1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Mukundan, V.T.
Phan, A.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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.Am.Chem.Soc.
JACSAT
0004
0002-7863
135
5017
5028
10.1021/ja310251r
23521617
Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences.
2013
10.2210/pdb2m4p/pdb
pdb_00002m4p
6034.862
DNA (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
1
syn
polymer
no
no
(DT)(DT)(DG)(DT)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)
TTGTGGTGGGTGGGTGGGT
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
7.784
3
6
A
12
A
16
-88.359
A_DG12:DG16_A
1
-5.556
1.610
-0.002
3.584
-1.304
3
6
A
13
A
17
-88.583
A_DG13:DG17_A
2
-2.966
1.602
-0.027
3.657
-1.546
3
6
A
14
A
18
-93.672
A_DG14:DG18_A
3
-1.692
0.795
0.013
3.717
6.348
3
6
A
10
A
6
94.091
A_DG10:DG6_A
4
2.068
-0.869
0.038
-3.707
-6.267
3
6
A
3
A
8
-91.191
A_DG3:DG8_A
5
-6.813
1.702
0.275
3.458
3.972
32.583
A
A
12
13
-3.818
A
A
16
17
3.853
-2.139
-0.825
-1.232
AA_DG12DG13:DG17DG16_AA
1
-2.380
4.248
32.430
-1.750
0.974
3.250
31.825
A
A
13
14
0.604
A
A
17
18
3.251
0.331
-0.182
-0.417
AA_DG13DG14:DG18DG17_AA
2
-0.960
1.751
31.809
-0.820
0.158
0.189
-179.507
A
A
14
10
0.187
A
A
18
6
0.188
-0.373
1.812
3.585
AA_DG14DG10:DG6DG18_AA
3
-3.719
-1.860
-179.507
-1.792
0.906
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
repository
Initial release
Data collection
Database references
Other
1
0
2013-06-19
1
1
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
BMRB
Y
PDBJ
2013-02-08
REL
REL
REL
REL
340
238
32
70
structures with the lowest energy
100
10
0.099
0.179
1
0.013
0.002
2D 1H-1H TOCSY
2D 1H-13C HSQC
2D 1H-1H NOESY
2D 1H-13C JR-HMBC
0.1-2.0
mM
.05
7.0
ambient
298
K
DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
1
lowest energy
0.1-2.0 mM DNA (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1, 90% H2O/10% D2O
90% H2O/10% D2O
Schwieters, Kuszewski, Tjandra and Clore
geometry optimization
X-PLOR NIH
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
600
Bruker
AVANCE
Bruker Avance
DT
1
n
1
DT
1
A
DT
2
n
2
DT
2
A
DG
3
n
3
DG
3
A
DT
4
n
4
DT
4
A
DG
5
n
5
DG
5
A
DG
6
n
6
DG
6
A
DT
7
n
7
DT
7
A
DG
8
n
8
DG
8
A
DG
9
n
9
DG
9
A
DG
10
n
10
DG
10
A
DT
11
n
11
DT
11
A
DG
12
n
12
DG
12
A
DG
13
n
13
DG
13
A
DG
14
n
14
DG
14
A
DT
15
n
15
DT
15
A
DG
16
n
16
DG
16
A
DG
17
n
17
DG
17
A
DG
18
n
18
DG
18
A
DT
19
n
19
DT
19
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
2
A
A
H1'
OP1
DT
DG
7
9
1.59
lowest energy, model1
Solution structure of an intramolecular propeller-type G-quadruplex containing a single bulge
1
N
N
hydrog
TYPE_6_PAIR
A
DG
3
A
N1
DG
3
1_555
A
DG
8
A
O6
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N2
DG
3
1_555
A
DG
8
A
N7
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N7
DG
3
1_555
A
DG
16
A
N2
DG
16
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
O6
DG
3
1_555
A
DG
16
A
N1
DG
16
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
N1
DG
5
1_555
A
DG
9
A
O6
DG
9
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
N2
DG
5
1_555
A
DG
9
A
N7
DG
9
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
N7
DG
5
1_555
A
DG
17
A
N2
DG
17
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
O6
DG
5
1_555
A
DG
17
A
N1
DG
17
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
6
A
N7
DG
6
1_555
A
DG
18
A
N2
DG
18
1_555
hydrog
TYPE_6_PAIR
A
DG
6
A
O6
DG
6
1_555
A
DG
18
A
N1
DG
18
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N1
DG
8
1_555
A
DG
12
A
O6
DG
12
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N2
DG
8
1_555
A
DG
12
A
N7
DG
12
1_555
hydrog
TYPE_6_PAIR
A
DG
9
A
N1
DG
9
1_555
A
DG
13
A
O6
DG
13
1_555
hydrog
TYPE_6_PAIR
A
DG
9
A
N2
DG
9
1_555
A
DG
13
A
N7
DG
13
1_555
hydrog
TYPE_6_PAIR
A
DG
10
A
N1
DG
10
1_555
A
DG
14
A
O6
DG
14
1_555
hydrog
TYPE_6_PAIR
A
DG
10
A
N2
DG
10
1_555
A
DG
14
A
N7
DG
14
1_555
hydrog
TYPE_6_PAIR
A
DG
12
A
N1
DG
12
1_555
A
DG
16
A
O6
DG
16
1_555
hydrog
TYPE_6_PAIR
A
DG
12
A
N2
DG
12
1_555
A
DG
16
A
N7
DG
16
1_555
hydrog
TYPE_6_PAIR
A
DG
13
A
N1
DG
13
1_555
A
DG
17
A
O6
DG
17
1_555
hydrog
TYPE_6_PAIR
A
DG
13
A
N2
DG
13
1_555
A
DG
17
A
N7
DG
17
1_555
hydrog
TYPE_6_PAIR
A
DG
14
A
N1
DG
14
1_555
A
DG
18
A
O6
DG
18
1_555
hydrog
TYPE_6_PAIR
A
DG
14
A
N2
DG
14
1_555
A
DG
18
A
N7
DG
18
1_555
DNA
G-quadruplex, Bulges, DNA
2M4P
PDB
1
2M4P
1
19
2M4P
1
19
2M4P
A
1
1
19