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/pdb1a4d/pdb
pdb_00001a4d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
6857.093
RNA (5'-R(*GP*GP*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*GP*UP*C)-3')
LOOP D/LOOP E ARM
1
man
polymer
6397.871
RNA (5'-R(P*UP*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*GP*CP*C)-3')
LOOP D/LOOP E ARM
1
man
polymer
no
no
GGCCGAUGGUAGUGUGGGGUC
GGCCGAUGGUAGUGUGGGGUC
A
polyribonucleotide
no
no
UCCCCAUGCGAGAGUAGGCC
UCCCCAUGCGAGAGUAGGCC
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
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
Escherichia
Escherichia
sample
CYTOPLASM
562
Escherichia coli
562
Escherichia coli
JM101
PAD3
-0.591
1
19
A
68
B
108
0.408
A_G68:C108_B
1
-3.453
-0.394
0.044
-0.250
-2.016
1
19
A
69
B
107
0.789
A_G69:C107_B
2
0.238
-0.891
-0.115
-0.446
3.121
1
19
A
70
B
106
-0.450
A_C70:G106_B
3
-0.027
0.743
-0.219
-0.371
-5.044
1
19
A
71
B
105
2.343
A_C71:G105_B
4
-5.772
0.235
-0.278
-0.248
4.084
10
11
A
72
B
104
-4.152
A_G72:A104_B
5
-1.328
6.909
0.188
-3.932
2.893
4
24
A
73
B
103
-108.004
A_A73:U103_B
6
-10.183
-3.550
-0.024
-0.999
-4.940
2
A
74
B
102
-93.929
A_U74:G102_B
7
-7.970
-4.202
-0.426
0.991
-1.294
A
75
B
101
-70.254
A_G75:A101_B
8
-2.028
-2.011
-0.091
2.182
2.719
A
76
B
100
-95.070
A_G76:G100_B
9
0.235
4.433
-0.314
0.927
2.902
4
24
A
77
B
99
-94.507
A_U77:A99_B
10
-6.526
3.991
-0.476
-1.669
3.285
9
11
A
78
B
98
0.732
A_A78:G98_B
11
-0.231
-6.756
-0.148
-4.333
-2.523
1
19
A
79
B
97
1.692
A_G79:C97_B
12
-6.682
-0.821
-0.254
-0.440
3.373
1
28
A
80
B
96
-4.522
A_U80:G96_B
13
-7.611
1.531
0.450
-0.379
-10.735
1
28
A
81
B
95
-5.652
A_G81:U95_B
14
-8.759
-1.089
-1.078
-0.736
1.555
1
20
A
82
B
94
0.644
A_U82:A94_B
15
-6.520
0.062
0.077
-0.244
5.085
1
19
A
83
B
93
-8.429
A_G83:C93_B
16
-16.711
-0.397
0.888
-0.751
-0.547
1
19
A
84
B
92
-0.045
A_G84:C92_B
17
-9.958
-0.344
-0.065
-0.263
-6.985
1
19
A
85
B
91
1.452
A_G85:C91_B
18
-5.107
-0.979
-0.046
-0.450
-10.354
1
A
86
B
90
53.777
A_G86:C90_B
19
6.472
0.842
-1.196
2.197
2.297
40.553
A
A
68
69
21.834
B
B
108
107
3.083
14.809
0.173
-1.655
AA_G68G69:C107C108_BB
1
-1.261
1.859
37.839
-3.798
-0.370
2.505
39.013
A
A
69
70
29.856
B
B
107
106
3.111
19.135
-0.072
-0.480
AA_G69C70:G106C107_BB
2
0.938
-1.463
34.145
-2.849
0.212
2.491
37.523
A
A
70
71
20.531
B
B
106
105
3.312
12.950
0.205
-1.903
AA_C70C71:G105G106_BB
3
1.589
-2.518
35.259
-4.510
-0.128
3.053
60.092
A
A
71
72
8.776
B
B
105
104
3.078
8.763
-0.457
0.038
AA_C71G72:A104G105_BB
4
0.344
-0.345
59.508
-0.369
0.472
-1.285
-14.665
A
A
72
73
11.322
B
B
104
103
2.889
-2.700
-6.189
-0.634
AA_G72A73:U103A104_BB
5
-8.307
-34.839
-11.791
3.123
-26.214
2.759
57.445
A
A
73
74
9.758
B
B
103
102
3.276
9.343
0.836
-3.323
AA_A73U74:G102U103_BB
6
1.206
-1.259
56.732
-3.928
-0.809
3.080
39.558
A
A
74
75
-1.451
B
B
102
101
3.015
-0.982
1.252
-2.253
AA_U74G75:A101G102_BB
7
0.414
-0.611
39.545
-3.222
-1.804
3.247
59.722
A
A
75
76
0.584
B
B
101
100
3.277
0.582
-0.551
-2.712
AA_G75G76:G100A101_BB
8
0.684
-0.686
59.716
-2.753
0.588
3.378
46.043
A
A
76
77
-5.261
B
B
100
99
3.128
-4.102
-0.775
-2.322
AA_G76U77:A99G100_BB
9
-5.289
6.784
45.580
-2.616
0.536
3.466
-18.664
A
A
77
78
-6.764
B
B
99
98
3.134
2.188
5.491
-0.933
AA_U77A78:G98A99_BB
10
-0.850
-2.629
-18.517
1.688
16.472
3.166
66.009
A
A
78
79
6.608
B
B
98
97
3.250
7.182
-0.202
-0.777
AA_A78G79:C97G98_BB
11
-4.862
4.473
65.501
-0.999
-0.008
3.086
43.556
A
A
79
80
2.900
B
B
97
96
3.117
2.151
-0.366
-0.659
AA_G79U80:G96C97_BB
12
-0.393
0.530
43.503
-1.084
0.457
4.080
20.093
A
A
80
81
-15.964
B
B
96
95
4.025
-5.390
-0.418
-2.192
AA_U80G81:U95G96_BB
13
6.803
-20.149
18.139
-3.037
5.296
2.953
40.962
A
A
81
82
-9.041
B
B
95
94
2.976
-6.271
0.374
-0.822
AA_G81U82:A94U95_BB
14
-7.467
10.765
39.833
-0.543
-1.285
3.014
29.988
A
A
82
83
-1.116
B
B
94
93
2.933
-0.576
-0.620
-1.524
AA_U82G83:C93A94_BB
15
-3.710
7.189
29.757
-2.837
0.500
3.910
33.906
A
A
83
84
-14.058
B
B
93
92
3.637
-8.108
0.415
-1.501
AA_G83G84:C92C93_BB
16
3.638
-6.307
32.754
-1.043
-0.026
4.036
29.150
A
A
84
85
-17.966
B
B
92
91
3.695
-8.887
0.275
-1.872
AA_G84G85:C91C92_BB
17
-3.079
6.224
27.622
-1.362
-1.363
3.514
34.895
A
A
85
86
10.933
B
B
91
90
3.463
6.503
2.655
-1.076
AA_G85G86:C90C91_BB
18
4.462
-7.502
34.019
-2.860
-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
1998-04-29
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
ENSEMBLE OF 9 STRUCTURES
Y
BNL
1998-01-29
REL
REL
NO NOE, DIHEDRAL VIOLATIONS, LOW OVERALL ENERGY STRUCTURES, GOOD LOCAL GEOMETRY
60
1
7.2
283
K
5.5
283
K
FOR REFINEMENT DETAILS, SEE JRNL REFERENCE ABOVE.
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
1
U
89
B
C
90
n
2
C
90
B
C
91
n
3
C
91
B
C
92
n
4
C
92
B
C
93
n
5
C
93
B
A
94
n
6
A
94
B
U
95
n
7
U
95
B
G
96
n
8
G
96
B
C
97
n
9
C
97
B
G
98
n
10
G
98
B
A
99
n
11
A
99
B
G
100
n
12
G
100
B
A
101
n
13
A
101
B
G
102
n
14
G
102
B
U
103
n
15
U
103
B
A
104
n
16
A
104
B
G
105
n
17
G
105
B
G
106
n
18
G
106
B
C
107
n
19
C
107
B
C
108
n
20
C
108
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
A
B
O4
H1
U
G
74
102
1.39
1
A
B
O3'
P
C
U
88
89
1.61
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
LOOP D/LOOP E ARM OF ESCHERICHIA COLI 5S RRNA, NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
68
A
N1
G
1
1_555
B
C
108
B
N3
C
20
1_555
hydrog
WATSON-CRICK
A
G
68
A
N2
G
1
1_555
B
C
108
B
O2
C
20
1_555
hydrog
WATSON-CRICK
A
G
68
A
O6
G
1
1_555
B
C
108
B
N4
C
20
1_555
hydrog
WATSON-CRICK
A
G
69
A
N1
G
2
1_555
B
C
107
B
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
69
A
N2
G
2
1_555
B
C
107
B
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
69
A
O6
G
2
1_555
B
C
107
B
N4
C
19
1_555
hydrog
WATSON-CRICK
A
C
70
A
N3
C
3
1_555
B
G
106
B
N1
G
18
1_555
hydrog
WATSON-CRICK
A
C
70
A
N4
C
3
1_555
B
G
106
B
O6
G
18
1_555
hydrog
WATSON-CRICK
A
C
70
A
O2
C
3
1_555
B
G
106
B
N2
G
18
1_555
hydrog
WATSON-CRICK
A
C
71
A
N3
C
4
1_555
B
G
105
B
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
71
A
N4
C
4
1_555
B
G
105
B
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
71
A
O2
C
4
1_555
B
G
105
B
N2
G
17
1_555
hydrog
TYPE_11_PAIR
A
G
72
A
N2
G
5
1_555
B
A
104
B
N7
A
16
1_555
hydrog
TYPE_11_PAIR
A
G
72
A
N3
G
5
1_555
B
A
104
B
N6
A
16
1_555
hydrog
REVERSED HOOGSTEEN
A
A
73
A
N6
A
6
1_555
B
U
103
B
O2
U
15
1_555
hydrog
REVERSED HOOGSTEEN
A
A
73
A
N7
A
6
1_555
B
U
103
B
N3
U
15
1_555
hydrog
U-G MISPAIR
A
U
74
A
O4
U
7
1_555
B
G
102
B
N1
G
14
1_555
hydrog
G-A MISPAIR
A
G
75
A
O6
G
8
1_555
B
A
101
B
N6
A
13
1_555
hydrog
G-G MISPAIR
A
G
76
A
N1
G
9
1_555
B
G
100
B
O6
G
12
1_555
hydrog
REVERSED HOOGSTEEN
A
U
77
A
N3
U
10
1_555
B
A
99
B
N7
A
11
1_555
hydrog
REVERSED HOOGSTEEN
A
U
77
A
O2
U
10
1_555
B
A
99
B
N6
A
11
1_555
hydrog
TYPE_11_PAIR
A
A
78
A
N6
A
11
1_555
B
G
98
B
N3
G
10
1_555
hydrog
TYPE_11_PAIR
A
A
78
A
N7
A
11
1_555
B
G
98
B
N2
G
10
1_555
hydrog
WATSON-CRICK
A
G
79
A
N1
G
12
1_555
B
C
97
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
79
A
N2
G
12
1_555
B
C
97
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
79
A
O6
G
12
1_555
B
C
97
B
N4
C
9
1_555
hydrog
TYPE_28_PAIR
A
U
80
A
N3
U
13
1_555
B
G
96
B
O6
G
8
1_555
hydrog
TYPE_28_PAIR
A
U
80
A
O2
U
13
1_555
B
G
96
B
N1
G
8
1_555
hydrog
TYPE_28_PAIR
A
G
81
A
N1
G
14
1_555
B
U
95
B
O2
U
7
1_555
hydrog
TYPE_28_PAIR
A
G
81
A
O6
G
14
1_555
B
U
95
B
N3
U
7
1_555
hydrog
WATSON-CRICK
A
U
82
A
N3
U
15
1_555
B
A
94
B
N1
A
6
1_555
hydrog
WATSON-CRICK
A
U
82
A
O4
U
15
1_555
B
A
94
B
N6
A
6
1_555
hydrog
WATSON-CRICK
A
G
83
A
N1
G
16
1_555
B
C
93
B
N3
C
5
1_555
hydrog
WATSON-CRICK
A
G
83
A
N2
G
16
1_555
B
C
93
B
O2
C
5
1_555
hydrog
WATSON-CRICK
A
G
83
A
O6
G
16
1_555
B
C
93
B
N4
C
5
1_555
hydrog
WATSON-CRICK
A
G
84
A
N1
G
17
1_555
B
C
92
B
N3
C
4
1_555
hydrog
WATSON-CRICK
A
G
84
A
N2
G
17
1_555
B
C
92
B
O2
C
4
1_555
hydrog
WATSON-CRICK
A
G
84
A
O6
G
17
1_555
B
C
92
B
N4
C
4
1_555
hydrog
WATSON-CRICK
A
G
85
A
N1
G
18
1_555
B
C
91
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
85
A
N2
G
18
1_555
B
C
91
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
85
A
O6
G
18
1_555
B
C
91
B
N4
C
3
1_555
hydrog
G-C PAIR
A
G
86
A
N2
G
19
1_555
B
C
90
B
O2
C
2
1_555
RNA
5S RRNA, INTERNAL LOOP, CROSS-STRAND STACK, TRANSLATION, RIBOSOME, RIBOSOMAL RNA COMPLEX, RNA
1A4D
PDB
1
1A4D
1A4D
PDB
2
1A4D
68
88
1A4D
68
88
1A4D
A
1
1
21
89
108
1A4D
89
108
1A4D
B
2
1
20
1
P 1