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
C10 H14 N5 O5 P S2
379.352
n
GUANOSINE-5'-DITHIOPHOSPHORATE
DNA linking
C10 H15 N2 O6 P S2
354.340
n
THYMIDINE-5'-DITHIOPHOSPHORATE
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/pdb1k8l/pdb
pdb_00001k8l
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
4314.044
FIRST STRAND OF CK14 DNA DUPLEX
DITHIOATED AT T10, C11
DITHIOATED AT T10, C11
1
syn
polymer
CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1
4440.326
SECOND STRAND OF CK14 DNA DUPLEX
DITHIOATED AT G17, C22, C24, G27
DITHIOATED AT G17, C22, C24, G27
1
syn
polymer
no
yes
(DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DT)(T2S)(C2S)(DC)(DA)(DC)
CCAGGAGATTCCAC
A
polydeoxyribonucleotide
no
yes
(DG)(DT)(G2S)(DG)(DA)(DA)(DT)(C2S)(DT)(C2S)(DC)(DT)(G2S)(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
3.476
1
19
A
1
B
28
0.320
A_DC1:DG28_B
1
-9.454
0.459
0.198
-0.213
0.468
1
19
A
2
B
27
-0.838
A_DC2:G2S27_B
2
-11.881
0.215
-0.004
-0.199
4.025
1
20
A
3
B
26
-4.832
A_DA3:DT26_B
3
-1.795
0.210
-0.151
-0.069
8.173
1
19
A
4
B
25
-0.672
A_DG4:DC25_B
4
-0.256
-0.381
0.097
-0.208
-1.859
1
19
A
5
B
24
-0.540
A_DG5:C2S24_B
5
-6.693
-0.492
-0.177
-0.260
-5.788
1
20
A
6
B
23
-1.340
A_DA6:DT23_B
6
-7.764
0.163
-0.159
-0.094
-2.788
1
19
A
7
B
22
-1.133
A_DG7:C2S22_B
7
-5.687
-0.365
-0.003
-0.218
-0.340
1
20
A
8
B
21
-0.130
A_DA8:DT21_B
8
-10.564
0.077
-0.208
-0.114
-5.511
1
20
A
9
B
20
-0.441
A_DT9:DA20_B
9
-10.748
-0.090
-0.110
-0.120
-0.595
1
20
A
10
B
19
-2.384
A_T2S10:DA19_B
10
-10.870
-0.102
-0.452
-0.140
-5.916
1
19
A
11
B
18
-0.676
A_C2S11:DG18_B
11
-2.151
0.398
0.139
-0.221
-3.966
1
19
A
12
B
17
-0.624
A_DC12:G2S17_B
12
0.539
0.379
0.218
-0.223
-2.233
1
20
A
13
B
16
-1.896
A_DA13:DT16_B
13
-6.055
0.193
-0.123
-0.106
-3.382
1
19
A
14
B
15
-0.164
A_DC14:DG15_B
14
0.805
0.453
0.265
-0.227
3.320
41.593
A
A
1
2
-3.290
B
B
28
27
3.347
-2.333
-0.089
0.129
AA_DC1DC2:G2S27DG28_BB
1
3.163
-4.461
41.415
0.433
0.468
2.564
29.499
A
A
2
3
28.995
B
B
27
26
3.174
14.176
-0.934
-0.445
AA_DC2DA3:DT26G2S27_BB
2
0.724
-1.481
25.926
-3.704
1.979
3.019
28.608
A
A
3
4
2.561
B
B
26
25
3.167
1.263
0.658
-1.430
AA_DA3DG4:DC25DT26_BB
3
-2.970
6.023
28.429
-3.165
-1.970
3.355
37.548
A
A
4
5
5.761
B
B
25
24
3.494
3.701
0.063
-1.282
AA_DG4DG5:C2S24DC25_BB
4
1.954
-3.041
37.323
-2.499
0.169
3.240
38.555
A
A
5
6
6.843
B
B
24
23
3.342
4.508
-0.531
-0.863
AA_DG5DA6:DT23C2S24_BB
5
-1.376
2.089
38.276
-1.870
0.632
2.667
24.314
A
A
6
7
14.434
B
B
23
22
3.169
6.018
0.647
-1.669
AA_DA6DG7:C2S22DT23_BB
6
0.053
-0.126
23.568
-5.678
-1.520
3.082
41.160
A
A
7
8
15.396
B
B
22
21
3.296
10.709
-0.234
-0.418
AA_DG7DA8:DT21C2S22_BB
7
0.954
-1.371
39.790
-1.745
0.435
3.292
26.102
A
A
8
9
5.362
B
B
21
20
3.426
2.418
-0.197
-1.334
AA_DA8DT9:DA20DT21_BB
8
-0.297
0.658
25.990
-3.633
0.354
3.072
40.685
A
A
9
10
10.321
B
B
20
19
3.060
7.114
0.555
0.047
AA_DT9T2S10:DA19DA20_BB
9
6.368
-9.238
39.595
-0.682
-0.127
3.130
32.160
A
A
10
11
10.796
B
B
19
18
3.457
5.935
0.364
-1.152
AA_T2S10C2S11:DG18DA19_BB
10
-3.707
6.742
31.409
-3.162
-1.332
3.269
39.638
A
A
11
12
-0.633
B
B
18
17
3.259
-0.429
-0.080
-0.941
AA_C2S11DC12:G2S17DG18_BB
11
-0.386
0.569
39.634
-1.338
0.073
3.032
31.959
A
A
12
13
3.550
B
B
17
16
3.165
1.951
-0.699
-0.811
AA_DC12DA13:DT16G2S17_BB
12
3.091
-5.626
31.754
-1.808
1.801
3.405
40.840
A
A
13
14
-4.164
B
B
16
15
3.412
-2.896
0.234
-0.812
AA_DA13DC14:DG15DT16_BB
13
-5.238
7.531
40.418
-0.830
-0.939
chem_comp
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
pdbx_struct_mod_residue
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Derived calculations
1
0
2003-04-15
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
1
4
2022-06-22
_chem_comp.type
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_pdbx_struct_mod_residue.parent_comp_id
NMR Structure of CK14, the non-thioated analog of XBY6
NMR Structure of CK14, an analog with 2 phosphorodithioates
RCSB
Y
RCSB
2001-10-24
REL
REL
SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY
sample
SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY
sample
This structure was determined using standard 2D homonuclear techniques.
Proton resonances were assigned using COSY, TOCSY, and NOESY data
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 approach.
AMBER 5 was used for MD and minimization. The deposited structure represents
the average of ten 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, 56mM NaCl, 50 uM NaN3
99.96% D2O
Gorenstein
iterative matrix relaxation
MORASS
2.5
Case,Kollman, et al
structure solution
Amber
5
Case,Kollman, et al
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
T2S
10
n
10
T2S
10
A
C2S
11
n
11
C2S
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
G2S
17
n
3
G2S
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
G2S
27
n
13
G2S
27
B
G
28
n
14
DG
28
B
author_defined_assembly
2
dimeric
A
T2S
10
THYMIDINE-5'-DITHIOPHOSPHORATE
A
T2S
10
DT
A
C2S
11
CYTIDINE-5'-DITHIOPHOSPHORATE
A
C2S
11
DC
B
G2S
17
GUANOSINE-5'-DITHIOPHOSPHORATE
B
G2S
3
DG
B
C2S
22
CYTIDINE-5'-DITHIOPHOSPHORATE
B
C2S
8
DC
B
C2S
24
CYTIDINE-5'-DITHIOPHOSPHORATE
B
C2S
10
DC
B
G2S
27
GUANOSINE-5'-DITHIOPHOSPHORATE
B
G2S
13
DG
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
1.40
1
-6.51
1.00
110.10
103.59
A
A
A
C1'
O4'
C4'
DC
DC
DC
1
1
1
N
1
-5.21
0.80
102.40
97.19
A
A
A
C3'
C2'
C1'
DC
DC
DC
1
1
1
N
1
-5.46
0.80
105.90
100.44
A
A
A
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
1
6.83
0.30
108.30
115.13
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-4.25
0.70
121.90
117.65
A
A
A
N3
C2
O2
DC
DC
DC
1
1
1
N
1
3.97
0.30
108.30
112.27
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
3.22
0.50
117.70
120.92
A
A
A
C5
C6
N1
DA
DA
DA
3
3
3
N
1
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
1.92
0.30
108.30
110.22
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
3.84
0.30
108.30
112.14
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
4.00
0.30
108.30
112.30
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
-3.74
0.60
122.90
119.16
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
1
2.83
0.30
108.30
111.13
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
2.32
0.30
108.30
110.62
B
B
B
O4'
C1'
N9
DA
DA
DA
19
19
19
N
1
4.80
0.30
108.30
113.10
B
B
B
O4'
C1'
N1
DT
DT
DT
21
21
21
N
1
-3.81
0.60
122.90
119.09
B
B
B
C6
C5
C7
DT
DT
DT
21
21
21
N
1
1.86
0.30
108.30
110.16
B
B
B
O4'
C1'
N1
DT
DT
DT
23
23
23
N
1
-4.00
0.60
122.90
118.90
B
B
B
C6
C5
C7
DT
DT
DT
23
23
23
N
1
2.06
0.30
108.30
110.36
B
B
B
O4'
C1'
N9
DG
DG
DG
28
28
28
N
minimized average
XBY6: An analog of CK14 containing 6 dithiophosphate groups
1
N
N
2
N
N
covale
1.623
both
A
DT
9
A
O3'
DT
9
1_555
A
T2S
10
A
P
T2S
10
1_555
covale
1.618
both
A
T2S
10
A
O3'
T2S
10
1_555
A
C2S
11
A
P
C2S
11
1_555
covale
1.618
both
A
C2S
11
A
O3'
C2S
11
1_555
A
DC
12
A
P
DC
12
1_555
covale
1.617
both
B
DT
16
B
O3'
DT
2
1_555
B
G2S
17
B
P
G2S
3
1_555
covale
1.616
both
B
G2S
17
B
O3'
G2S
3
1_555
B
DG
18
B
P
DG
4
1_555
covale
1.622
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
1.620
both
B
DT
23
B
O3'
DT
9
1_555
B
C2S
24
B
P
C2S
10
1_555
covale
1.617
both
B
C2S
24
B
O3'
C2S
10
1_555
B
DC
25
B
P
DC
11
1_555
covale
1.617
both
B
DT
26
B
O3'
DT
12
1_555
B
G2S
27
B
P
G2S
13
1_555
covale
1.611
both
B
G2S
27
B
O3'
G2S
13
1_555
B
DG
28
B
P
DG
14
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
G2S
27
B
N1
G2S
13
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
G2S
27
B
O6
G2S
13
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
G2S
27
B
N2
G2S
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
T2S
10
A
N3
T2S
10
1_555
B
DA
19
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
T2S
10
A
O4
T2S
10
1_555
B
DA
19
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
C2S
11
A
N3
C2S
11
1_555
B
DG
18
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
C2S
11
A
N4
C2S
11
1_555
B
DG
18
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
C2S
11
A
O2
C2S
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
G2S
17
B
N1
G2S
3
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N4
DC
12
1_555
B
G2S
17
B
O6
G2S
3
1_555
hydrog
WATSON-CRICK
A
DC
12
A
O2
DC
12
1_555
B
G2S
17
B
N2
G2S
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
XBY6, CK14, CK1, PHOSPHORODITHIOATE, NF-KB, DNA
1K8L
PDB
1
1K8L
1K8L
PDB
2
1K8L
1
14
1K8L
1
14
1K8L
A
1
1
14
15
28
1K8L
15
28
1K8L
B
2
1
14