1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Volk, D.E.
Yang, X.
Fennewald, S.M.
King, D.J.
Bassett, S.E.
Venkitachalam, S.
Herzog, N.
Luxon, B.A.
Gorenstein, D.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C9 H14 N3 O5 P S2
339.328
n
CYTIDINE-5'-DITHIOPHOSPHORATE
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
US
Bioorg.Chem.
BOCMBM
0368
0045-2068
30
396
419
10.1016/S0045-2068(02)00510-2
12642125
Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB
2002
10.2210/pdb1k8n/pdb
pdb_00001k8n
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1
4249.781
FIRST STRAND OF CK14 DNA DUPLEX
1
syn
polymer
CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1
4376.063
SECOND STRAND OF CK14 DNA DUPLEX
DITHIOATED AT C22 and C24
DITHIOATED AT C22 and C24
1
syn
polymer
no
no
(DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DT)(DT)(DC)(DC)(DA)(DC)
CCAGGAGATTCCAC
A
polydeoxyribonucleotide
no
yes
(DG)(DT)(DG)(DG)(DA)(DA)(DT)(C2S)(DT)(C2S)(DC)(DT)(DG)(DG)
GTGGAATCTCCTGG
B
polydeoxyribonucleotide
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
33.540
1
19
A
1
B
28
1.266
A_DC1:DG28_B
1
-17.943
0.650
-0.607
-0.140
3.532
1
19
A
2
B
27
-1.320
A_DC2:DG27_B
2
8.410
0.386
-0.315
-0.226
-2.377
1
20
A
3
B
26
-5.926
A_DA3:DT26_B
3
-1.949
0.412
-0.282
-0.015
11.403
1
19
A
4
B
25
0.826
A_DG4:DC25_B
4
0.047
-0.447
-0.063
-0.211
17.891
1
19
A
5
B
24
-0.719
A_DG5:C2S24_B
5
4.489
-0.302
0.291
-0.145
17.601
1
20
A
6
B
23
1.959
A_DA6:DT23_B
6
-13.297
0.043
-0.219
-0.143
2.674
1
19
A
7
B
22
-0.823
A_DG7:C2S22_B
7
-4.831
-0.294
-0.138
-0.197
4.209
1
20
A
8
B
21
-2.042
A_DA8:DT21_B
8
-11.873
0.073
0.083
-0.109
-1.331
1
20
A
9
B
20
-4.791
A_DT9:DA20_B
9
-12.268
-0.166
0.039
-0.094
-0.607
1
20
A
10
B
19
-2.865
A_DT10:DA19_B
10
-12.855
-0.183
-0.198
-0.099
-8.160
1
19
A
11
B
18
-0.723
A_DC11:DG18_B
11
-3.718
0.338
-0.055
-0.211
-6.008
1
19
A
12
B
17
-0.014
A_DC12:DG17_B
12
-1.402
0.384
0.175
-0.206
4.726
1
20
A
13
B
16
-1.609
A_DA13:DT16_B
13
-6.327
0.108
0.058
-0.115
0.610
1
19
A
14
B
15
-0.040
A_DC14:DG15_B
14
-4.148
0.507
0.207
-0.240
6.124
38.049
A
A
1
2
-3.331
B
B
28
27
6.281
-2.156
0.473
-1.336
AA_DC1DC2:DG27DG28_BB
1
-7.874
12.165
37.194
-1.523
-2.645
3.700
33.783
A
A
2
3
-5.661
B
B
27
26
3.597
-3.284
-1.595
-0.560
AA_DC2DA3:DT26DG27_BB
2
-1.511
2.604
33.594
-0.369
2.472
3.037
23.744
A
A
3
4
-9.200
B
B
26
25
3.144
-3.753
1.125
-1.021
AA_DA3DG4:DC25DT26_BB
3
-3.947
9.678
23.119
-1.296
-3.981
3.442
39.073
A
A
4
5
-8.822
B
B
25
24
3.252
-5.857
-1.076
-0.684
AA_DG4DG5:C2S24DC25_BB
4
-6.157
9.274
38.174
-0.293
0.841
2.832
28.352
A
A
5
6
17.758
B
B
24
23
3.356
8.565
-0.025
-1.246
AA_DG5DA6:DT23C2S24_BB
5
1.298
-2.692
27.023
-4.460
0.342
3.472
40.603
A
A
6
7
20.122
B
B
23
22
3.398
13.604
-1.883
-0.182
AA_DA6DG7:C2S22DT23_BB
6
-8.820
13.045
37.351
-1.926
1.636
3.132
35.313
A
A
7
8
11.408
B
B
22
21
3.265
6.870
0.099
-0.284
AA_DG7DA8:DT21C2S22_BB
7
-3.151
5.232
34.520
-1.474
-0.625
3.298
29.797
A
A
8
9
4.912
B
B
21
20
3.384
2.522
-0.750
-1.136
AA_DA8DT9:DA20DT21_BB
8
-0.880
1.714
29.680
-2.747
1.270
3.136
37.675
A
A
9
10
1.717
B
B
20
19
3.154
1.108
0.018
-0.373
AA_DT9DT10:DA19DA20_BB
9
2.734
-4.238
37.563
-0.715
0.313
3.426
46.620
A
A
10
11
2.956
B
B
19
18
3.410
2.338
0.611
0.257
AA_DT10DC11:DG18DA19_BB
10
0.596
-0.753
46.561
0.120
-0.720
3.227
25.442
A
A
11
12
1.687
B
B
18
17
3.256
0.742
-0.118
-1.014
AA_DC11DC12:DG17DG18_BB
11
-1.519
3.451
25.386
-2.515
-0.166
3.035
39.145
A
A
12
13
2.344
B
B
17
16
2.993
1.565
0.444
0.294
AA_DC12DA13:DT16DG17_BB
12
5.649
-8.461
38.721
0.264
-0.036
3.537
42.471
A
A
13
14
-7.170
B
B
16
15
3.482
-5.175
0.214
-0.949
AA_DA13DC14:DG15DT16_BB
13
-3.851
5.335
42.001
-0.744
-0.717
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
2003-04-15
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
NMR Structure of CK14, the non-thioated analog of XBY6
NMR Structure of CK14, an analog with 6 phosphorodithioates
RCSB
Y
RCSB
2001-10-24
REL
REL
SYNTHESIZED WITH NORMAL PHOSPHOROAMIDITE CHEMISTRY
sample
SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY
sample
Standard 2D homonuclear methods were used
structures with the lowest energy
10
1
2D NOESY
2D NOESY
DQF-COSY
100 mM
6.7
ambient
278
K
100 mM
6.7
ambient
288
K
Distance restraints were derived by MORASS 2.5 using a total relaxation
matrix method. The deposited structure represents the average of 10 final
structures
molecular dynamics
1
minimized average structure
1 mM duplex, 12 mM Na2HPO4, 8 mM NaH2PO4, 56 mM NaCl, 50 uM NaN3
90% H2O/10% D2O
1 mM duplex, 12 mM Na2HPO4,8 mM NaH2PO4, 56 mM NaCl, 50 uM NaN3
99.96% D2O
Gorenstein
iterative matrix relaxation
MORASS
2.5
Case and Kollman
structure solution
Amber
5
Case and Kollman
refinement
Amber
5
750
Varian
UNITYPLUS
600
Varian
UNITYPLUS
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
G
4
n
4
DG
4
A
G
5
n
5
DG
5
A
A
6
n
6
DA
6
A
G
7
n
7
DG
7
A
A
8
n
8
DA
8
A
T
9
n
9
DT
9
A
T
10
n
10
DT
10
A
C
11
n
11
DC
11
A
C
12
n
12
DC
12
A
A
13
n
13
DA
13
A
C
14
n
14
DC
14
A
G
15
n
1
DG
15
B
T
16
n
2
DT
16
B
G
17
n
3
DG
17
B
G
18
n
4
DG
18
B
A
19
n
5
DA
19
B
A
20
n
6
DA
20
B
T
21
n
7
DT
21
B
C2S
22
n
8
C2S
22
B
T
23
n
9
DT
23
B
C2S
24
n
10
C2S
24
B
C
25
n
11
DC
25
B
T
26
n
12
DT
26
B
G
27
n
13
DG
27
B
G
28
n
14
DG
28
B
author_defined_assembly
2
dimeric
B
C2S
22
CYTIDINE-5'-DITHIOPHOSPHORATE
B
C2S
8
DC
B
C2S
24
CYTIDINE-5'-DITHIOPHOSPHORATE
B
C2S
10
DC
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
HO5'
OP2
DC
DC
1
2
1.33
1
A
DC
1
0.063
SIDE CHAIN
1
A
DC
2
0.067
SIDE CHAIN
1
A
DG
4
0.059
SIDE CHAIN
1
5.50
0.30
108.30
113.80
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
4.16
0.30
108.30
112.46
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
3.35
0.50
117.70
121.05
A
A
A
C5
C6
N1
DA
DA
DA
3
3
3
N
1
5.45
0.30
108.30
113.75
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
4.05
0.30
108.30
112.35
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
-3.64
0.60
118.60
114.96
A
A
A
N1
C6
N6
DA
DA
DA
6
6
6
N
1
3.99
0.30
108.30
112.29
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
3.21
0.30
108.30
111.51
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
4.92
0.30
108.30
113.22
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.41
0.30
108.30
112.71
B
B
B
O4'
C1'
N1
DT
DT
DT
21
21
21
N
1
-3.76
0.60
122.90
119.14
B
B
B
C6
C5
C7
DT
DT
DT
21
21
21
N
1
2.64
0.30
108.30
110.94
B
B
B
O4'
C1'
N1
DT
DT
DT
23
23
23
N
1
-3.87
0.60
122.90
119.03
B
B
B
C6
C5
C7
DT
DT
DT
23
23
23
N
1
3.83
0.30
108.30
112.13
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
1
1.90
0.30
108.30
110.20
B
B
B
O4'
C1'
N1
DT
DT
DT
26
26
26
N
1
6.17
0.30
108.30
114.47
B
B
B
O4'
C1'
N9
DG
DG
DG
27
27
27
N
1
2.52
0.30
108.30
110.82
B
B
B
O4'
C1'
N9
DG
DG
DG
28
28
28
N
minimized average
NMR structure of the XBY2 DNA duplex, an analog of CK14 containing phosphorodithioate groups at C22 and C24
1
N
N
2
N
N
covale
1.620
both
B
DT
21
B
O3'
DT
7
1_555
B
C2S
22
B
P
C2S
8
1_555
covale
1.616
both
B
C2S
22
B
O3'
C2S
8
1_555
B
DT
23
B
P
DT
9
1_555
covale
1.618
both
B
DT
23
B
O3'
DT
9
1_555
B
C2S
24
B
P
C2S
10
1_555
covale
1.619
both
B
C2S
24
B
O3'
C2S
10
1_555
B
DC
25
B
P
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
28
B
N1
DG
14
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
28
B
O6
DG
14
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
28
B
N2
DG
14
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
27
B
N1
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
27
B
O6
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
27
B
N2
DG
13
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
26
B
N3
DT
12
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
26
B
O4
DT
12
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
25
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
25
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
25
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
C2S
24
B
N3
C2S
10
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
C2S
24
B
O2
C2S
10
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
C2S
24
B
N4
C2S
10
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
23
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
23
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
C2S
22
B
N3
C2S
8
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
C2S
22
B
O2
C2S
8
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
C2S
22
B
N4
C2S
8
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
21
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
21
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
20
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
20
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
10
A
N3
DT
10
1_555
B
DA
19
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
10
A
O4
DT
10
1_555
B
DA
19
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
18
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
18
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
18
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N3
DC
12
1_555
B
DG
17
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N4
DC
12
1_555
B
DG
17
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
12
A
O2
DC
12
1_555
B
DG
17
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N1
DA
13
1_555
B
DT
16
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N6
DA
13
1_555
B
DT
16
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DC
14
A
N3
DC
14
1_555
B
DG
15
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
14
A
N4
DC
14
1_555
B
DG
15
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
14
A
O2
DC
14
1_555
B
DG
15
B
N2
DG
1
1_555
DNA
phosphorodithioate, CK14, CK1, NF-kB, XBY6, XBY2, thiophosphate, DNA
1K8N
PDB
1
1K8N
1K8N
PDB
2
1K8N
1
14
1K8N
1
14
1K8N
A
1
1
14
15
28
1K8N
15
28
1K8N
B
2
1
14