1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kaluarachchi, K.
Gorenstein, D.G.
Luxon, B.A.
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
J.Biomol.Struct.Dyn.
JBSDD6
0646
0739-1102
Conversation 11
123
133
-1
How Do Proteins Recognize DNA? Solution Structure and Local Conformational Dynamics of Lac Operators by 2D NMR
2000
10.2210/pdb1k9h/pdb
pdb_00001k9h
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
This sequence has been derived from the natural Lac Operator sequence by symmetrizing the minimum required length for lac repressor binding.
4280.792
5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3'
2
syn
polymer
no
no
(DT)(DG)(DT)(DG)(DA)(DG)(DC)(DG)(DC)(DT)(DC)(DA)(DC)(DA)
TGTGAGCGCTCACA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
23.054
1
20
A
1
B
28
5.687
A_DT1:DA28_B
1
-41.343
0.419
-0.275
-0.183
-5.776
1
19
A
2
B
27
-0.940
A_DG2:DC27_B
2
-8.346
-0.382
0.143
-0.265
-2.009
1
20
A
3
B
26
3.780
A_DT3:DA26_B
3
-12.567
0.110
0.185
-0.202
-21.363
1
19
A
4
B
25
0.029
A_DG4:DC25_B
4
-28.448
-0.391
-0.715
-0.336
-27.297
1
20
A
5
B
24
3.054
A_DA5:DT24_B
5
-13.066
-0.074
-0.416
-0.127
-3.060
1
19
A
6
B
23
-0.151
A_DG6:DC23_B
6
-7.235
-0.264
0.095
-0.214
-11.475
1
19
A
7
B
22
-3.467
A_DC7:DG22_B
7
0.479
0.195
0.282
-0.255
13.643
1
19
A
8
B
21
-2.777
A_DG8:DC21_B
8
1.109
-0.155
0.426
-0.232
4.128
1
19
A
9
B
20
-0.502
A_DC9:DG20_B
9
-6.864
0.278
0.039
-0.218
7.988
1
20
A
10
B
19
5.300
A_DT10:DA19_B
10
-1.703
0.039
0.239
-0.161
1.895
1
19
A
11
B
18
-3.053
A_DC11:DG18_B
11
-14.175
0.326
0.106
-0.287
2.525
1
20
A
12
B
17
-2.326
A_DA12:DT17_B
12
-13.667
-0.266
0.226
-0.277
1.562
1
19
A
13
B
16
1.339
A_DC13:DG16_B
13
-6.546
0.528
0.404
-0.241
0.170
1
20
A
14
B
15
-3.574
A_DA14:DT15_B
14
-31.247
-0.011
0.050
-0.216
2.855
46.966
A
A
1
2
34.482
B
B
28
27
3.619
25.932
-0.828
-0.548
AA_DT1DG2:DC27DA28_BB
1
-8.301
11.039
38.638
-3.044
0.285
3.053
35.399
A
A
2
3
7.738
B
B
27
26
3.127
4.692
0.013
-0.381
AA_DG2DT3:DA26DC27_BB
2
0.075
-0.124
35.096
-1.281
-0.011
2.922
38.626
A
A
3
4
27.937
B
B
26
25
3.575
17.661
0.193
-0.501
AA_DT3DG4:DC25DA26_BB
3
8.931
-14.128
33.338
-3.094
0.889
3.247
33.361
A
A
4
5
8.443
B
B
25
24
3.296
4.830
0.464
-0.003
AA_DG4DA5:DT24DC25_BB
4
-1.030
1.801
33.004
-0.811
-0.980
2.345
32.651
A
A
5
6
29.758
B
B
24
23
2.808
15.802
-0.451
-0.262
AA_DA5DG6:DC23DT24_BB
5
-9.311
17.534
27.129
-2.840
-0.595
3.360
41.028
A
A
6
7
6.633
B
B
23
22
3.432
4.638
-0.481
-0.633
AA_DG6DC7:DG22DC23_BB
6
-1.743
2.493
40.741
-1.430
0.488
2.623
26.912
A
A
7
8
0.289
B
B
22
21
2.634
0.134
0.002
-0.427
AA_DC7DG8:DC21DG22_BB
7
-2.161
4.649
26.826
-0.944
-0.450
3.470
39.753
A
A
8
9
3.692
B
B
21
20
3.469
2.505
0.525
-0.433
AA_DG8DC9:DG20DC21_BB
8
3.846
-5.667
39.497
-0.946
-0.297
2.447
39.370
A
A
9
10
48.121
B
B
20
19
3.481
28.880
1.206
-0.133
AA_DC9DT10:DA19DG20_BB
9
6.517
-10.858
26.248
-3.984
-0.936
3.123
32.847
A
A
10
11
19.873
B
B
19
18
3.373
11.026
-0.270
-0.140
AA_DT10DC11:DG18DA19_BB
10
1.731
-3.120
30.942
-2.183
0.781
3.072
32.798
A
A
11
12
9.343
B
B
18
17
3.144
5.252
-0.502
-0.357
AA_DC11DA12:DT17DG18_BB
11
-1.687
3.001
32.343
-1.495
0.612
3.335
37.514
A
A
12
13
1.065
B
B
17
16
3.347
0.685
0.225
0.038
AA_DA12DC13:DG16DT17_BB
12
-1.566
2.435
37.476
-0.033
-0.559
2.862
33.169
A
A
13
14
21.124
B
B
16
15
3.157
11.693
0.406
-0.300
AA_DC13DA14:DT15DG16_BB
13
7.939
-14.343
30.083
-2.427
0.581
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
2001-11-07
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
1k9l is the Solution structure of the DNA oligomer TATGAGCGCTCATA.
RCSB
Y
RCSB
2001-10-29
REL
This structure was determined using standard homonuclear techniques.
back calculated data agree with experimental NOESY spectrum,structures with the lowest energy
2
1
2D NOESY
2D TOCSY
150 mM KCl
7.4
ambient
298
K
molecular dynamics,
matrix relaxation,
simulated annealing
closest to the average
3.6 mM oligonucleotide, 55 mM potassium phosphate, 150 mM KCl, 0.1mM NaN3
99.96% D2O
Kollman. P.
refinement
Amber
versions 3-5
Meadows. R.P.
refinement
MORASS
1.0
500
Varian
VXRS
600
Varian
VXRS
THY
1
n
1
DT
1
A
GUA
2
n
2
DG
2
A
THY
3
n
3
DT
3
A
GUA
4
n
4
DG
4
A
ADE
5
n
5
DA
5
A
GUA
6
n
6
DG
6
A
CYT
7
n
7
DC
7
A
GUA
8
n
8
DG
8
A
CYT
9
n
9
DC
9
A
THY
10
n
10
DT
10
A
CYT
11
n
11
DC
11
A
ADE
12
n
12
DA
12
A
CYT
13
n
13
DC
13
A
ADE
14
n
14
DA
14
A
THY
15
n
1
DT
15
B
GUA
16
n
2
DG
16
B
THY
17
n
3
DT
17
B
GUA
18
n
4
DG
18
B
ADE
19
n
5
DA
19
B
GUA
20
n
6
DG
20
B
CYT
21
n
7
DC
21
B
GUA
22
n
8
DG
22
B
CYT
23
n
9
DC
23
B
THY
24
n
10
DT
24
B
CYT
25
n
11
DC
25
B
ADE
26
n
12
DA
26
B
CYT
27
n
13
DC
27
B
ADE
28
n
14
DA
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
A
DG
4
0.079
SIDE CHAIN
1
A
DA
5
0.076
SIDE CHAIN
1
A
DC
7
0.074
SIDE CHAIN
1
A
DA
12
0.094
SIDE CHAIN
1
B
DT
15
0.088
SIDE CHAIN
1
B
DG
16
0.067
SIDE CHAIN
1
B
DG
18
0.097
SIDE CHAIN
1
B
DA
19
0.056
SIDE CHAIN
1
B
DC
25
0.093
SIDE CHAIN
1
3.86
0.30
108.30
112.16
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
8.21
0.30
108.30
116.51
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
3.18
0.50
113.10
116.28
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-3.24
0.40
106.40
103.16
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
3.66
0.30
108.30
111.96
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
14.99
1.60
120.90
135.89
A
A
A
P
O5'
C5'
DC
DC
DC
9
9
9
N
1
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-4.25
0.70
102.20
97.95
A
A
A
C4'
C3'
C2'
DT
DT
DT
10
10
10
N
1
7.93
1.20
102.50
110.43
A
A
A
C3'
C2'
C1'
DT
DT
DT
10
10
10
N
1
3.18
0.30
108.30
111.48
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
4.48
0.60
106.00
110.48
A
A
A
O4'
C4'
C3'
DA
DA
DA
12
12
12
N
1
-9.90
0.70
102.20
92.30
A
A
A
C4'
C3'
C2'
DA
DA
DA
12
12
12
N
1
-4.93
0.80
105.90
100.97
A
A
A
O4'
C1'
C2'
DA
DA
DA
12
12
12
N
1
4.30
0.30
108.30
112.60
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
1
3.64
0.30
108.30
111.94
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N9
DA
DA
DA
14
14
14
N
1
2.41
0.30
108.30
110.71
B
B
B
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
7.56
0.30
108.30
115.86
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
-2.49
0.40
106.40
103.91
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
3.24
0.30
108.30
111.54
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.24
0.60
106.00
110.24
B
B
B
O4'
C4'
C3'
DT
DT
DT
24
24
24
N
1
-4.93
0.70
102.20
97.27
B
B
B
C4'
C3'
C2'
DT
DT
DT
24
24
24
N
1
7.99
1.20
102.50
110.49
B
B
B
C3'
C2'
C1'
DT
DT
DT
24
24
24
N
1
4.71
0.30
108.30
113.01
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
1
2.86
0.30
108.30
111.16
B
B
B
O4'
C1'
N1
DC
DC
DC
27
27
27
N
1
2.38
0.30
108.30
110.68
B
B
B
O4'
C1'
N9
DA
DA
DA
28
28
28
N
1
A
A
O5'
C5'
DT
DT
1
1
-0.371
0.025
1.418
1.047
N
1
A
A
O4'
C4'
DT
DT
1
1
-0.071
0.010
1.446
1.375
N
1
A
A
O3'
C3'
DT
DT
1
1
-0.041
0.006
1.419
1.378
N
1
A
A
O4'
C4'
DT
DT
3
3
-0.063
0.010
1.446
1.383
N
1
A
A
P
OP1
DC
DC
9
9
-0.132
0.017
1.485
1.353
N
1
A
A
P
O5'
DC
DC
9
9
-0.125
0.010
1.593
1.468
N
1
A
A
O4'
C4'
DC
DC
9
9
-0.062
0.010
1.446
1.384
N
1
B
B
O4'
C4'
DT
DT
15
15
-0.068
0.010
1.446
1.378
N
1
B
B
O4'
C4'
DT
DT
24
24
-0.060
0.010
1.446
1.386
N
1
B
B
O3'
C3'
DA
DA
28
28
-0.050
0.006
1.419
1.369
N
1
B
B
C4
C5
DA
DA
28
28
-0.046
0.007
1.383
1.337
N
NMR structure of DNA TGTGAGCGCTCACA
1
N
N
1
N
N
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
DA
28
B
N1
DA
14
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
DA
28
B
N6
DA
14
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
27
B
N3
DC
13
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
27
B
O2
DC
13
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
27
B
N4
DC
13
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
26
B
N1
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
26
B
N6
DA
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
DA
5
A
N1
DA
5
1_555
B
DT
24
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
24
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
23
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
23
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
23
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
DG
22
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
22
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
22
B
N2
DG
8
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N1
DG
8
1_555
B
DC
21
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N2
DG
8
1_555
B
DC
21
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
8
A
O6
DG
8
1_555
B
DC
21
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
20
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
20
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
20
B
N2
DG
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
DA
12
A
N1
DA
12
1_555
B
DT
17
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N6
DA
12
1_555
B
DT
17
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N3
DC
13
1_555
B
DG
16
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N4
DC
13
1_555
B
DG
16
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
13
A
O2
DC
13
1_555
B
DG
16
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DA
14
A
N1
DA
14
1_555
B
DT
15
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
A
DA
14
A
N6
DA
14
1_555
B
DT
15
B
O4
DT
1
1_555
DNA
Lac operator, Double helix, DNA
1K9H
PDB
1
1K9H
1
14
1K9H
1
14
1K9H
A
1
1
14
15
28
1K9H
15
28
1K9H
B
1
1
14