0.030497
0.017608
0.000000
0.000000
0.035215
0.000000
0.000000
0.000000
0.009311
0.00000
0.00000
0.00000
Shalev, M.
Kondo, J.
Adir, N.
Baasov, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
32.790
32.790
107.400
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C21 H41 N5 O11
539.577
APRAMYCIN
NEBRAMYCIN II; 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE
non-polymer
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
H2 O
18.015
WATER
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
S
C
N
39
R
C
N
40
N
C
N
41
S
C
N
42
R
C
N
43
R
C
N
44
S
C
N
45
R
C
N
46
N
C
N
47
N
O
N
48
N
O
N
49
N
N
N
50
N
N
N
51
N
O
N
52
N
O
N
53
N
O
N
54
R
C
N
55
R
C
N
56
S
C
N
57
S
C
N
58
S
C
N
59
N
C
N
60
N
O
N
61
N
N
N
62
N
O
N
63
N
O
N
64
N
O
N
65
R
C
N
66
R
C
N
67
S
C
N
68
R
C
N
69
N
C
N
70
S
C
N
71
N
N
N
72
N
N
N
73
N
O
N
74
N
O
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
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
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
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
O
N
117
N
P
N
118
N
O
N
119
N
O
N
120
N
O
N
121
N
C
N
122
R
C
N
123
N
O
N
124
S
C
N
125
N
O
N
126
R
C
N
127
N
O
N
128
R
C
N
129
N
N
N
130
N
C
N
131
N
O
N
132
N
N
N
133
N
C
N
134
N
N
N
135
N
C
N
136
N
C
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
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
O
N
152
N
P
N
153
N
O
N
154
N
O
N
155
N
O
N
156
N
C
N
157
R
C
N
158
N
O
N
159
S
C
N
160
N
O
N
161
R
C
N
162
N
O
N
163
R
C
Y
164
N
N
Y
165
N
C
Y
166
N
N
Y
167
N
C
N
168
N
C
N
169
N
O
N
170
N
N
N
171
N
C
N
172
N
N
N
173
N
N
Y
174
N
C
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
O
N
190
N
H
N
191
N
H
N
192
N
O
N
193
N
P
N
194
N
O
N
195
N
O
N
196
N
O
N
197
N
C
N
198
R
C
N
199
N
O
N
200
S
C
N
201
N
O
N
202
R
C
N
203
N
O
N
204
R
C
N
205
N
N
N
206
N
C
N
207
N
O
N
208
N
N
N
209
N
C
N
210
N
O
N
211
N
C
N
212
N
C
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
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
sing
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
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
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
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
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
doub
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
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
doub
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
doub
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
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
Y
181
N
sing
Y
182
N
sing
Y
183
N
doub
N
184
N
sing
Y
185
N
sing
N
186
N
sing
Y
187
N
doub
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
doub
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
doub
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
doub
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
110
13333
13338
10.1073/pnas.1307365110
23898171
Identification of the molecular attributes required for aminoglycoside activity against Leishmania.
2013
10.2210/pdb4k31/pdb
pdb_00004k31
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
2012-01-01
ADSC QUANTUM 315r
SINGLE WAVELENGTH
M
x-ray
1
0.9394
1.0
ID14-4
ESRF
0.9394
SYNCHROTRON
ESRF BEAMLINE ID14-4
7356.393
RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
2
syn
polymer
539.577
APRAMYCIN
4
syn
non-polymer
18.015
water
209
nat
water
no
no
UUGCGUCGUUCCGGAAAAGUCGC
UUGCGUCGUUCCGGAAAAGUCGC
B,C
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
2.27
45.71
VAPOR DIFFUSION, HANGING DROP
7.0
50 mM Na cacodylate, 1 mM spermine tetrahydrochloride, 1% 2-methyl-2,4-pentadiol (vs. 40% reservoir), 100-250 mM NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
293.15
-2.870
1
19
B
3
C
23
-0.905
B_G3:C23_C
1
3.569
-0.174
0.082
-0.157
4.920
1
19
B
4
C
22
-0.303
B_C4:G22_C
2
-5.312
0.123
-0.014
-0.113
-5.027
1
19
B
5
C
21
2.575
B_G5:C21_C
3
-18.351
-0.135
-0.118
-0.130
-1.625
1
16
B
6
C
20
6.521
B_U6:U20_C
4
-14.583
2.477
0.219
-1.699
6.215
1
19
B
7
C
19
-1.032
B_C7:G19_C
5
-11.712
0.240
-0.112
-0.178
9.899
1
8
B
8
C
17
-17.870
B_G8:A17_C
6
-5.092
0.250
-0.140
1.629
17.014
1
20
B
9
C
16
-4.935
B_U9:A16_C
7
-17.682
0.055
0.086
0.006
15.313
1
20
B
10
C
15
-0.609
B_U10:A15_C
8
-16.466
-0.140
-0.019
0.054
2.686
1
19
B
11
C
14
1.365
B_C11:G14_C
9
-10.951
0.249
0.183
-0.149
-4.606
1
19
B
12
C
13
0.675
B_C12:G13_C
10
-6.268
-0.006
0.266
-0.170
1.366
1
19
B
13
C
12
1.392
B_G13:C12_C
11
-9.164
0.044
0.410
-0.179
-8.965
1
19
B
14
C
11
2.187
B_G14:C11_C
12
-14.344
-0.130
-0.405
-0.053
-12.583
1
20
B
15
C
10
0.729
B_A15:U10_C
13
-13.128
0.184
-0.126
-0.021
-20.769
1
20
B
16
C
9
-2.822
B_A16:U9_C
14
-16.228
0.041
0.246
-0.069
-6.822
1
8
B
17
C
8
-10.736
B_A17:G8_C
15
-8.910
-0.263
-0.201
1.612
-5.572
1
19
B
19
C
7
0.042
B_G19:C7_C
16
-11.891
-0.206
-0.059
-0.145
2.180
1
16
B
20
C
6
6.054
B_U20:U6_C
17
-14.955
-2.439
0.242
-1.677
5.113
1
19
B
21
C
5
2.296
B_C21:G5_C
18
-18.185
0.151
-0.136
-0.152
-5.063
1
19
B
22
C
4
-0.338
B_G22:C4_C
19
-5.630
-0.128
-0.029
-0.111
2.922
1
19
B
23
C
3
-0.953
B_C23:G3_C
20
3.169
0.207
0.104
-0.160
3.253
32.808
B
B
3
4
-1.778
C
C
23
22
3.205
-1.004
-0.281
-1.829
BB_G3C4:G22C23_CC
1
0.576
-1.020
32.788
-3.068
0.595
2.497
29.661
B
B
4
5
22.138
C
C
22
21
3.407
11.070
-0.186
-1.849
BB_C4G5:C21G22_CC
2
-0.622
1.244
27.554
-5.799
0.241
3.059
46.214
B
B
5
6
6.291
C
C
21
20
3.176
4.929
0.515
-0.931
BB_G5U6:U20C21_CC
3
-0.660
0.842
45.960
-1.587
-0.710
2.431
27.054
B
B
6
7
8.636
C
C
20
19
2.895
3.969
-0.218
-1.725
BB_U6C7:G19U20_CC
4
7.877
-17.140
25.601
-4.532
2.140
2.599
33.110
B
B
7
8
10.028
C
C
19
17
3.395
5.667
0.776
-3.573
BB_C7G8:A17G19_CC
5
-5.042
8.923
32.253
-7.158
-2.151
2.294
28.878
B
B
8
9
15.432
C
C
17
16
2.867
7.533
-0.381
-1.884
BB_G8U9:A16A17_CC
6
-7.006
14.351
27.020
-5.145
-0.508
2.904
36.760
B
B
9
10
9.868
C
C
16
15
3.259
6.183
0.296
-1.603
BB_U9U10:A15A16_CC
7
-4.098
6.541
36.029
-3.345
-1.001
2.943
34.800
B
B
10
11
12.174
C
C
15
14
3.345
7.231
-0.239
-1.652
BB_U10C11:G14A15_CC
8
-0.072
0.121
34.063
-3.834
0.389
2.813
32.306
B
B
11
12
12.144
C
C
14
13
3.264
6.704
-0.041
-1.835
BB_C11C12:G13G14_CC
9
2.504
-4.535
31.524
-4.416
0.491
2.087
24.810
B
B
12
13
24.596
C
C
13
12
3.249
10.260
0.017
-2.152
BB_C12G13:C12G13_CC
10
-0.095
0.227
22.619
-7.658
-0.064
2.741
34.133
B
B
13
14
19.839
C
C
12
11
3.505
11.429
-0.033
-1.740
BB_G13G14:C11C12_CC
11
1.537
-2.668
32.181
-4.748
0.296
2.670
34.261
B
B
14
15
15.296
C
C
11
10
3.171
8.900
0.125
-1.474
BB_G14A15:U10C11_CC
12
-3.300
5.673
32.958
-3.778
-0.685
3.185
36.916
B
B
15
16
5.270
C
C
10
9
3.320
3.332
-0.317
-1.490
BB_A15A16:U9U10_CC
13
-0.991
1.568
36.757
-2.801
0.368
2.347
31.103
B
B
16
17
9.886
C
C
9
8
2.772
5.156
0.307
-1.905
BB_A16A17:G8U9_CC
14
11.473
-21.997
28.504
-4.361
1.224
2.268
30.920
B
B
17
19
15.597
C
C
8
7
3.427
8.195
-0.760
-3.513
BB_A17G19:C7G8_CC
15
4.182
-7.960
29.552
-8.004
2.148
2.461
26.903
B
B
19
20
8.328
C
C
7
6
2.900
3.808
0.173
-1.729
BB_G19U20:U6C7_CC
16
-7.788
17.032
25.492
-4.539
-2.055
3.075
45.641
B
B
20
21
6.223
C
C
6
5
3.199
4.818
-0.516
-0.952
BB_U20C21:G5U6_CC
17
1.125
-1.453
45.387
-1.632
0.759
2.492
29.655
B
B
21
22
22.246
C
C
5
4
3.408
11.118
0.211
-1.855
BB_C21G22:C4G5_CC
18
0.882
-1.765
27.521
-5.822
-0.239
3.250
33.018
B
B
22
23
-1.603
C
C
4
3
3.210
-0.911
0.309
-1.819
BB_G22C23:G3C4_CC
19
-0.782
1.376
32.996
-3.047
-0.675
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
Structure summary
1
0
2013-07-31
1
1
2013-09-04
1
2
2023-09-20
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2013-04-10
REL
REL
AM2
APRAMYCIN
HOH
water
38568
Leishmania
sample
2G5K
pdb entry 2G5K
PDB
experimental model
AM2
51
2
AM2
AM2
101
B
AM2
54
2
AM2
AM2
102
B
AM2
52
2
AM2
AM2
101
C
AM2
53
2
AM2
AM2
102
C
HOH
3
3
HOH
HOH
201
B
HOH
6
3
HOH
HOH
202
B
HOH
8
3
HOH
HOH
203
B
HOH
10
3
HOH
HOH
204
B
HOH
11
3
HOH
HOH
205
B
HOH
15
3
HOH
HOH
206
B
HOH
19
3
HOH
HOH
207
B
HOH
22
3
HOH
HOH
208
B
HOH
24
3
HOH
HOH
209
B
HOH
25
3
HOH
HOH
210
B
HOH
26
3
HOH
HOH
211
B
HOH
27
3
HOH
HOH
212
B
HOH
30
3
HOH
HOH
213
B
HOH
32
3
HOH
HOH
214
B
HOH
34
3
HOH
HOH
215
B
HOH
35
3
HOH
HOH
216
B
HOH
37
3
HOH
HOH
217
B
HOH
38
3
HOH
HOH
218
B
HOH
40
3
HOH
HOH
219
B
HOH
41
3
HOH
HOH
220
B
HOH
44
3
HOH
HOH
221
B
HOH
46
3
HOH
HOH
222
B
HOH
48
3
HOH
HOH
223
B
HOH
49
3
HOH
HOH
224
B
HOH
52
3
HOH
HOH
225
B
HOH
56
3
HOH
HOH
226
B
HOH
57
3
HOH
HOH
227
B
HOH
59
3
HOH
HOH
228
B
HOH
61
3
HOH
HOH
229
B
HOH
62
3
HOH
HOH
230
B
HOH
67
3
HOH
HOH
231
B
HOH
68
3
HOH
HOH
232
B
HOH
69
3
HOH
HOH
233
B
HOH
71
3
HOH
HOH
234
B
HOH
75
3
HOH
HOH
235
B
HOH
77
3
HOH
HOH
236
B
HOH
78
3
HOH
HOH
237
B
HOH
79
3
HOH
HOH
238
B
HOH
80
3
HOH
HOH
239
B
HOH
81
3
HOH
HOH
240
B
HOH
83
3
HOH
HOH
241
B
HOH
87
3
HOH
HOH
242
B
HOH
90
3
HOH
HOH
243
B
HOH
93
3
HOH
HOH
244
B
HOH
97
3
HOH
HOH
245
B
HOH
98
3
HOH
HOH
246
B
HOH
99
3
HOH
HOH
247
B
HOH
101
3
HOH
HOH
248
B
HOH
102
3
HOH
HOH
249
B
HOH
104
3
HOH
HOH
250
B
HOH
105
3
HOH
HOH
251
B
HOH
107
3
HOH
HOH
252
B
HOH
108
3
HOH
HOH
253
B
HOH
109
3
HOH
HOH
254
B
HOH
110
3
HOH
HOH
255
B
HOH
115
3
HOH
HOH
256
B
HOH
117
3
HOH
HOH
257
B
HOH
119
3
HOH
HOH
258
B
HOH
120
3
HOH
HOH
259
B
HOH
121
3
HOH
HOH
260
B
HOH
123
3
HOH
HOH
261
B
HOH
125
3
HOH
HOH
262
B
HOH
128
3
HOH
HOH
263
B
HOH
129
3
HOH
HOH
264
B
HOH
130
3
HOH
HOH
265
B
HOH
131
3
HOH
HOH
266
B
HOH
133
3
HOH
HOH
267
B
HOH
134
3
HOH
HOH
268
B
HOH
136
3
HOH
HOH
269
B
HOH
139
3
HOH
HOH
270
B
HOH
141
3
HOH
HOH
271
B
HOH
145
3
HOH
HOH
272
B
HOH
146
3
HOH
HOH
273
B
HOH
149
3
HOH
HOH
274
B
HOH
151
3
HOH
HOH
275
B
HOH
152
3
HOH
HOH
276
B
HOH
155
3
HOH
HOH
277
B
HOH
158
3
HOH
HOH
278
B
HOH
160
3
HOH
HOH
279
B
HOH
161
3
HOH
HOH
280
B
HOH
162
3
HOH
HOH
281
B
HOH
165
3
HOH
HOH
282
B
HOH
166
3
HOH
HOH
283
B
HOH
167
3
HOH
HOH
284
B
HOH
168
3
HOH
HOH
285
B
HOH
170
3
HOH
HOH
286
B
HOH
171
3
HOH
HOH
287
B
HOH
172
3
HOH
HOH
288
B
HOH
173
3
HOH
HOH
289
B
HOH
174
3
HOH
HOH
290
B
HOH
177
3
HOH
HOH
291
B
HOH
178
3
HOH
HOH
292
B
HOH
183
3
HOH
HOH
293
B
HOH
185
3
HOH
HOH
294
B
HOH
186
3
HOH
HOH
295
B
HOH
189
3
HOH
HOH
296
B
HOH
190
3
HOH
HOH
297
B
HOH
192
3
HOH
HOH
298
B
HOH
194
3
HOH
HOH
299
B
HOH
195
3
HOH
HOH
300
B
HOH
197
3
HOH
HOH
301
B
HOH
199
3
HOH
HOH
302
B
HOH
201
3
HOH
HOH
303
B
HOH
202
3
HOH
HOH
304
B
HOH
204
3
HOH
HOH
305
B
HOH
208
3
HOH
HOH
306
B
HOH
209
3
HOH
HOH
307
B
HOH
1
3
HOH
HOH
308
B
HOH
2
3
HOH
HOH
201
C
HOH
12
3
HOH
HOH
202
C
HOH
4
3
HOH
HOH
203
C
HOH
5
3
HOH
HOH
204
C
HOH
7
3
HOH
HOH
205
C
HOH
9
3
HOH
HOH
206
C
HOH
13
3
HOH
HOH
207
C
HOH
14
3
HOH
HOH
208
C
HOH
16
3
HOH
HOH
209
C
HOH
17
3
HOH
HOH
210
C
HOH
18
3
HOH
HOH
211
C
HOH
20
3
HOH
HOH
212
C
HOH
21
3
HOH
HOH
213
C
HOH
23
3
HOH
HOH
214
C
HOH
28
3
HOH
HOH
215
C
HOH
29
3
HOH
HOH
216
C
HOH
31
3
HOH
HOH
217
C
HOH
33
3
HOH
HOH
218
C
HOH
36
3
HOH
HOH
219
C
HOH
39
3
HOH
HOH
220
C
HOH
42
3
HOH
HOH
221
C
HOH
43
3
HOH
HOH
222
C
HOH
45
3
HOH
HOH
223
C
HOH
47
3
HOH
HOH
224
C
HOH
50
3
HOH
HOH
225
C
HOH
51
3
HOH
HOH
226
C
HOH
53
3
HOH
HOH
227
C
HOH
54
3
HOH
HOH
228
C
HOH
55
3
HOH
HOH
229
C
HOH
58
3
HOH
HOH
230
C
HOH
60
3
HOH
HOH
231
C
HOH
63
3
HOH
HOH
232
C
HOH
64
3
HOH
HOH
233
C
HOH
65
3
HOH
HOH
234
C
HOH
66
3
HOH
HOH
235
C
HOH
70
3
HOH
HOH
236
C
HOH
72
3
HOH
HOH
237
C
HOH
73
3
HOH
HOH
238
C
HOH
74
3
HOH
HOH
239
C
HOH
76
3
HOH
HOH
240
C
HOH
82
3
HOH
HOH
241
C
HOH
84
3
HOH
HOH
242
C
HOH
85
3
HOH
HOH
243
C
HOH
86
3
HOH
HOH
244
C
HOH
88
3
HOH
HOH
245
C
HOH
89
3
HOH
HOH
246
C
HOH
91
3
HOH
HOH
247
C
HOH
92
3
HOH
HOH
248
C
HOH
94
3
HOH
HOH
249
C
HOH
95
3
HOH
HOH
250
C
HOH
96
3
HOH
HOH
251
C
HOH
100
3
HOH
HOH
252
C
HOH
103
3
HOH
HOH
253
C
HOH
106
3
HOH
HOH
254
C
HOH
111
3
HOH
HOH
255
C
HOH
112
3
HOH
HOH
256
C
HOH
113
3
HOH
HOH
257
C
HOH
114
3
HOH
HOH
258
C
HOH
116
3
HOH
HOH
259
C
HOH
118
3
HOH
HOH
260
C
HOH
122
3
HOH
HOH
261
C
HOH
124
3
HOH
HOH
262
C
HOH
126
3
HOH
HOH
263
C
HOH
127
3
HOH
HOH
264
C
HOH
132
3
HOH
HOH
265
C
HOH
135
3
HOH
HOH
266
C
HOH
137
3
HOH
HOH
267
C
HOH
138
3
HOH
HOH
268
C
HOH
140
3
HOH
HOH
269
C
HOH
142
3
HOH
HOH
270
C
HOH
143
3
HOH
HOH
271
C
HOH
144
3
HOH
HOH
272
C
HOH
147
3
HOH
HOH
273
C
HOH
148
3
HOH
HOH
274
C
HOH
150
3
HOH
HOH
275
C
HOH
153
3
HOH
HOH
276
C
HOH
154
3
HOH
HOH
277
C
HOH
156
3
HOH
HOH
278
C
HOH
157
3
HOH
HOH
279
C
HOH
159
3
HOH
HOH
280
C
HOH
163
3
HOH
HOH
281
C
HOH
164
3
HOH
HOH
282
C
HOH
169
3
HOH
HOH
283
C
HOH
175
3
HOH
HOH
284
C
HOH
176
3
HOH
HOH
285
C
HOH
179
3
HOH
HOH
286
C
HOH
180
3
HOH
HOH
287
C
HOH
181
3
HOH
HOH
288
C
HOH
182
3
HOH
HOH
289
C
HOH
184
3
HOH
HOH
290
C
HOH
187
3
HOH
HOH
291
C
HOH
188
3
HOH
HOH
292
C
HOH
191
3
HOH
HOH
293
C
HOH
193
3
HOH
HOH
294
C
HOH
196
3
HOH
HOH
295
C
HOH
198
3
HOH
HOH
296
C
HOH
200
3
HOH
HOH
297
C
HOH
203
3
HOH
HOH
298
C
HOH
205
3
HOH
HOH
299
C
HOH
206
3
HOH
HOH
300
C
HOH
207
3
HOH
HOH
301
C
n
1
1
B
U
2
n
2
U
2
B
G
3
n
3
G
3
B
C
4
n
4
C
4
B
G
5
n
5
G
5
B
U
6
n
6
U
6
B
C
7
n
7
C
7
B
G
8
n
8
G
8
B
U
9
n
9
U
9
B
U
10
n
10
U
10
B
C
11
n
11
C
11
B
C
12
n
12
C
12
B
G
13
n
13
G
13
B
G
14
n
14
G
14
B
A
15
n
15
A
15
B
A
16
n
16
A
16
B
A
17
n
17
A
17
B
A
18
n
18
A
18
B
G
19
n
19
G
19
B
U
20
n
20
U
20
B
C
21
n
21
C
21
B
G
22
n
22
G
22
B
C
23
n
23
C
23
B
n
1
1
C
U
2
n
2
U
2
C
G
3
n
3
G
3
C
C
4
n
4
C
4
C
G
5
n
5
G
5
C
U
6
n
6
U
6
C
C
7
n
7
C
7
C
G
8
n
8
G
8
C
U
9
n
9
U
9
C
U
10
n
10
U
10
C
C
11
n
11
C
11
C
C
12
n
12
C
12
C
G
13
n
13
G
13
C
G
14
n
14
G
14
C
A
15
n
15
A
15
C
A
16
n
16
A
16
C
A
17
n
17
A
17
C
A
18
n
18
A
18
C
G
19
n
19
G
19
C
U
20
n
20
U
20
C
C
21
n
21
C
21
C
G
22
n
22
G
22
C
C
23
n
23
C
23
C
author_and_software_defined_assembly
PISA
2
dimeric
5040
-63
8260
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
B
U
1
A
U
1
1
Y
1
C
U
1
B
U
1
1
Y
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.2644
0.2258
0.2277
1.415
19.510
1190
22089
23271
5.11
94.51
0.19
RANDOM
1
2.00
MOLECULAR REPLACEMENT
21.40
0.90
1.11
pdb entry 2G5K
ML
FLAT BULK SOLVENT MODEL
80.000
0.600
1.415
19.510
209
1295
148
938
0
0.006
1208
0.976
1872
15.785
638
0.051
288
0.009
44
0.2827
0.2456
1.4795
165
2826
98.00
0.2323
0.2222
1.5574
167
2929
100.00
0.2402
0.2165
1.6549
144
2921
100.00
0.2234
0.2077
1.7826
157
2908
100.00
0.2291
0.2114
1.9619
137
2941
100.00
0.2239
0.2052
2.2454
167
2904
100.00
0.2846
0.2219
2.8276
159
2912
99.00
0.3155
0.2566
19.5116
94
1740
60.00
1.4
35.8
4K31
67545
23325
21.5
21.5
0.048
1
14.1
2.9
94.5
0.137
1.42
1.49
5.7
1
98
refinement
PHENIX
(phenix.refine: 1.6.1_357)
Crystal structure of apramycin bound to the leishmanial rRNA A-site
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
hydrog
WATSON-CRICK
B
G
3
A
N1
G
3
1_555
C
C
23
B
N3
C
23
1_555
hydrog
WATSON-CRICK
B
G
3
A
N2
G
3
1_555
C
C
23
B
O2
C
23
1_555
hydrog
WATSON-CRICK
B
G
3
A
O6
G
3
1_555
C
C
23
B
N4
C
23
1_555
hydrog
WATSON-CRICK
B
C
4
A
N3
C
4
1_555
C
G
22
B
N1
G
22
1_555
hydrog
WATSON-CRICK
B
C
4
A
N4
C
4
1_555
C
G
22
B
O6
G
22
1_555
hydrog
WATSON-CRICK
B
C
4
A
O2
C
4
1_555
C
G
22
B
N2
G
22
1_555
hydrog
WATSON-CRICK
B
G
5
A
N1
G
5
1_555
C
C
21
B
N3
C
21
1_555
hydrog
WATSON-CRICK
B
G
5
A
N2
G
5
1_555
C
C
21
B
O2
C
21
1_555
hydrog
WATSON-CRICK
B
G
5
A
O6
G
5
1_555
C
C
21
B
N4
C
21
1_555
hydrog
TYPE_16_PAIR
B
U
6
A
N3
U
6
1_555
C
U
20
B
O4
U
20
1_555
hydrog
TYPE_16_PAIR
B
U
6
A
O2
U
6
1_555
C
U
20
B
N3
U
20
1_555
hydrog
WATSON-CRICK
B
C
7
A
N3
C
7
1_555
C
G
19
B
N1
G
19
1_555
hydrog
WATSON-CRICK
B
C
7
A
N4
C
7
1_555
C
G
19
B
O6
G
19
1_555
hydrog
WATSON-CRICK
B
C
7
A
O2
C
7
1_555
C
G
19
B
N2
G
19
1_555
hydrog
TYPE_8_PAIR
B
G
8
A
N1
G
8
1_555
C
A
17
B
N1
A
17
1_555
hydrog
TYPE_8_PAIR
B
G
8
A
O6
G
8
1_555
C
A
17
B
N6
A
17
1_555
hydrog
WATSON-CRICK
B
U
9
A
N3
U
9
1_555
C
A
16
B
N1
A
16
1_555
hydrog
WATSON-CRICK
B
U
9
A
O4
U
9
1_555
C
A
16
B
N6
A
16
1_555
hydrog
WATSON-CRICK
B
U
10
A
N3
U
10
1_555
C
A
15
B
N1
A
15
1_555
hydrog
WATSON-CRICK
B
U
10
A
O4
U
10
1_555
C
A
15
B
N6
A
15
1_555
hydrog
WATSON-CRICK
B
C
11
A
N3
C
11
1_555
C
G
14
B
N1
G
14
1_555
hydrog
WATSON-CRICK
B
C
11
A
N4
C
11
1_555
C
G
14
B
O6
G
14
1_555
hydrog
WATSON-CRICK
B
C
11
A
O2
C
11
1_555
C
G
14
B
N2
G
14
1_555
hydrog
WATSON-CRICK
B
C
12
A
N3
C
12
1_555
C
G
13
B
N1
G
13
1_555
hydrog
WATSON-CRICK
B
C
12
A
N4
C
12
1_555
C
G
13
B
O6
G
13
1_555
hydrog
WATSON-CRICK
B
C
12
A
O2
C
12
1_555
C
G
13
B
N2
G
13
1_555
hydrog
WATSON-CRICK
B
G
13
A
N1
G
13
1_555
C
C
12
B
N3
C
12
1_555
hydrog
WATSON-CRICK
B
G
13
A
N2
G
13
1_555
C
C
12
B
O2
C
12
1_555
hydrog
WATSON-CRICK
B
G
13
A
O6
G
13
1_555
C
C
12
B
N4
C
12
1_555
hydrog
WATSON-CRICK
B
G
14
A
N1
G
14
1_555
C
C
11
B
N3
C
11
1_555
hydrog
WATSON-CRICK
B
G
14
A
N2
G
14
1_555
C
C
11
B
O2
C
11
1_555
hydrog
WATSON-CRICK
B
G
14
A
O6
G
14
1_555
C
C
11
B
N4
C
11
1_555
hydrog
WATSON-CRICK
B
A
15
A
N1
A
15
1_555
C
U
10
B
N3
U
10
1_555
hydrog
WATSON-CRICK
B
A
15
A
N6
A
15
1_555
C
U
10
B
O4
U
10
1_555
hydrog
WATSON-CRICK
B
A
16
A
N1
A
16
1_555
C
U
9
B
N3
U
9
1_555
hydrog
WATSON-CRICK
B
A
16
A
N6
A
16
1_555
C
U
9
B
O4
U
9
1_555
hydrog
TYPE_8_PAIR
B
A
17
A
N1
A
17
1_555
C
G
8
B
N1
G
8
1_555
hydrog
TYPE_8_PAIR
B
A
17
A
N6
A
17
1_555
C
G
8
B
O6
G
8
1_555
hydrog
WATSON-CRICK
B
G
19
A
N1
G
19
1_555
C
C
7
B
N3
C
7
1_555
hydrog
WATSON-CRICK
B
G
19
A
N2
G
19
1_555
C
C
7
B
O2
C
7
1_555
hydrog
WATSON-CRICK
B
G
19
A
O6
G
19
1_555
C
C
7
B
N4
C
7
1_555
hydrog
TYPE_16_PAIR
B
U
20
A
N3
U
20
1_555
C
U
6
B
O2
U
6
1_555
hydrog
TYPE_16_PAIR
B
U
20
A
O4
U
20
1_555
C
U
6
B
N3
U
6
1_555
hydrog
WATSON-CRICK
B
C
21
A
N3
C
21
1_555
C
G
5
B
N1
G
5
1_555
hydrog
WATSON-CRICK
B
C
21
A
N4
C
21
1_555
C
G
5
B
O6
G
5
1_555
hydrog
WATSON-CRICK
B
C
21
A
O2
C
21
1_555
C
G
5
B
N2
G
5
1_555
hydrog
WATSON-CRICK
B
G
22
A
N1
G
22
1_555
C
C
4
B
N3
C
4
1_555
hydrog
WATSON-CRICK
B
G
22
A
N2
G
22
1_555
C
C
4
B
O2
C
4
1_555
hydrog
WATSON-CRICK
B
G
22
A
O6
G
22
1_555
C
C
4
B
N4
C
4
1_555
hydrog
WATSON-CRICK
B
C
23
A
N3
C
23
1_555
C
G
3
B
N1
G
3
1_555
hydrog
WATSON-CRICK
B
C
23
A
N4
C
23
1_555
C
G
3
B
O6
G
3
1_555
hydrog
WATSON-CRICK
B
C
23
A
O2
C
23
1_555
C
G
3
B
N2
G
3
1_555
RNA/antibiotic
rRNA duplex, Ribosomal A-site, Aminoglycoside, Ribosome, RNA, RNA-antibiotic complex
4K31
PDB
1
4K31
1
23
4K31
1
23
4K31
B
1
1
23
1
23
4K31
1
23
4K31
C
1
1
23
BINDING SITE FOR RESIDUE AM2 B 101
B
AM2
101
Software
13
BINDING SITE FOR RESIDUE AM2 B 102
B
AM2
102
Software
24
BINDING SITE FOR RESIDUE AM2 C 101
C
AM2
101
Software
23
BINDING SITE FOR RESIDUE AM2 C 102
C
AM2
102
Software
17
B
C
4
A
C
4
13
1_555
B
G
5
A
G
5
13
1_555
B
U
6
A
U
6
13
1_555
B
G
8
A
G
8
13
1_555
B
HOH
207
G
HOH
13
1_555
B
HOH
211
G
HOH
13
1_555
B
HOH
239
G
HOH
13
1_555
B
HOH
258
G
HOH
13
1_555
B
HOH
295
G
HOH
13
1_555
C
A
17
B
A
17
13
1_555
C
G
19
B
G
19
13
1_555
C
U
20
B
U
20
13
1_555
C
HOH
219
H
HOH
13
1_555
B
U
9
A
U
9
24
1_555
B
U
10
A
U
10
24
1_555
B
C
11
A
C
11
24
1_555
B
HOH
205
G
HOH
24
1_555
B
HOH
225
G
HOH
24
1_555
B
HOH
232
G
HOH
24
1_555
B
HOH
233
G
HOH
24
1_555
B
HOH
235
G
HOH
24
1_555
B
HOH
240
G
HOH
24
1_555
B
HOH
253
G
HOH
24
1_555
B
HOH
260
G
HOH
24
1_555
B
HOH
274
G
HOH
24
1_555
B
HOH
287
G
HOH
24
1_555
B
HOH
297
G
HOH
24
1_555
B
HOH
301
G
HOH
24
1_555
B
HOH
308
G
HOH
24
1_555
C
G
8
B
G
8
24
1_555
C
U
9
B
U
9
24
1_555
C
C
23
B
C
23
24
2_545
C
HOH
201
H
HOH
24
1_555
C
HOH
210
H
HOH
24
1_555
C
HOH
215
H
HOH
24
1_555
C
HOH
274
H
HOH
24
1_555
C
HOH
280
H
HOH
24
1_555
B
G
8
A
G
8
23
1_555
B
U
9
A
U
9
23
1_555
B
C
23
A
C
23
23
3_544
B
HOH
210
G
HOH
23
1_555
B
HOH
294
G
HOH
23
1_555
B
HOH
308
G
HOH
23
1_555
C
U
9
B
U
9
23
1_555
C
U
10
B
U
10
23
1_555
C
C
11
B
C
11
23
1_555
C
HOH
202
H
HOH
23
1_555
C
HOH
204
H
HOH
23
1_555
C
HOH
205
H
HOH
23
1_555
C
HOH
225
H
HOH
23
1_555
C
HOH
236
H
HOH
23
1_555
C
HOH
238
H
HOH
23
1_555
C
HOH
240
H
HOH
23
1_555
C
HOH
257
H
HOH
23
1_555
C
HOH
262
H
HOH
23
1_555
C
HOH
269
H
HOH
23
1_555
C
HOH
270
H
HOH
23
1_555
C
HOH
275
H
HOH
23
1_555
C
HOH
283
H
HOH
23
1_555
C
HOH
295
H
HOH
23
1_555
B
G
14
A
G
14
17
1_555
B
A
17
A
A
17
17
1_555
B
G
19
A
G
19
17
1_555
B
U
20
A
U
20
17
1_555
B
HOH
218
G
HOH
17
1_555
B
HOH
227
G
HOH
17
1_555
C
C
4
B
C
4
17
1_555
C
G
5
B
G
5
17
1_555
C
U
6
B
U
6
17
1_555
C
G
8
B
G
8
17
1_555
C
HOH
216
H
HOH
17
1_555
C
HOH
239
H
HOH
17
1_555
C
HOH
247
H
HOH
17
1_555
C
HOH
278
H
HOH
17
1_555
C
HOH
282
H
HOH
17
1_555
C
HOH
284
H
HOH
17
1_555
C
HOH
296
H
HOH
17
1_555
144
P 31