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/pdb2m92/pdb
pdb_00002m92
10702.835
34-MER DNA
1
syn
polymer
no
no
(DA)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DG)(DC)(DT)(DG)(DG)(DG)(DG)(DC)(DG)(DC)(DG)
(DA)(DA)(DG)(DC)(DA)(DT)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DG)
AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG
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
n
n
n
n
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[GGGAAGGGCGCGAAGCATTCGCGAGGTAGG] quadruplex-duplex HYBRID (CONSTRUCT III)
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
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
600
Bruker
AVANCE
Bruker Avance
700
Bruker
AVANCE
Bruker Avance
DA
1
n
1
DA
1
A
DG
2
n
2
DG
2
A
DG
3
n
3
DG
3
A
DG
4
n
4
DG
4
A
DT
5
n
5
DT
5
A
DG
6
n
6
DG
6
A
DG
7
n
7
DG
7
A
DG
8
n
8
DG
8
A
DT
9
n
9
DT
9
A
DG
10
n
10
DG
10
A
DC
11
n
11
DC
11
A
DT
12
n
12
DT
12
A
DG
13
n
13
DG
13
A
DG
14
n
14
DG
14
A
DG
15
n
15
DG
15
A
DG
16
n
16
DG
16
A
DC
17
n
17
DC
17
A
DG
18
n
18
DG
18
A
DC
19
n
19
DC
19
A
DG
20
n
20
DG
20
A
DA
21
n
21
DA
21
A
DA
22
n
22
DA
22
A
DG
23
n
23
DG
23
A
DC
24
n
24
DC
24
A
DA
25
n
25
DA
25
A
DT
26
n
26
DT
26
A
DT
27
n
27
DT
27
A
DC
28
n
28
DC
28
A
DG
29
n
29
DG
29
A
DC
30
n
30
DC
30
A
DG
31
n
31
DG
31
A
DA
32
n
32
DA
32
A
DG
33
n
33
DG
33
A
DG
34
n
34
DG
34
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
4
A
A
OP2
H5'
DC
DG
11
33
1.44
4
A
A
H1'
OP2
DG
DT
8
9
1.59
2
-3.84
0.60
122.90
119.06
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
4
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
10
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
lowest energy, model1
Structure of d[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] quadruplex-duplex hybrid
1
N
N
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
A
DT
12
A
N3
DT
12
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
A
DT
12
A
O4
DT
12
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
13
A
N2
DG
13
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
O6
DG
2
1_555
A
DG
13
A
N1
DG
13
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N1
DG
3
1_555
A
DG
7
A
O6
DG
7
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N2
DG
3
1_555
A
DG
7
A
N7
DG
7
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N7
DG
3
1_555
A
DG
14
A
N2
DG
14
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
O6
DG
3
1_555
A
DG
14
A
N1
DG
14
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N1
DG
4
1_555
A
DG
8
A
O6
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N2
DG
4
1_555
A
DG
8
A
N7
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N7
DG
4
1_555
A
DG
15
A
N2
DG
15
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
O6
DG
4
1_555
A
DG
15
A
N1
DG
15
1_555
hydrog
TYPE_6_PAIR
A
DG
6
A
N1
DG
6
1_555
A
DG
10
A
O6
DG
10
1_555
hydrog
TYPE_6_PAIR
A
DG
6
A
N2
DG
6
1_555
A
DG
10
A
N7
DG
10
1_555
hydrog
TYPE_6_PAIR
A
DG
7
A
N1
DG
7
1_555
A
DG
33
A
O6
DG
33
1_555
hydrog
TYPE_6_PAIR
A
DG
7
A
N2
DG
7
1_555
A
DG
33
A
N7
DG
33
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N1
DG
8
1_555
A
DG
34
A
O6
DG
34
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N2
DG
8
1_555
A
DG
34
A
N7
DG
34
1_555
hydrog
TYPE_6_PAIR
A
DG
10
A
N1
DG
10
1_555
A
DG
13
A
O6
DG
13
1_555
hydrog
TYPE_6_PAIR
A
DG
10
A
N2
DG
10
1_555
A
DG
13
A
N7
DG
13
1_555
hydrog
TYPE_6_PAIR
A
DG
14
A
N7
DG
14
1_555
A
DG
33
A
N2
DG
33
1_555
hydrog
TYPE_6_PAIR
A
DG
14
A
O6
DG
14
1_555
A
DG
33
A
N1
DG
33
1_555
hydrog
TYPE_6_PAIR
A
DG
15
A
N7
DG
15
1_555
A
DG
34
A
N2
DG
34
1_555
hydrog
TYPE_6_PAIR
A
DG
15
A
O6
DG
15
1_555
A
DG
34
A
N1
DG
34
1_555
hydrog
TYPE_8_PAIR
A
DG
16
A
N1
DG
16
1_555
A
DA
32
A
N1
DA
32
1_555
hydrog
TYPE_8_PAIR
A
DG
16
A
O6
DG
16
1_555
A
DA
32
A
N6
DA
32
1_555
hydrog
WATSON-CRICK
A
DC
17
A
N3
DC
17
1_555
A
DG
31
A
N1
DG
31
1_555
hydrog
WATSON-CRICK
A
DC
17
A
N4
DC
17
1_555
A
DG
31
A
O6
DG
31
1_555
hydrog
WATSON-CRICK
A
DC
17
A
O2
DC
17
1_555
A
DG
31
A
N2
DG
31
1_555
hydrog
WATSON-CRICK
A
DG
18
A
N1
DG
18
1_555
A
DC
30
A
N3
DC
30
1_555
hydrog
WATSON-CRICK
A
DG
18
A
N2
DG
18
1_555
A
DC
30
A
O2
DC
30
1_555
hydrog
WATSON-CRICK
A
DG
18
A
O6
DG
18
1_555
A
DC
30
A
N4
DC
30
1_555
hydrog
WATSON-CRICK
A
DC
19
A
N3
DC
19
1_555
A
DG
29
A
N1
DG
29
1_555
hydrog
WATSON-CRICK
A
DC
19
A
N4
DC
19
1_555
A
DG
29
A
O6
DG
29
1_555
hydrog
WATSON-CRICK
A
DC
19
A
O2
DC
19
1_555
A
DG
29
A
N2
DG
29
1_555
hydrog
WATSON-CRICK
A
DG
20
A
N1
DG
20
1_555
A
DC
28
A
N3
DC
28
1_555
hydrog
WATSON-CRICK
A
DG
20
A
N2
DG
20
1_555
A
DC
28
A
O2
DC
28
1_555
hydrog
WATSON-CRICK
A
DG
20
A
O6
DG
20
1_555
A
DC
28
A
N4
DC
28
1_555
hydrog
WATSON-CRICK
A
DA
21
A
N1
DA
21
1_555
A
DT
27
A
N3
DT
27
1_555
hydrog
WATSON-CRICK
A
DA
21
A
N6
DA
21
1_555
A
DT
27
A
O4
DT
27
1_555
hydrog
DA-DA MISPAIR
A
DA
22
A
N1
DA
22
1_555
A
DA
25
A
N6
DA
25
1_555
hydrog
WATSON-CRICK
A
DA
22
A
N1
DA
22
1_555
A
DT
26
A
N3
DT
26
1_555
hydrog
WATSON-CRICK
A
DA
22
A
N6
DA
22
1_555
A
DT
26
A
O4
DT
26
1_555
DNA
quadruplex-duplex hybrid, duplex, quadruplex, DNA
2M92
PDB
1
2M92
1
34
2M92
1
34
2M92
A
1
1
34