1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lynch, S.R.
Puglisi, J.D.
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
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C23 H45 N5 O14
615.628
PAROMOMYCIN
PAROMOMYCIN I; AMMINOSIDIN; CATENULIN; CRESTOMYCIN; MONOMYCIN A; NEOMYCIN E
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
306
1037
1058
10.1006/jmbi.2000.4420
11237617
Structural origins of aminoglycoside specificity for prokaryotic ribosomes.
2001
10.2210/pdb1fyp/pdb
pdb_00001fyp
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
EUKARYOTIC DECODING REGION A-SITE RNA
8672.185
FRAGMENT OF 18S RIBOSOMAL RNA
18S RNA - NUCLEOTIDES 1404-1412, 1488-1497 (E. COLI NUMBERING)
U1410A, A1490U
1
syn
polymer
615.628
PAROMOMYCIN
PAROMOMYCIN
1
syn
non-polymer
no
no
GGCGUCGCACCUUCGGGUGAAGUCGCC
GGCGUCGCACCUUCGGGUGAAGUCGCC
A
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
n
n
3.247
1
19
A
1
A
27
-1.816
A_G1:C27_A
1
-22.660
-0.286
-0.060
-0.222
-0.640
1
19
A
2
A
26
-4.658
A_G2:C26_A
2
-10.567
-0.425
0.021
-0.313
9.244
1
19
A
3
A
25
-1.687
A_C3:G25_A
3
-19.296
0.566
-0.058
-0.333
-21.306
1
19
A
4
A
24
-5.591
A_G4:C24_A
4
-37.146
-0.238
-0.036
-0.273
-16.032
1
19
A
6
A
22
0.561
A_C6:G22_A
5
-20.148
0.425
-0.068
-0.330
-19.146
1
8
A
7
A
21
-11.700
A_G7:A21_A
6
-0.306
0.471
0.932
1.277
1.833
1
19
A
8
A
19
-10.312
A_C8:G19_A
7
-20.512
0.191
0.574
-0.293
-1.868
1
20
A
9
A
18
-11.460
A_A9:U18_A
8
-31.325
0.151
0.252
-0.243
1.317
1
19
A
10
A
17
-3.410
A_C10:G17_A
9
-15.274
0.092
0.103
-0.152
8.426
1
19
A
11
A
16
-2.421
A_C11:G16_A
10
-11.329
0.474
-0.309
-0.312
-12.693
A
12
A
15
-79.759
A_U12:G15_A
11
-32.331
1.853
0.947
-4.892
2.827
44.775
A
A
1
2
16.117
A
A
27
26
2.852
12.027
-1.701
-0.939
AA_G1G2:C26C27_AA
1
-10.776
14.440
41.902
-2.219
1.349
2.738
36.706
A
A
2
3
6.352
A
A
26
25
2.856
3.993
0.281
-1.006
AA_G2C3:G25C26_AA
2
0.508
-0.808
36.492
-2.066
-0.387
2.416
48.752
A
A
3
4
32.056
A
A
25
24
3.454
25.259
0.591
-1.263
AA_C3G4:C24G25_AA
3
5.126
-6.505
41.740
-3.418
-0.333
5.154
64.938
A
A
4
6
10.901
A
A
24
22
5.563
11.653
-0.827
-2.167
AA_G4C6:G22C24_AA
4
-0.999
0.934
63.989
-2.824
0.701
2.230
31.831
A
A
6
7
19.554
A
A
22
21
2.828
10.532
0.813
-1.356
AA_C6G7:A21G22_AA
5
-0.293
0.544
30.080
-4.005
-1.525
2.643
54.117
A
A
7
8
19.163
A
A
21
19
3.799
16.928
1.325
-1.516
AA_G7C8:G19A21_AA
6
-16.478
18.653
49.043
-2.753
-2.514
2.462
39.618
A
A
8
9
21.066
A
A
19
18
3.004
13.990
-0.166
-1.037
AA_C8A9:U18G19_AA
7
1.557
-2.344
37.127
-2.946
0.403
3.116
37.244
A
A
9
10
-5.310
A
A
18
17
3.020
-3.386
0.886
-0.975
AA_A9C10:G17U18_AA
8
1.031
-1.616
37.082
-1.104
-1.258
2.632
31.939
A
A
10
11
12.105
A
A
17
16
2.930
6.610
-0.343
-1.036
AA_C10C11:G16G17_AA
9
2.117
-3.877
31.195
-2.914
0.954
2.864
101.392
A
A
11
12
9.919
A
A
16
15
2.938
15.309
0.606
-0.814
AA_C11U12:G15G16_AA
10
9.033
-5.853
100.247
-0.733
-0.269
chem_comp
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Structure summary
1
0
2001-03-14
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Eukaryotic decoding region A-site RNA, free in solution
Prokaryotic decoding region A-site RNA, bound to paromomycin
Prokaryotic decoding region A-site RNA, free in solution
RCSB
Y
RCSB
2000-10-02
REL
PAR
PAROMOMYCIN
This sequence of 18S RNA occurs in Tetrahymena thermophila
sample
structures with the least restraint violations,structures with the lowest energy
100
29
DQF-COSY
3D_15N-separated_NOESY
3D_13C-separated_NOESY
2D NOESY
10 mM
6.3
1
atm
308
K
605 NOEs, 122 dihedral constraints, and 36 hydrogen bonds
simulated annealing molecular dynamics
11
3 mM RNA, 3 mM paromomycin, 10 mM Naphosphate, pH 6.3, 13C/15N RNA
10% D2O/ 90% H2O; 100% D2O
collection
VNMR
6.1
processing
VNMR
6.1
processing
Felix
98
Brunger
refinement
X-PLOR
3.83
Brunger
structure solution
X-PLOR
3.83
500
Varian
INOVA
800
Varian
INOVA
PAR
28
2
PAR
PAR
28
A
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
U
5
n
5
U
5
A
C
6
n
6
C
6
A
G
7
n
7
G
7
A
C
8
n
8
C
8
A
A
9
n
9
A
9
A
C
10
n
10
C
10
A
C
11
n
11
C
11
A
U
12
n
12
U
12
A
U
13
n
13
U
13
A
C
14
n
14
C
14
A
G
15
n
15
G
15
A
G
16
n
16
G
16
A
G
17
n
17
G
17
A
U
18
n
18
U
18
A
G
19
n
19
G
19
A
A
20
n
20
A
20
A
A
21
n
21
A
21
A
G
22
n
22
G
22
A
U
23
n
23
U
23
A
C
24
n
24
C
24
A
G
25
n
25
G
25
A
C
26
n
26
C
26
A
C
27
n
27
C
27
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
17
A
A
HO2'
O4'
A
A
20
21
1.57
28
A
A
HO2'
O4'
A
A
20
21
1.53
EUKARYOTIC DECODING REGION A-SITE RNA-PAROMOMYCIN COMPLEX
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
27
A
N3
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
27
A
O2
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
27
A
N4
C
27
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
26
A
N3
C
26
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
26
A
O2
C
26
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
26
A
N4
C
26
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
25
A
N1
G
25
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
25
A
O6
G
25
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
25
A
N2
G
25
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
24
A
N3
C
24
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
24
A
O2
C
24
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
24
A
N4
C
24
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
A
G
22
A
N1
G
22
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
A
G
22
A
O6
G
22
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
A
G
22
A
N2
G
22
1_555
hydrog
TYPE_8_PAIR
A
G
7
A
N1
G
7
1_555
A
A
21
A
N1
A
21
1_555
hydrog
TYPE_8_PAIR
A
G
7
A
O6
G
7
1_555
A
A
21
A
N6
A
21
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
A
G
19
A
N1
G
19
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
A
G
19
A
O6
G
19
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
A
G
19
A
N2
G
19
1_555
hydrog
C-A MISPAIR
A
C
8
A
O2
C
8
1_555
A
A
20
A
N6
A
20
1_555
hydrog
WATSON-CRICK
A
A
9
A
N1
A
9
1_555
A
U
18
A
N3
U
18
1_555
hydrog
WATSON-CRICK
A
A
9
A
N6
A
9
1_555
A
U
18
A
O4
U
18
1_555
hydrog
WATSON-CRICK
A
C
10
A
N3
C
10
1_555
A
G
17
A
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
10
A
N4
C
10
1_555
A
G
17
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
10
A
O2
C
10
1_555
A
G
17
A
N2
G
17
1_555
hydrog
WATSON-CRICK
A
C
11
A
N3
C
11
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
11
A
N4
C
11
1_555
A
G
16
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
11
A
O2
C
11
1_555
A
G
16
A
N2
G
16
1_555
hydrog
U-G MISPAIR
A
U
12
A
O2
U
12
1_555
A
G
15
A
N1
G
15
1_555
RNA
RNA-paromomycin complex, aminoglycoside, stem-internal loop-stem-tetraloop, RNA-drug, G-A base pair, RNA
1FYP
PDB
1
1FYP
1
27
1FYP
1
27
1FYP
A
1
1
27
BINDING SITE FOR RESIDUE PAR A 28
A
PAR
28
Software
13
A
G
2
A
G
2
13
1_555
A
C
3
A
C
3
13
1_555
A
G
4
A
G
4
13
1_555
A
U
5
A
U
5
13
1_555
A
C
6
A
C
6
13
1_555
A
G
7
A
G
7
13
1_555
A
G
17
A
G
17
13
1_555
A
U
18
A
U
18
13
1_555
A
G
19
A
G
19
13
1_555
A
A
20
A
A
20
13
1_555
A
A
21
A
A
21
13
1_555
A
G
22
A
G
22
13
1_555
A
U
23
A
U
23
13
1_555
1
P 1