
18
3.648
9.502
-0.422
-1.561
BB_C5U6:A18G19_BB
18
-9.432
22.886
21.244
-6.546
-1.955
2.196
38.650
B
B
6
7
16.618
B
B
18
17
2.682
10.807
0.686
-1.713
BB_U6G7:C17A18_BB
19
6.782
-10.428
36.560
-3.610
-0.395
2.224
29.373
C
C
10
11
21.572
D
D
15
14
3.171
10.543
-0.267
-1.928
CC_G10U11:A14C15_DD
20
-8.455
17.299
26.141
-5.785
-1.064
2.388
56.561
C
C
11
12
24.705
D
D
14
13
3.415
22.713
-0.586
-1.643
CC_U11G12:C13A14_DD
21
10.805
-11.753
51.080
-2.935
1.189
2.422
20.817
C
C
12
13
-3.915
D
D
13
12
2.903
-1.314
-0.051
-1.642
CC_G12C13:G12C13_DD
22
-12.829
38.235
16.375
-4.029
-4.904
3.055
30.036
C
C
13
14
-8.264
D
D
12
11
2.862
-4.267
0.158
-1.560
CC_C13A14:U11G12_DD
23
1.475
-2.857
29.702
-2.213
-0.029
2.966
33.356
C
C
14
15
11.525
D
D
11
10
3.304
6.574
0.762
-1.468
CC_A14C15:G10U11_DD
24
0.222
-0.390
32.719
-3.615
-1.292
2.895
54.262
D
D
1
2
9.461
D
D
23
22
3.400
8.551
1.277
-1.237
DD_U1U2:A22U23_DD
25
-10.554
11.678
52.660
-1.868
-2.032
2.729
29.545
D
D
2
3
9.164
D
D
22
21
2.946
4.645
0.439
-1.380
DD_U2U3:A21A22_DD
26
3.271
-6.453
29.006
-3.570
-0.252
2.925
30.922
D
D
3
4
14.178
D
D
21
20
3.409
7.485
-0.030
-1.625
DD_U3G4:C20A21_DD
27
-1.418
2.686
29.991
-4.474
-0.215
3.309
36.618
D
D
4
5
10.066
D
D
20
19
3.626
6.292
0.361
-1.450
DD_G4C5:G19C20_DD
28
-2.124
3.399
36.031
-3.232
-0.887
2.616
43.361
D
D
5
6
14.325
D
D
19
18
2.852
10.465
0.659
-0.930
DD_C5U6:A18G19_DD
29
5.171
-7.078
41.833
-2.126
-0.464
1.913
19.919
D
D
6
7
10.399
D
D
18
17
2.391
3.479
-0.328
-2.151
DD_U6G7:C17A18_DD
30
-7.946
23.752
17.948
-7.352
-1.639
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-11-30
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
HIV-1(Mal) DIS kissing-complex
HIV-1(Lai) DIS kissing-complex
RCSB
Y
RCSB
2001-10-31
REL
REL
MG
MAGNESIUM ION
HIV-1(Mal) sequence with U265 and U287 mutations
sample
MG
101
2
MG
MG
101
B
MG
103
2
MG
MG
103
B
MG
104
2
MG
MG
104
B
MG
102
2
MG
MG
102
D
U
1
n
1
U
1
A
U
2
n
2
U
2
A
U
3
n
3
U
3
A
G
4
n
4
G
4
A
C
5
n
5
C
5
A
U
6
n
6
U
6
A
G
7
n
7
G
7
A
A
8
n
8
A
8
A
G
9
n
9
G
9
A
G
10
n
10
G
10
A
U
11
n
11
U
11
A
G
12
n
12
G
12
A
C
13
n
13
C
13
A
A
14
n
14
A
14
A
C
15
n
15
C
15
A
A
16
n
16
A
16
A
C
17
n
17
C
17
A
A
18
n
18
A
18
A
G
19
n
19
G
19
A
C
20
n
20
C
20
A
A
21
n
21
A
21
A
A
22
n
22
A
22
A
U
23
n
23
U
23
A
U
1
n
1
U
1
B
U
2
n
2
U
2
B
U
3
n
3
U
3
B
G
4
n
4
G
4
B
C
5
n
5
C
5
B
U
6
n
6
U
6
B
G
7
n
7
G
7
B
A
8
n
8
A
8
B
G
9
n
9
G
9
B
G
10
n
10
G
10
B
U
11
n
11
U
11
B
G
12
n
12
G
12
B
C
13
n
13
C
13
B
A
14
n
14
A
14
B
C
15
n
15
C
15
B
A
16
n
16
A
16
B
C
17
n
17
C
17
B
A
18
n
18
A
18
B
G
19
n
19
G
19
B
C
20
n
20
C
20
B
A
21
n
21
A
21
B
A
22
n
22
A
22
B
U
23
n
23
U
23
B
U
1
n
1
U
1
C
U
2
n
2
U
2
C
U
3
n
3
U
3
C
G
4
n
4
G
4
C
C
5
n
5
C
5
C
U
6
n
6
U
6
C
G
7
n
7
G
7
C
A
8
n
8
A
8
C
G
9
n
9
G
9
C
G
10
n
10
G
10
C
U
11
n
11
U
11
C
G
12
n
12
G
12
C
C
13
n
13
C
13
C
A
14
n
14
A
14
C
C
15
n
15
C
15
C
A
16
n
16
A
16
C
C
17
n
17
C
17
C
A
18
n
18
A
18
C
G
19
n
19
G
19
C
C
20
n
20
C
20
C
A
21
n
21
A
21
C
A
22
n
22
A
22
C
U
23
n
23
U
23
C
U
1
n
1
U
1
D
U
2
n
2
U
2
D
U
3
n
3
U
3
D
G
4
n
4
G
4
D
C
5
n
5
C
5
D
U
6
n
6
U
6
D
G
7
n
7
G
7
D
A
8
n
8
A
8
D
G
9
n
9
G
9
D
G
10
n
10
G
10
D
U
11
n
11
U
11
D
G
12
n
12
G
12
D
C
13
n
13
C
13
D
A
14
n
14
A
14
D
C
15
n
15
C
15
D
A
16
n
16
A
16
D
C
17
n
17
C
17
D
A
18
n
18
A
18
D
G
19
n
19
G
19
D
C
20
n
20
C
20
D
A
21
n
21
A
21
D
A
22
n
22
A
22
D
U
23
n
23
U
23
D
author_defined_assembly
2
dimeric
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
O3'
C
20
A
O3'
C
20
0
Y
1
A
U
1
A
U
1
0
Y
1
A
U
2
A
U
2
0
Y
1
A
A
21
A
A
21
0
Y
1
A
A
22
A
A
22
0
Y
1
A
U
23
A
U
23
0
Y
1
C
U
1
C
U
1
0
Y
1
C
U
2
C
U
2
0
Y
1
C
U
3
C
U
3
0
Y
1
C
C
20
C
C
20
0
Y
1
C
A
21
C
A
21
0
Y
1
C
A
22
C
A
22
0
Y
1
C
U
23
C
U
23
0
Y
1
A
A
8
0.053
SIDE CHAIN
1
A
G
9
0.055
SIDE CHAIN
1
A
U
11
0.069
SIDE CHAIN
1
B
A
8
0.072
SIDE CHAIN
1
B
G
9
0.065
SIDE CHAIN
1
B
A
16
0.055
SIDE CHAIN
1
B
A
22
0.054
SIDE CHAIN
1
C
G
9
0.057
SIDE CHAIN
1
D
U
6
0.065
SIDE CHAIN
LUC.PARAM
DNA-RNA.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
64.2
2.70
0.00
-10.14
-17.19
0.00
14.49
0.2650000
0.013
0.2270000
3.10
8.00
436
5458
4967
8.8
91.0
RANDOM
422155.84
0.000000
1
RESTRAINED
THROUGHOUT
2.0
MOLECULAR REPLACEMENT
FLAT MODEL
10
0.09661481
0.48
0.39
8.00
0.26
-0.02
3.10
8.00
0
1952
4
1948
0
0.006
1.2
14.7
1.51
0.3710000
0.048
0.2540000
3.28
60
741
6
7.5
90.2
2.9
15
1K9W
6955
0
0
0.0420000
1
2.9
96.3
2.90
3.03
909
0.2960000
98.9
phasing
AMoRE
refinement
CNS
0.4
data reduction
DENZO
data scaling
SCALEPACK
HIV-1(MAL) RNA Dimerization Initiation Site
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
metalc
3.136
B
U
11
B
OP1
U
11
1_555
B
MG
103
F
MG
MG
1_555
metalc
2.955
D
G
9
D
N7
G
9
1_555
D
MG
102
H
MG
MG
1_555
hydrog
U-U MISPAIR
A
U
1
A
N3
U
1
1_555
C
U
2
C
O2
U
2
1_555
hydrog
G-C PAIR
A
G
4
A
N1
G
4
1_555
A
C
20
A
N3
C
20
1_555
hydrog
C-G PAIR
A
C
5
A
N4
C
5
1_555
A
G
19
A
O6
G
19
1_555
hydrog
WATSON-CRICK
A
U
6
A
N3
U
6
1_555
A
A
18
A
N1
A
18
1_555
hydrog
WATSON-CRICK
A
U
6
A
O4
U
6
1_555
A
A
18
A
N6
A
18
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
A
C
17
A
N3
C
17
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
A
C
17
A
O2
C
17
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
A
C
17
A
N4
C
17
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
B
C
15
B
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
B
C
15
B
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
B
C
15
B
N4
C
15
1_555
hydrog
WATSON-CRICK
A
U
11
A
N3
U
11
1_555
B
A
14
B
N1
A
14
1_555
hydrog
WATSON-CRICK
A
U
11
A
O4
U
11
1_555
B
A
14
B
N6
A
14
1_555
hydrog
WATSON-CRICK
A
G
12
A
N1
G
12
1_555
B
C
13
B
N3
C
13
1_555
hydrog
WATSON-CRICK
A
G
12
A
N2
G
12
1_555
B
C
13
B
O2
C
13
1_555
hydrog
WATSON-CRICK
A
G
12
A
O6
G
12
1_555
B
C
13
B
N4
C
13
1_555
hydrog
WATSON-CRICK
A
C
13
A
N3
C
13
1_555
B
G
12
B
N1
G
12
1_555
hydrog
WATSON-CRICK
A
C
13
A
N4
C
13
1_555
B
G
12
B
O6
G
12
1_555
hydrog
WATSON-CRICK
A
C
13
A
O2
C
13
1_555
B
G
12
B
N2
G
12
1_555
hydrog
WATSON-CRICK
A
A
14
A
N1
A
14
1_555
B
U
11
B
N3
U
11
1_555
hydrog
WATSON-CRICK
A
A
14
A
N6
A
14
1_555
B
U
11
B
O4
U
11
1_555
hydrog
WATSON-CRICK
A
C
15
A
N3
C
15
1_555
B
G
10
B
N1
G
10
1_555
hydrog
WATSON-CRICK
A
C
15
A
N4
C
15
1_555
B
G
10
B
O6
G
10
1_555
hydrog
WATSON-CRICK
A
C
15
A
O2
C
15
1_555
B
G
10
B
N2
G
10
1_555
hydrog
U-U MISPAIR
B
U
1
B
O4
U
1
1_555
B
U
23
B
N3
U
23
1_555
hydrog
WATSON-CRICK
B
U
2
B
N3
U
2
1_555
B
A
22
B
N1
A
22
1_555
hydrog
WATSON-CRICK
B
U
2
B
O4
U
2
1_555
B
A
22
B
N6
A
22
1_555
hydrog
WATSON-CRICK
B
U
3
B
N3
U
3
1_555
B
A
21
B
N1
A
21
1_555
hydrog
WATSON-CRICK
B
U
3
B
O4
U
3
1_555
B
A
21
B
N6
A
21
1_555
hydrog
WATSON-CRICK
B
G
4
B
N1
G
4
1_555
B
C
20
B
N3
C
20
1_555
hydrog
WATSON-CRICK
B
G
4
B
N2
G
4
1_555
B
C
20
B
O2
C
20
1_555
hydrog
WATSON-CRICK
B
G
4
B
O6
G
4
1_555
B
C
20
B
N4
C
20
1_555
hydrog
WATSON-CRICK
B
C
5
B
N3
C
5
1_555
B
G
19
B
N1
G
19
1_555
hydrog
WATSON-CRICK
B
C
5
B
N4
C
5
1_555
B
G
19
B
O6
G
19
1_555
hydrog
WATSON-CRICK
B
C
5
B
O2
C
5
1_555
B
G
19
B
N2
G
19
1_555
hydrog
WATSON-CRICK
B
U
6
B
N3
U
6
1_555
B
A
18
B
N1
A
18
1_555
hydrog
WATSON-CRICK
B
U
6
B
O4
U
6
1_555
B
A
18
B
N6
A
18
1_555
hydrog
WATSON-CRICK
B
G
7
B
N1
G
7
1_555
B
C
17
B
N3
C
17
1_555
hydrog
WATSON-CRICK
B
G
7
B
N2
G
7
1_555
B
C
17
B
O2
C
17
1_555
hydrog
WATSON-CRICK
B
G
7
B
O6
G
7
1_555
B
C
17
B
N4
C
17
1_555
hydrog
WATSON-CRICK
C
U
2
C
N3
U
2
1_555
C
A
22
C
N1
A
22
1_555
hydrog
WATSON-CRICK
C
U
2
C
O4
U
2
1_555
C
A
22
C
N6
A
22
1_555
hydrog
U-A PAIR
C
U
3
C
O2
U
3
1_555
C
A
21
C
N6
A
21
1_555
hydrog
G-C PAIR
C
G
4
C
N1
G
4
1_555
C
C
20
C
O2
C
20
1_555
hydrog
C-G PAIR
C
C
5
C
O2
C
5
1_555
C
G
19
C
N2
G
19
1_555
hydrog
WATSON-CRICK
C
U
6
C
N3
U
6
1_555
C
A
18
C
N1
A
18
1_555
hydrog
WATSON-CRICK
C
U
6
C
O4
U
6
1_555
C
A
18
C
N6
A
18
1_555
hydrog
WATSON-CRICK
C
G
7
C
N1
G
7
1_555
C
C
17
C
N3
C
17
1_555
hydrog
WATSON-CRICK
C
G
7
C
N2
G
7
1_555
C
C
17
C
O2
C
17
1_555
hydrog
WATSON-CRICK
C
G
7
C
O6
G
7
1_555
C
C
17
C
N4
C
17
1_555
hydrog
WATSON-CRICK
C
G
10
C
N1
G
10
1_555
D
C
15
D
N3
C
15
1_555
hydrog
WATSON-CRICK
C
G
10
C
N2
G
10
1_555
D
C
15
D
O2
C
15
1_555
hydrog
WATSON-CRICK
C
G
10
C
O6
G
10
1_555
D
C
15
D
N4
C
15
1_555
hydrog
WATSON-CRICK
C
U
11
C
N3
U
11
1_555
D
A
14
D
N1
A
14
1_555
hydrog
WATSON-CRICK
C
U
11
C
O4
U
11
1_555
D
A
14
D
N6
A
14
1_555
hydrog
G-C PAIR
C
G
12
C
N1
G
12
1_555
D
C
13
D
N3
C
13
1_555
hydrog
WATSON-CRICK
C
C
13
C
N3
C
13
1_555
D
G
12
D
N1
G
12
1_555
hydrog
WATSON-CRICK
C
C
13
C
N4
C
13
1_555
D
G
12
D
O6
G
12
1_555
hydrog
WATSON-CRICK
C
C
13
C
O2
C
13
1_555
D
G
12
D
N2
G
12
1_555
hydrog
WATSON-CRICK
C
A
14
C
N1
A
14
1_555
D
U
11
D
N3
U
11
1_555
hydrog
WATSON-CRICK
C
A
14
C
N6
A
14
1_555
D
U
11
D
O4
U
11
1_555
hydrog
WATSON-CRICK
C
C
15
C
N3
C
15
1_555
D
G
10
D
N1
G
10
1_555
hydrog
WATSON-CRICK
C
C
15
C
N4
C
15
1_555
D
G
10
D
O6
G
10
1_555
hydrog
WATSON-CRICK
C
C
15
C
O2
C
15
1_555
D
G
10
D
N2
G
10
1_555
hydrog
U-U MISPAIR
D
U
1
D
O4
U
1
1_555
D
U
23
D
N3
U
23
1_555
hydrog
WATSON-CRICK
D
U
2
D
N3
U
2
1_555
D
A
22
D
N1
A
22
1_555
hydrog
WATSON-CRICK
D
U
2
D
O4
U
2
1_555
D
A
22
D
N6
A
22
1_555
hydrog
WATSON-CRICK
D
U
3
D
N3
U
3
1_555
D
A
21
D
N1
A
21
1_555
hydrog
WATSON-CRICK
D
U
3
D
O4
U
3
1_555
D
A
21
D
N6
A
21
1_555
hydrog
WATSON-CRICK
D
G
4
D
N1
G
4
1_555
D
C
20
D
N3
C
20
1_555
hydrog
WATSON-CRICK
D
G
4
D
N2
G
4
1_555
D
C
20
D
O2
C
20
1_555
hydrog
WATSON-CRICK
D
G
4
D
O6
G
4
1_555
D
C
20
D
N4
C
20
1_555
hydrog
WATSON-CRICK
D
C
5
D
N3
C
5
1_555
D
G
19
D
N1
G
19
1_555
hydrog
WATSON-CRICK
D
C
5
D
N4
C
5
1_555
D
G
19
D
O6
G
19
1_555
hydrog
WATSON-CRICK
D
C
5
D
O2
C
5
1_555
D
G
19
D
N2
G
19
1_555
hydrog
U-A PAIR
D
U
6
D
N3
U
6
1_555
D
A
18
D
N1
A
18
1_555
hydrog
WATSON-CRICK
D
G
7
D
N1
G
7
1_555
D
C
17
D
N3
C
17
1_555
hydrog
WATSON-CRICK
D
G
7
D
N2
G
7
1_555
D
C
17
D
O2
C
17
1_555
hydrog
WATSON-CRICK
D
G
7
D
O6
G
7
1_555
D
C
17
D
N4
C
17
1_555
RNA
HIV, RNA, hairpin
1K9W
PDB
1
1K9W
1
23
1K9W
1
23
1K9W
A
1
1
23
1
23
1K9W
1
23
1K9W
B
1
1
23
1
23
1K9W
1
23
1K9W
C
1
1
23
1
23
1K9W
1
23
1K9W
D
1
1
23
BINDING SITE FOR RESIDUE MG D 102
D
MG
102
Software
2
BINDING SITE FOR RESIDUE MG B 103
B
MG
103
Software
2
BINDING SITE FOR RESIDUE MG B 104
B
MG
104
Software
1
D
A
8
D
A
8
2
1_555
D
G
9
D
G
9
2
1_555
B
A
8
B
A
8
2
1_555
B
U
11
B
U
11
2
1_555
B
C
15
B
C
15
1
1_555
5
C 1 2 1