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
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/pdb1k8j/pdb
pdb_00001k8j
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
4311.802
SECOND STRAND OF CK14 DNA DUPLEX
1
syn
polymer
no
no
(DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DT)(DT)(DC)(DC)(DA)(DC)
CCAGGAGATTCCAC
A
polydeoxyribonucleotide
no
no
(DG)(DT)(DG)(DG)(DA)(DA)(DT)(DC)(DT)(DC)(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
17.458
1
19
A
1
B
28
-1.057
A_DC1:DG28_B
1
-15.057
0.392
-0.019
-0.196
2.782
1
19
A
2
B
27
-0.647
A_DC2:DG27_B
2
-10.959
0.375
0.188
-0.230
-2.199
1
20
A
3
B
26
-3.296
A_DA3:DT26_B
3
-6.685
0.165
-0.139
-0.099
6.144
1
19
A
4
B
25
-0.926
A_DG4:DC25_B
4
-2.578
-0.320
0.278
-0.209
-4.831
1
19
A
5
B
24
-0.864
A_DG5:DC24_B
5
-11.270
-0.423
-0.200
-0.247
-5.359
1
20
A
6
B
23
-3.526
A_DA6:DT23_B
6
-9.673
0.272
-0.215
-0.066
-0.472
1
19
A
7
B
22
-0.511
A_DG7:DC22_B
7
-15.897
-0.405
0.121
-0.239
-6.342
1
20
A
8
B
21
-3.096
A_DA8:DT21_B
8
-9.385
0.192
0.000
-0.079
-7.378
1
20
A
9
B
20
-4.384
A_DT9:DA20_B
9
-11.127
-0.168
0.176
-0.089
-8.022
1
20
A
10
B
19
-2.260
A_DT10:DA19_B
10
-14.229
-0.169
-0.153
-0.103
-11.268
1
19
A
11
B
18
-1.552
A_DC11:DG18_B
11
-2.066
0.315
0.160
-0.188
-7.739
1
19
A
12
B
17
-0.220
A_DC12:DG17_B
12
4.468
0.353
0.063
-0.204
0.826
1
20
A
13
B
16
-3.164
A_DA13:DT16_B
13
-4.719
0.270
0.057
-0.078
7.011
1
19
A
14
B
15
-0.077
A_DC14:DG15_B
14
-4.395
0.478
0.114
-0.229
3.466
42.002
A
A
1
2
5.095
B
B
28
27
3.572
3.643
-0.258
-1.235
AA_DC1DC2:DG27DG28_BB
1
-3.755
5.251
41.689
-2.132
-0.061
2.769
30.115
A
A
2
3
18.830
B
B
27
26
3.229
9.618
-0.744
-0.865
AA_DC2DA3:DT26DG27_BB
2
1.075
-2.105
28.552
-3.517
1.638
2.963
33.231
A
A
3
4
0.286
B
B
26
25
3.023
0.163
0.291
-0.649
AA_DA3DG4:DC25DT26_BB
3
-4.119
7.220
32.982
-1.160
-1.143
3.409
36.701
A
A
4
5
7.402
B
B
25
24
3.528
4.634
0.453
-0.995
AA_DG4DG5:DC24DC25_BB
4
5.237
-8.365
36.051
-2.259
0.047
3.250
40.565
A
A
5
6
4.002
B
B
24
23
3.248
2.772
-0.883
-0.341
AA_DG5DA6:DT23DC24_BB
5
-1.591
2.296
40.444
-0.799
1.097
3.004
30.063
A
A
6
7
6.210
B
B
23
22
3.163
3.208
0.554
-0.562
AA_DA6DG7:DC22DT23_BB
6
-3.480
6.736
29.697
-1.708
-1.745
3.303
37.582
A
A
7
8
2.045
B
B
22
21
3.326
1.317
-0.773
-0.898
AA_DG7DA8:DT21DC22_BB
7
-0.467
0.725
37.557
-1.567
1.138
3.296
31.396
A
A
8
9
-0.662
B
B
21
20
3.281
-0.358
-0.228
-1.009
AA_DA8DT9:DA20DT21_BB
8
-0.655
1.210
31.387
-1.797
0.297
3.166
38.334
A
A
9
10
-0.383
B
B
20
19
3.169
-0.251
0.104
-0.369
AA_DT9DT10:DA19DA20_BB
9
3.946
-6.020
38.137
-0.532
0.321
3.376
37.720
A
A
10
11
3.000
B
B
19
18
3.414
1.939
0.775
-0.347
AA_DT10DC11:DG18DA19_BB
10
-0.812
1.257
37.663
-0.797
-1.308
3.320
41.520
A
A
11
12
-2.429
B
B
18
17
3.302
-1.721
0.527
-0.045
AA_DC11DC12:DG17DG18_BB
11
1.820
-2.569
41.448
0.122
-0.548
3.126
31.723
A
A
12
13
-2.413
B
B
17
16
3.069
-1.318
-1.743
0.038
AA_DC12DA13:DT16DG17_BB
12
-1.178
2.156
31.675
0.300
2.984
3.197
36.078
A
A
13
14
-3.521
B
B
16
15
3.197
-2.179
0.852
-0.757
AA_DA13DC14:DG15DT16_BB
13
-1.570
2.537
35.982
-0.920
-1.594
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
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
NMR Structure of CK14, an analog with 6 phosphorodithioates
NMR Structure of CK14, an analog with 2 phosphorodithioates
RCSB
Y
RCSB
2001-10-24
REL
REL
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
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. The deposited
structure represents the average of 10
final structures.
molecular dynamics
1
minimized average structure
2 mM DNA DUPLEX; 12 mM Na2HPO4; 8 mM NaH2PO4; 56 mM NaCl; 50 uM NaN3
90% H2O/10% D2O
2 mM DNA 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
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
C
22
n
8
DC
22
B
T
23
n
9
DT
23
B
C
24
n
10
DC
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
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
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
2.83
0.30
108.30
111.13
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
2.31
0.30
108.30
110.61
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
4.82
0.30
108.30
113.12
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
1
3.01
0.50
117.70
120.71
B
B
B
C5
C6
N1
DA
DA
DA
20
20
20
N
1
-3.72
0.60
122.90
119.18
B
B
B
C6
C5
C7
DT
DT
DT
21
21
21
N
1
3.77
0.30
108.30
112.07
B
B
B
O4'
C1'
N1
DC
DC
DC
22
22
22
N
1
4.02
0.30
108.30
112.32
B
B
B
O4'
C1'
N9
DG
DG
DG
27
27
27
N
minimized average
NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1
1
N
N
2
N
N
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
DC
24
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
24
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
24
B
N4
DC
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
DC
22
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
22
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
22
B
N4
DC
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
DNA DUPLEX, CK14, CK1, NF-KB, DNA
1K8J
PDB
1
1K8J
1K8J
PDB
2
1K8J
1
14
1K8J
1
14
1K8J
A
1
1
14
15
28
1K8J
15
28
1K8J
B
2
1
14