1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Dallas, A.
Moore, P.B.
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
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
UK
Structure
STRUE6
2005
0969-2126
5
1639
1653
10.1016/S0969-2126(97)00311-0
9438864
The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins.
1997
10.2210/pdb1a51/pdb
pdb_00001a51
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
13299.919
5S RRNA LOOP D/LOOP E
LOOP D/LOOP E ARM
1
man
polymer
no
no
GGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGCC
GGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGCC
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Escherichia
Escherichia
sample
CYTOPLASM
562
Escherichia coli
562
Escherichia coli
JM101
PAD3
-0.600
1
19
A
68
A
108
0.410
A_G68:C108_A
1
-3.479
-0.394
0.043
-0.250
-2.016
1
19
A
69
A
107
0.791
A_G69:C107_A
2
0.245
-0.892
-0.115
-0.447
3.116
1
19
A
70
A
106
-0.448
A_C70:G106_A
3
-0.027
0.743
-0.219
-0.371
-5.038
1
19
A
71
A
105
2.351
A_C71:G105_A
4
-5.757
0.236
-0.279
-0.248
4.080
10
11
A
72
A
104
-4.157
A_G72:A104_A
5
-1.333
6.909
0.188
-3.933
2.884
4
24
A
73
A
103
-108.003
A_A73:U103_A
6
-10.184
-3.550
-0.023
-1.000
-4.942
2
A
74
A
102
-93.930
A_U74:G102_A
7
-7.955
-4.202
-0.425
0.992
-1.291
A
75
A
101
-70.262
A_G75:A101_A
8
-2.036
-2.011
-0.092
2.182
2.725
A
76
A
100
-95.071
A_G76:G100_A
9
0.241
4.433
-0.314
0.927
2.904
4
24
A
77
A
99
-94.504
A_U77:A99_A
10
-6.535
3.991
-0.477
-1.669
3.284
9
11
A
78
A
98
0.735
A_A78:G98_A
11
-0.220
-6.757
-0.148
-4.333
-2.535
1
19
A
79
A
97
1.697
A_G79:C97_A
12
-6.681
-0.822
-0.254
-0.440
3.385
1
28
A
80
A
96
-4.524
A_U80:G96_A
13
-7.621
1.531
0.450
-0.379
-10.725
1
28
A
81
A
95
-5.646
A_G81:U95_A
14
-8.760
-1.089
-1.078
-0.736
1.559
1
20
A
82
A
94
0.642
A_U82:A94_A
15
-6.516
0.062
0.077
-0.244
5.084
1
19
A
83
A
93
-8.434
A_G83:C93_A
16
-16.718
-0.397
0.888
-0.751
-0.551
1
19
A
84
A
92
-0.041
A_G84:C92_A
17
-9.955
-0.344
-0.066
-0.263
-6.994
1
19
A
85
A
91
1.449
A_G85:C91_A
18
-5.108
-0.979
-0.046
-0.450
-10.347
1
A
86
A
90
53.777
A_G86:C90_A
19
6.482
0.842
-1.197
2.197
2.298
40.541
A
A
68
69
21.820
A
A
108
107
3.083
14.795
0.173
-1.654
AA_G68G69:C107C108_AA
1
-1.258
1.855
37.831
-3.798
-0.369
2.505
39.020
A
A
69
70
29.860
A
A
107
106
3.111
19.141
-0.072
-0.480
AA_G69C70:G106C107_AA
2
0.935
-1.459
34.150
-2.848
0.211
2.490
37.526
A
A
70
71
20.535
A
A
106
105
3.311
12.953
0.205
-1.903
AA_C70C71:G105G106_AA
3
1.590
-2.520
35.260
-4.510
-0.128
3.053
60.089
A
A
71
72
8.774
A
A
105
104
3.078
8.760
-0.457
0.039
AA_C71G72:A104G105_AA
4
0.343
-0.343
59.505
-0.369
0.473
-1.284
-14.669
A
A
72
73
11.314
A
A
104
103
2.889
-2.698
-6.189
-0.634
AA_G72A73:U103A104_AA
5
-8.309
-34.835
-11.795
3.121
-26.207
2.759
57.445
A
A
73
74
9.758
A
A
103
102
3.276
9.344
0.836
-3.323
AA_A73U74:G102U103_AA
6
1.201
-1.254
56.733
-3.928
-0.809
3.080
39.561
A
A
74
75
-1.453
A
A
102
101
3.014
-0.983
1.251
-2.254
AA_U74G75:A101G102_AA
7
0.415
-0.614
39.548
-3.222
-1.804
3.247
59.720
A
A
75
76
0.578
A
A
101
100
3.277
0.575
-0.551
-2.712
AA_G75G76:G100A101_AA
8
0.688
-0.691
59.714
-2.752
0.588
3.378
46.046
A
A
76
77
-5.261
A
A
100
99
3.128
-4.102
-0.774
-2.322
AA_G76U77:A99G100_AA
9
-5.294
6.790
45.583
-2.616
0.535
3.465
-18.668
A
A
77
78
-6.779
A
A
99
98
3.134
2.193
5.492
-0.932
AA_U77A78:G98A99_AA
10
-0.845
-2.613
-18.521
1.685
16.471
3.166
66.009
A
A
78
79
6.612
A
A
98
97
3.251
7.187
-0.202
-0.777
AA_A78G79:C97G98_AA
11
-4.869
4.479
65.500
-0.999
-0.009
3.085
43.556
A
A
79
80
2.892
A
A
97
96
3.116
2.145
-0.366
-0.659
AA_G79U80:G96C97_AA
12
-0.390
0.526
43.504
-1.084
0.458
4.080
20.091
A
A
80
81
-15.935
A
A
96
95
4.025
-5.380
-0.418
-2.192
AA_U80G81:U95G96_AA
13
6.797
-20.132
18.142
-3.043
5.293
2.953
40.961
A
A
81
82
-9.048
A
A
95
94
2.976
-6.276
0.374
-0.821
AA_G81U82:A94U95_AA
14
-7.470
10.770
39.831
-0.543
-1.285
3.015
29.992
A
A
82
83
-1.113
A
A
94
93
2.933
-0.574
-0.620
-1.524
AA_U82G83:C93A94_AA
15
-3.711
7.189
29.762
-2.837
0.500
3.910
33.901
A
A
83
84
-14.068
A
A
93
92
3.638
-8.113
0.416
-1.500
AA_G83G84:C92C93_AA
16
3.641
-6.314
32.748
-1.041
-0.025
4.036
29.153
A
A
84
85
-17.953
A
A
92
91
3.695
-8.882
0.275
-1.871
AA_G84G85:C91C92_AA
17
-3.083
6.232
27.627
-1.363
-1.364
3.514
34.892
A
A
85
86
10.923
A
A
91
90
3.463
6.497
2.655
-1.076
AA_G85G86:C90C91_AA
18
4.463
-7.504
34.017
-2.859
-3.697
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1998-05-27
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
MINIMIZED AVERAGE STRUCTURE
Y
BNL
1998-02-19
REL
REL
NO NOE, DIHEDRAL VIOLATIONS, LOW OVERALL ENERGY STRUCTURES, GOOD LOCAL GEOMETRY
60
9
7.2
283
K
5.5
283
K
FOR REFINEMENT DETAILS, SEE STRUCTURE,5,P.1639
TORSION ANGLE MOLECULAR DYNAMICS
BRUNGER
refinement
X-PLOR
structure solution
X-PLOR
500
Varian
UNITY
600
GE
UNITYPLUS
600
GE
OMEGA
G
68
n
1
G
68
A
G
69
n
2
G
69
A
C
70
n
3
C
70
A
C
71
n
4
C
71
A
G
72
n
5
G
72
A
A
73
n
6
A
73
A
U
74
n
7
U
74
A
G
75
n
8
G
75
A
G
76
n
9
G
76
A
U
77
n
10
U
77
A
A
78
n
11
A
78
A
G
79
n
12
G
79
A
U
80
n
13
U
80
A
G
81
n
14
G
81
A
U
82
n
15
U
82
A
G
83
n
16
G
83
A
G
84
n
17
G
84
A
G
85
n
18
G
85
A
G
86
n
19
G
86
A
U
87
n
20
U
87
A
C
88
n
21
C
88
A
U
89
n
22
U
89
A
C
90
n
23
C
90
A
C
91
n
24
C
91
A
C
92
n
25
C
92
A
C
93
n
26
C
93
A
A
94
n
27
A
94
A
U
95
n
28
U
95
A
G
96
n
29
G
96
A
C
97
n
30
C
97
A
G
98
n
31
G
98
A
A
99
n
32
A
99
A
G
100
n
33
G
100
A
A
101
n
34
A
101
A
G
102
n
35
G
102
A
U
103
n
36
U
103
A
A
104
n
37
A
104
A
G
105
n
38
G
105
A
G
106
n
39
G
106
A
C
107
n
40
C
107
A
C
108
n
41
C
108
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
1
A
A
O4
H1
U
G
74
102
1.39
2
A
A
O4
H1
U
G
74
102
1.50
3
A
A
O4
H1
U
G
74
102
1.40
4
A
A
O4
H1
U
G
74
102
1.47
5
A
A
O4
H1
U
G
74
102
1.51
6
A
A
O4
H1
U
G
74
102
1.43
7
A
A
O4
H1
U
G
74
102
1.43
8
A
A
HO2'
O2
C
C
88
90
1.57
9
A
A
O4
H1
U
G
74
102
1.41
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
LOOP D/LOOP E ARM OF E. COLI 5S RRNA, NMR, 9 STRUCTURES
1
N
N
hydrog
WATSON-CRICK
A
G
68
A
N1
G
1
1_555
A
C
108
A
N3
C
41
1_555
hydrog
WATSON-CRICK
A
G
68
A
N2
G
1
1_555
A
C
108
A
O2
C
41
1_555
hydrog
WATSON-CRICK
A
G
68
A
O6
G
1
1_555
A
C
108
A
N4
C
41
1_555
hydrog
WATSON-CRICK
A
G
69
A
N1
G
2
1_555
A
C
107
A
N3
C
40
1_555
hydrog
WATSON-CRICK
A
G
69
A
N2
G
2
1_555
A
C
107
A
O2
C
40
1_555
hydrog
WATSON-CRICK
A
G
69
A
O6
G
2
1_555
A
C
107
A
N4
C
40
1_555
hydrog
WATSON-CRICK
A
C
70
A
N3
C
3
1_555
A
G
106
A
N1
G
39
1_555
hydrog
WATSON-CRICK
A
C
70
A
N4
C
3
1_555
A
G
106
A
O6
G
39
1_555
hydrog
WATSON-CRICK
A
C
70
A
O2
C
3
1_555
A
G
106
A
N2
G
39
1_555
hydrog
WATSON-CRICK
A
C
71
A
N3
C
4
1_555
A
G
105
A
N1
G
38
1_555
hydrog
WATSON-CRICK
A
C
71
A
N4
C
4
1_555
A
G
105
A
O6
G
38
1_555
hydrog
WATSON-CRICK
A
C
71
A
O2
C
4
1_555
A
G
105
A
N2
G
38
1_555
hydrog
TYPE_11_PAIR
A
G
72
A
N2
G
5
1_555
A
A
104
A
N7
A
37
1_555
hydrog
TYPE_11_PAIR
A
G
72
A
N3
G
5
1_555
A
A
104
A
N6
A
37
1_555
hydrog
REVERSED HOOGSTEEN
A
A
73
A
N6
A
6
1_555
A
U
103
A
O2
U
36
1_555
hydrog
REVERSED HOOGSTEEN
A
A
73
A
N7
A
6
1_555
A
U
103
A
N3
U
36
1_555
hydrog
U-G MISPAIR
A
U
74
A
O4
U
7
1_555
A
G
102
A
N1
G
35
1_555
hydrog
G-A MISPAIR
A
G
75
A
O6
G
8
1_555
A
A
101
A
N6
A
34
1_555
hydrog
G-G MISPAIR
A
G
76
A
N1
G
9
1_555
A
G
100
A
O6
G
33
1_555
hydrog
REVERSED HOOGSTEEN
A
U
77
A
N3
U
10
1_555
A
A
99
A
N7
A
32
1_555
hydrog
REVERSED HOOGSTEEN
A
U
77
A
O2
U
10
1_555
A
A
99
A
N6
A
32
1_555
hydrog
TYPE_11_PAIR
A
A
78
A
N6
A
11
1_555
A
G
98
A
N3
G
31
1_555
hydrog
TYPE_11_PAIR
A
A
78
A
N7
A
11
1_555
A
G
98
A
N2
G
31
1_555
hydrog
WATSON-CRICK
A
G
79
A
N1
G
12
1_555
A
C
97
A
N3
C
30
1_555
hydrog
WATSON-CRICK
A
G
79
A
N2
G
12
1_555
A
C
97
A
O2
C
30
1_555
hydrog
WATSON-CRICK
A
G
79
A
O6
G
12
1_555
A
C
97
A
N4
C
30
1_555
hydrog
TYPE_28_PAIR
A
U
80
A
N3
U
13
1_555
A
G
96
A
O6
G
29
1_555
hydrog
TYPE_28_PAIR
A
U
80
A
O2
U
13
1_555
A
G
96
A
N1
G
29
1_555
hydrog
TYPE_28_PAIR
A
G
81
A
N1
G
14
1_555
A
U
95
A
O2
U
28
1_555
hydrog
TYPE_28_PAIR
A
G
81
A
O6
G
14
1_555
A
U
95
A
N3
U
28
1_555
hydrog
WATSON-CRICK
A
U
82
A
N3
U
15
1_555
A
A
94
A
N1
A
27
1_555
hydrog
WATSON-CRICK
A
U
82
A
O4
U
15
1_555
A
A
94
A
N6
A
27
1_555
hydrog
WATSON-CRICK
A
G
83
A
N1
G
16
1_555
A
C
93
A
N3
C
26
1_555
hydrog
WATSON-CRICK
A
G
83
A
N2
G
16
1_555
A
C
93
A
O2
C
26
1_555
hydrog
WATSON-CRICK
A
G
83
A
O6
G
16
1_555
A
C
93
A
N4
C
26
1_555
hydrog
WATSON-CRICK
A
G
84
A
N1
G
17
1_555
A
C
92
A
N3
C
25
1_555
hydrog
WATSON-CRICK
A
G
84
A
N2
G
17
1_555
A
C
92
A
O2
C
25
1_555
hydrog
WATSON-CRICK
A
G
84
A
O6
G
17
1_555
A
C
92
A
N4
C
25
1_555
hydrog
WATSON-CRICK
A
G
85
A
N1
G
18
1_555
A
C
91
A
N3
C
24
1_555
hydrog
WATSON-CRICK
A
G
85
A
N2
G
18
1_555
A
C
91
A
O2
C
24
1_555
hydrog
WATSON-CRICK
A
G
85
A
O6
G
18
1_555
A
C
91
A
N4
C
24
1_555
hydrog
G-C PAIR
A
G
86
A
N2
G
19
1_555
A
C
90
A
O2
C
23
1_555
RNA
5S RRNA, INTERNAL LOOP, CROSS-STRAND STACK, TRANSLATION, RIBOSOME, RIBONUCLEIC ACID, RNA
1A51
PDB
1
1A51
68
108
1A51
68
108
1A51
A
1
1
41
1
P 1