1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Sundaram, M.
Durant, P.C.
Davis, D.R.
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
n
PSEUDOURIDINE-5'-MONOPHOSPHATE
RNA linking
C15 H21 N6 O11 P
492.335
n
N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5'-MONOPHOSPHATE
N-(NEBULARIN-6-YLCARBAMOYL)-L-THREONINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
C11 H18 N3 O8 P S
383.315
n
5-METHYLAMINOMETHYL-2-THIOURIDINE-5'-MONOPHOSPHATE
RNA linking
US
Biochemistry
BICHAW
0033
0006-2960
39
12575
12584
10.1021/bi0014655
11027137
Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure.
2000
10.2210/pdb1fl8/pdb
pdb_00001fl8
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
RESIDUES 30-40 (TRNA NUMBERING) ARE IDENTICAL TO THOSE FOUND IN THE ANTICODON DOMAIN OF E. COLI TRNA(LYS) INCLUDING MODIFIED NUCLEOSIDES
5554.438
ANTICODON DOMAIN OF TRNA(LYS)
17-MER TRNA(LYS) ANTICODON DOMAIN
G27U, U28C, U29A, A41U, A42G, U43A
1
syn
polymer
no
yes
UCAGACU(U8U)UU(T6A)A(PSU)CUGA
UCAGACUUUUAAUCUGA
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-1.839
1
20
A
27
A
43
3.402
A_U27:A43_A
1
-11.710
0.651
-0.767
0.183
-2.299
1
19
A
28
A
42
-3.618
A_C28:G42_A
2
-21.698
-0.727
0.228
-0.170
0.130
1
20
A
29
A
41
-3.002
A_A29:U41_A
3
-18.295
0.820
0.187
-0.092
-12.282
1
19
A
30
A
40
-1.543
A_G30:C40_A
4
-25.398
0.640
-0.447
-0.168
-20.718
1
21
A
31
A
39
-18.979
A_A31:PSU39_A
5
-25.768
1.408
0.206
-0.158
2.953
25.617
A
A
27
28
22.482
A
A
43
42
3.758
9.682
-0.562
-1.536
AA_U27C28:G42A43_AA
1
-4.150
9.636
23.384
-6.411
0.004
2.837
38.272
A
A
28
29
19.782
A
A
42
41
3.401
12.740
0.113
-1.188
AA_C28A29:U41G42_AA
2
-0.219
0.339
36.164
-3.385
-0.199
3.484
31.866
A
A
29
30
18.831
A
A
41
40
4.189
10.119
0.128
-1.479
AA_A29G30:C40U41_AA
3
5.364
-9.983
29.787
-4.935
0.955
3.300
37.958
A
A
30
31
19.612
A
A
40
39
3.919
12.526
-0.863
-1.433
AA_G30A31:PSU39C40_AA
4
-2.248
3.520
35.835
-4.024
1.001
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-10-16
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
the same anticodon loop sequence but without modified nucleosides at position 34 and 37. Pseudouridine is present at postion 39
the same anticodon loop sequence but without modified nucleosides at position 34, 37 or 39
RCSB
Y
RCSB
2000-08-11
REL
REL
This structure was determined using standard 2D homonuclear techniques and standard 1H-31P 2D correlation experiments.
structures with the lowest energy
35
20
2D NOESY
2D NOESY
DQF-COSY
1H-31P-COSY
1H-31P-hetero-TOCSY-TOCSY
120mM
7
ambient
285
K
120mM
7
ambient
303
K
123 NOE-derived restraints, 15 hydrogen bond restraints, 102 lower/upper bound restraints, 161 dihedral restraints, 68 chiral restraints
used H5-H6 distances for distance calculations then simulated annealing/molecular dynamics in vacuo then restrained minimization in vacuo
4
closest to the average,lowest energy
1.5mM natural abundance RNA; 10mM phosphate buffer; 50mM KCl; 50mM NaCl; 10mM MgCl2
90% H2O/10% D2O
1.5mM natural abundance RNA; 10mM phosphate buffer; 50mM KCl; 50mM NaCl; 10mM MgCl2
99.99% D2O
Varian
collection
VNMR
6.1B
Varian
processing
VNMR
6.1B
Varian
data analysis
VNMR
6.1B
MSI
processing
Felix
MSI
data analysis
Felix
MSI
structure solution
Discover
MSI
refinement
Discover
600
Varian
UNITYPLUS
500
Varian
UNITY
U
27
n
1
U
27
A
C
28
n
2
C
28
A
A
29
n
3
A
29
A
G
30
n
4
G
30
A
A
31
n
5
A
31
A
C
32
n
6
C
32
A
U
33
n
7
U
33
A
U8U
34
n
8
U8U
34
A
U
35
n
9
U
35
A
U
36
n
10
U
36
A
T6A
37
n
11
T6A
37
A
A
38
n
12
A
38
A
PSU
39
n
13
PSU
39
A
C
40
n
14
C
40
A
U
41
n
15
U
41
A
G
42
n
16
G
42
A
A
43
n
17
A
43
A
author_defined_assembly
1
monomeric
A
U8U
34
A
U8U
8
U
A
T6A
37
A
T6A
11
A
A
PSU
39
PSEUDOURIDINE-5'-MONOPHOSPHATE
A
PSU
13
U
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
4.21
0.70
108.50
112.71
A
A
A
O4'
C1'
N1
C
C
C
32
32
32
N
1
-7.55
1.20
119.70
112.15
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
2
-7.64
1.20
119.70
112.06
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
3
-7.49
1.20
119.70
112.21
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
4
-7.51
1.20
119.70
112.19
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
5
-7.32
1.20
119.70
112.38
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
6
-7.53
1.20
119.70
112.17
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
7
4.25
0.70
108.50
112.75
A
A
A
O4'
C1'
N1
C
C
C
32
32
32
N
7
-7.33
1.20
119.70
112.37
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
8
-7.41
1.20
119.70
112.29
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
9
-7.51
1.20
119.70
112.19
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
10
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N1
C
C
C
32
32
32
N
10
-7.40
1.20
119.70
112.30
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
10
-7.21
1.20
119.70
112.49
A
A
A
C3'
O3'
P
PSU
PSU
C
39
39
40
Y
11
4.25
0.70
108.50
112.75
A
A
A
O4'
C1'
N1
C
C
C
32
32
32
N
11
-7.66
1.20
119.70
112.04
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
12
-7.41
1.20
119.70
112.29
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
13
-7.61
1.20
119.70
112.09
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
14
-7.56
1.20
119.70
112.14
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
15
4.20
0.70
108.50
112.70
A
A
A
O4'
C1'
N1
U
U
U
33
33
33
N
16
-7.52
1.20
119.70
112.18
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
17
-7.50
1.20
119.70
112.20
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
18
-7.42
1.20
119.70
112.28
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
19
-7.51
1.20
119.70
112.19
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
20
-7.54
1.20
119.70
112.16
A
A
A
C3'
O3'
P
U8U
U8U
U
34
34
35
Y
HYPERMODIFIED NUCLEOSIDES IN THE ANTICODON OF TRNALYS STABILIZE A CANONICAL U-TURN STRUCTURE
1
N
N
covale
1.612
both
A
U
33
A
O3'
U
7
1_555
A
U8U
34
A
P
U8U
8
1_555
covale
1.621
both
A
U8U
34
A
O3'
U8U
8
1_555
A
U
35
A
P
U
9
1_555
covale
1.615
both
A
U
36
A
O3'
U
10
1_555
A
T6A
37
A
P
T6A
11
1_555
covale
1.624
both
A
T6A
37
A
O3'
T6A
11
1_555
A
A
38
A
P
A
12
1_555
covale
1.615
both
A
A
38
A
O3'
A
12
1_555
A
PSU
39
A
P
PSU
13
1_555
covale
1.622
both
A
PSU
39
A
O3'
PSU
13
1_555
A
C
40
A
P
C
14
1_555
hydrog
WATSON-CRICK
A
U
27
A
N3
U
1
1_555
A
A
43
A
N1
A
17
1_555
hydrog
WATSON-CRICK
A
U
27
A
O4
U
1
1_555
A
A
43
A
N6
A
17
1_555
hydrog
WATSON-CRICK
A
C
28
A
N3
C
2
1_555
A
G
42
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
28
A
N4
C
2
1_555
A
G
42
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
28
A
O2
C
2
1_555
A
G
42
A
N2
G
16
1_555
hydrog
WATSON-CRICK
A
A
29
A
N1
A
3
1_555
A
U
41
A
N3
U
15
1_555
hydrog
WATSON-CRICK
A
A
29
A
N6
A
3
1_555
A
U
41
A
O4
U
15
1_555
hydrog
WATSON-CRICK
A
G
30
A
N1
G
4
1_555
A
C
40
A
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
30
A
N2
G
4
1_555
A
C
40
A
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
30
A
O6
G
4
1_555
A
C
40
A
N4
C
14
1_555
hydrog
REVERSED WATSON-CRICK
A
A
31
A
N1
A
5
1_555
A
PSU
39
A
N3
PSU
13
1_555
hydrog
REVERSED WATSON-CRICK
A
A
31
A
N6
A
5
1_555
A
PSU
39
A
O2
PSU
13
1_555
RNA
tRNA, anticodon, pseudouridine, mnm5s2U, t6a, RNA
1FL8
PDB
1
1FL8
27
43
1FL8
27
43
1FL8
A
1
1
17
1
P 1