1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lim, K.W.
Phan, A.T.
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
GE
Angew.Chem.Int.Ed.Engl.
ACIEAY
0179
1521-3773
52
8566
8569
10.1002/anie.201302995
23794476
Structural basis of DNA quadruplex-duplex junction formation.
2013
10.2210/pdb2m91/pdb
pdb_00002m91
9444.064
30-MER DNA
1
syn
polymer
no
no
(DG)(DG)(DG)(DA)(DA)(DG)(DG)(DG)(DC)(DG)(DC)(DG)(DA)(DA)(DG)(DC)(DA)(DT)(DT)(DC)
(DG)(DC)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DG)
GGGAAGGGCGCGAAGCATTCGCGAGGTAGG
A
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
n
n
-9.470
1
8
A
28
A
3
-16.970
A_DA28:DG3_A
1
-10.043
0.090
0.046
1.420
9.758
3
6
A
26
A
2
-95.926
A_DG26:DG2_A
2
-5.715
1.040
-0.115
3.427
-28.286
A
17
A
15
28.124
A_DA17:DG15_A
3
-7.546
-6.655
1.846
-3.430
0.187
1
20
A
18
A
14
4.654
A_DT18:DA14_A
4
10.705
-0.302
-0.593
-0.177
-0.557
1
20
A
19
A
13
-8.344
A_DT19:DA13_A
5
4.257
-0.778
-0.366
-0.082
2.941
1
19
A
20
A
12
-3.498
A_DC20:DG12_A
6
-6.219
0.178
-0.406
-0.172
1.021
1
19
A
21
A
11
-1.361
A_DG21:DC11_A
7
-1.763
-0.044
-0.276
-0.184
-3.331
1
19
A
22
A
10
-8.204
A_DC22:DG10_A
8
3.825
-0.293
-0.494
-0.075
-4.970
1
19
A
23
A
9
-7.890
A_DG23:DC9_A
9
-1.623
0.167
-0.477
-0.037
-2.494
1
8
A
24
A
8
-19.417
A_DA24:DG8_A
10
5.556
-0.787
-0.484
1.342
6.660
3
6
A
25
A
1
97.268
A_DG25:DG1_A
11
-1.615
-1.015
-0.197
-3.743
-0.634
3
6
A
30
A
7
-97.168
A_DG30:DG7_A
12
-5.944
0.806
0.059
3.548
9.841
3
6
A
29
A
6
92.492
A_DG29:DG6_A
13
0.943
-1.734
-0.335
-3.623
2.319
176.793
A
A
28
26
-74.870
A
A
3
2
1.836
-148.499
2.454
-3.306
AA_DA28DG26:DG2DG3_AA
1
-94.033
47.410
81.464
-0.849
-1.737
2.900
53.828
A
A
17
18
2.838
A
A
15
14
2.903
2.568
-1.258
1.180
AA_DA17DT18:DA14DG15_AA
2
2.286
-2.526
53.726
1.161
1.516
2.739
30.853
A
A
18
19
23.491
A
A
14
13
3.461
12.172
-1.246
-1.115
AA_DT18DT19:DA13DA14_AA
3
0.537
-1.036
28.399
-4.438
2.446
3.034
35.875
A
A
19
20
9.124
A
A
13
12
3.211
5.596
0.321
-1.008
AA_DT19DC20:DG12DA13_AA
4
1.886
-3.075
35.401
-2.408
-0.262
3.332
33.010
A
A
20
21
11.991
A
A
12
11
3.582
6.764
0.127
-0.834
AA_DC20DG21:DC11DG12_AA
5
-1.849
3.278
32.277
-2.694
-0.558
3.469
30.987
A
A
21
22
9.053
A
A
11
10
3.708
4.817
-0.727
-1.395
AA_DG21DC22:DG10DC11_AA
6
-0.703
1.321
30.612
-3.636
1.211
3.573
32.285
A
A
22
23
15.652
A
A
10
9
3.935
8.602
-0.302
-0.901
AA_DC22DG23:DC9DG10_AA
7
-1.109
2.018
31.128
-3.405
0.313
3.772
33.234
A
A
23
24
-14.283
A
A
9
8
3.596
-8.091
-0.738
-1.223
AA_DG23DA24:DG8DC9_AA
8
0.529
-0.934
32.257
-0.590
1.392
-4.079
-178.933
A
A
24
25
-42.762
A
A
8
1
-4.842
85.450
0.352
-3.590
AA_DA24DG25:DG1DG8_AA
9
-154.061
-77.097
-147.641
2.102
0.730
-0.351
-177.239
A
A
25
30
-1.272
A
A
1
7
-0.350
2.544
2.320
3.297
AA_DG25DG30:DG7DG1_AA
10
-2.302
-1.151
-177.238
-1.649
1.161
-0.283
178.135
A
A
30
29
79.065
A
A
7
6
0.595
157.712
4.353
0.245
AA_DG30DG29:DG6DG7_AA
11
-78.213
39.210
123.779
0.088
-2.194
citation
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_database_status
repository
Initial release
Data collection
Database references
Other
1
0
2013-07-10
1
1
2022-08-24
1
2
2023-06-14
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.title
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_pdbx_database_status.status_code_nmr_data
STRUCTURE OF D[CGCGAAGCATTCGCG] HAIRPIN (REFERENCE DUPLEX HAIRPIN)
STRUCTURE OF D[GGTTGGCGCGAAGCATTCGCGGGTTGG] quadruplex-duplex HYBRID (CONSTRUCT I)
STRUCTURE OF D[GCGCGAAGCATTCGCGGGGAGGTGGGGAAGGG] quadruplex-duplex HYBRID (CONSTRUCT II)
STRUCTURE OF D[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] quadruplex-duplex HYBRID (CONSTRUCT IV)
STRUCTURE OF D[TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT] quadruplex-duplex HYBRID (CONSTRUCT V)
BMRB
Y
PDBJ
2013-05-30
REL
REL
REL
REL
structures with the lowest energy
100
10
1
2D 1H-1H NOESY
2D 1H-1H JR NOESY
2D 1H-1H JR NOESY
2D 1H-1H COSY
2D 1H-1H TOCSY
2D 1H-13C HSQC
2D 1H-13C JR HMBC
2D 1H-31P HSQC
H-D EXCHANGE
15N-FILTERED
15N-FILTERED
D-LABELED
0.5-2.0
mM
0.5-2.0
mM
0.5-2.0
mM
[U-2% 15N]
0.2-1.0
mM
[U-100% 2H]
40 mM K+
7
ambient
278
K
40 mM K+
7
ambient
298
K
DGSA-distance geometry simulated annealing, Distance-restrained molecular dynamics
1
lowest energy
0.5-2.0 mM DNA-1, 90% H2O/10% D2O
90% H2O/10% D2O
0.5-2.0 mM DNA-2, 100% D2O
100% D2O
0.5-2.0 mM [U-2% 15N] DNA-3, 90% H2O/10% D2O
90% H2O/10% D2O
0.2-1.0 mM [U-100% 2H] DNA-4, 100% D2O
100% D2O
Bruker Biospin
processing
TopSpin
2.1
Felix NMR, Inc.
peak picking
Felix
2007
Schwieters, Kuszewski, Tjandra and Clore
processing
X-PLOR NIH
2.29
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
2.29
400
Bruker
AVANCE
Bruker Avance
600
Bruker
AVANCE
Bruker Avance
700
Bruker
AVANCE
Bruker Avance
DG
1
n
1
DG
1
A
DG
2
n
2
DG
2
A
DG
3
n
3
DG
3
A
DA
4
n
4
DA
4
A
DA
5
n
5
DA
5
A
DG
6
n
6
DG
6
A
DG
7
n
7
DG
7
A
DG
8
n
8
DG
8
A
DC
9
n
9
DC
9
A
DG
10
n
10
DG
10
A
DC
11
n
11
DC
11
A
DG
12
n
12
DG
12
A
DA
13
n
13
DA
13
A
DA
14
n
14
DA
14
A
DG
15
n
15
DG
15
A
DC
16
n
16
DC
16
A
DA
17
n
17
DA
17
A
DT
18
n
18
DT
18
A
DT
19
n
19
DT
19
A
DC
20
n
20
DC
20
A
DG
21
n
21
DG
21
A
DC
22
n
22
DC
22
A
DG
23
n
23
DG
23
A
DA
24
n
24
DA
24
A
DG
25
n
25
DG
25
A
DG
26
n
26
DG
26
A
DT
27
n
27
DT
27
A
DA
28
n
28
DA
28
A
DG
29
n
29
DG
29
A
DG
30
n
30
DG
30
A
author_defined_assembly
1
monomeric
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
3
A
A
H1'
OP2
DC
DA
16
17
1.58
1
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
27
27
27
N
5
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
19
19
19
N
lowest energy, model1
Structure of d[GGGAAGGGCGCGAAGCATTCGCGAGGTAGG] quadruplex-duplex hybrid
1
N
N
hydrog
TYPE_6_PAIR
A
DG
1
A
N7
DG
1
1_555
A
DG
7
A
N2
DG
7
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
O6
DG
1
1_555
A
DG
7
A
N1
DG
7
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
N1
DG
1
1_555
A
DG
25
A
O6
DG
25
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
N2
DG
1
1_555
A
DG
25
A
N7
DG
25
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N1
DG
2
1_555
A
DG
6
A
O6
DG
6
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N2
DG
2
1_555
A
DG
6
A
N7
DG
6
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N7
DG
2
1_555
A
DG
26
A
N2
DG
26
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
O6
DG
2
1_555
A
DG
26
A
N1
DG
26
1_555
hydrog
TYPE_8_PAIR
A
DG
3
A
N1
DG
3
1_555
A
DA
28
A
N1
DA
28
1_555
hydrog
TYPE_8_PAIR
A
DG
3
A
O6
DG
3
1_555
A
DA
28
A
N6
DA
28
1_555
hydrog
TYPE_6_PAIR
A
DG
6
A
N1
DG
6
1_555
A
DG
29
A
O6
DG
29
1_555
hydrog
TYPE_6_PAIR
A
DG
6
A
N2
DG
6
1_555
A
DG
29
A
N7
DG
29
1_555
hydrog
TYPE_6_PAIR
A
DG
7
A
N7
DG
7
1_555
A
DG
30
A
N2
DG
30
1_555
hydrog
TYPE_6_PAIR
A
DG
7
A
O6
DG
7
1_555
A
DG
30
A
N1
DG
30
1_555
hydrog
TYPE_8_PAIR
A
DG
8
A
N1
DG
8
1_555
A
DA
24
A
N1
DA
24
1_555
hydrog
TYPE_8_PAIR
A
DG
8
A
O6
DG
8
1_555
A
DA
24
A
N6
DA
24
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
A
DG
23
A
N1
DG
23
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
A
DG
23
A
O6
DG
23
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
A
DG
23
A
N2
DG
23
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
A
DC
22
A
N3
DC
22
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
A
DC
22
A
O2
DC
22
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
A
DC
22
A
N4
DC
22
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
A
DG
21
A
N1
DG
21
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
A
DG
21
A
O6
DG
21
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
A
DG
21
A
N2
DG
21
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
A
DC
20
A
N3
DC
20
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
A
DC
20
A
O2
DC
20
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
A
DC
20
A
N4
DC
20
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N1
DA
13
1_555
A
DT
19
A
N3
DT
19
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N6
DA
13
1_555
A
DT
19
A
O4
DT
19
1_555
hydrog
DA-DA MISPAIR
A
DA
14
A
N1
DA
14
1_555
A
DA
17
A
N6
DA
17
1_555
hydrog
WATSON-CRICK
A
DA
14
A
N1
DA
14
1_555
A
DT
18
A
N3
DT
18
1_555
hydrog
WATSON-CRICK
A
DA
14
A
N6
DA
14
1_555
A
DT
18
A
O4
DT
18
1_555
hydrog
DG-DA MISPAIR
A
DG
15
A
N3
DG
15
1_555
A
DA
17
A
N6
DA
17
1_555
hydrog
TYPE_6_PAIR
A
DG
25
A
N1
DG
25
1_555
A
DG
30
A
O6
DG
30
1_555
hydrog
TYPE_6_PAIR
A
DG
25
A
N2
DG
25
1_555
A
DG
30
A
N7
DG
30
1_555
hydrog
TYPE_6_PAIR
A
DG
26
A
N7
DG
26
1_555
A
DG
29
A
N2
DG
29
1_555
hydrog
TYPE_6_PAIR
A
DG
26
A
O6
DG
26
1_555
A
DG
29
A
N1
DG
29
1_555
DNA
quadruplex-duplex hybrid, duplex, quadruplex, DNA
2M91
PDB
1
2M91
1
30
2M91
1
30
2M91
A
1
1
30