1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Radhakrishnan, I.
Patel, D.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
UK
Structure
STRUE6
2005
0969-2126
1
135
152
10.1016/0969-2126(93)90028-F
8069626
Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples.
1993
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
115
1615
Solution Structure of an Intramolecular Purine(Dot)Purine(Dot)Pyrimidine DNA Triplex
1993
10.2210/pdb135d/pdb
pdb_0000135d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9552.122
DNA TRIPLEX
1
syn
polymer
DEOXYRIBONUCLEIC ACID
no
no
(DT)(DC)(DC)(DT)(DC)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DG)(DA)(DG)(DG)(DA)(DT)
(DT)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DG)(DG)(DT)
TCCTCCTTTTTTAGGAGGATTTTTTGGTGGT
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
-14.402
L
A
5
L
A
1
-10.408
A_DT5L:DT1L_A
1
-5.362
-2.477
0.755
-1.574
7.295
1
20
A
8
A
7
1.453
A_DA8:DT7_A
2
-7.242
0.032
0.112
-0.162
-1.477
1
19
A
9
A
6
0.949
A_DG9:DC6_A
3
-10.757
-0.683
-0.512
-0.339
-6.828
1
19
A
10
A
5
-2.597
A_DG10:DC5_A
4
-4.426
-0.393
0.176
-0.253
0.152
1
20
A
11
A
4
4.230
A_DA11:DT4_A
5
-13.855
0.003
0.233
-0.221
-7.273
1
19
A
12
A
3
2.937
A_DG12:DC3_A
6
-14.638
-0.755
-0.307
-0.349
-5.824
1
19
A
13
A
2
-3.751
A_DG13:DC2_A
7
-4.620
-0.291
-0.171
-0.175
-14.662
1
20
A
14
A
1
5.462
A_DA14:DT1_A
8
-17.342
-0.005
-1.180
-0.504
-38.856
2
13
L
A
6
L
A
10
152.402
A_DT6L:DT10L_A
9
-6.894
2.943
-0.849
3.435
3.188
40.398
L
A
A
5
8
-5.093
L
A
A
1
7
3.103
-3.506
0.380
-0.871
AA_DT5LDA8:DT7DT1L_AA
1
4.693
-6.818
39.989
-0.881
-0.040
4.175
21.832
A
A
8
9
-13.308
A
A
7
6
3.936
-4.994
-0.247
-1.603
AA_DA8DG9:DC6DT7_AA
2
1.291
-3.441
21.221
-1.777
1.288
3.561
31.744
A
A
9
10
4.399
A
A
6
5
3.667
2.401
-0.079
-1.184
AA_DG9DG10:DC5DC6_AA
3
-3.054
5.597
31.512
-2.654
-0.477
3.784
37.011
A
A
10
11
-14.419
A
A
5
4
3.701
-9.066
1.534
-0.783
AA_DG10DA11:DT4DC5_AA
4
0.053
-0.085
35.921
0.183
-2.408
3.243
21.635
A
A
11
12
3.297
A
A
4
3
3.735
1.216
-0.767
-1.039
AA_DA11DG12:DC3DT4_AA
5
6.857
-18.592
20.496
-3.298
5.035
3.209
35.858
A
A
12
13
-0.085
A
A
3
2
3.212
-0.052
0.144
-1.087
AA_DG12DG13:DC2DC3_AA
6
-0.791
1.285
35.850
-1.758
-0.345
3.275
36.450
A
A
13
14
15.374
A
A
2
1
3.634
9.509
0.665
-1.058
AA_DG13DA14:DT1DC2_AA
7
1.640
-2.651
35.191
-3.110
-0.819
3.526
-23.925
L
A
A
14
6
3.433
L
A
A
1
10
3.597
-1.420
-0.115
-1.010
AA_DA14DT6L:DT10LDT1_AA
8
2.395
5.791
-23.764
2.941
0.574
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1994-04-30
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
MINIMIZED AVERAGE STRUCTURE
ENSEMBLE OF 14 STRUCTURES
Y
BNL
1993-08-30
REL
CHEMICALLY SYNTHESIZED
sample
1
RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045.
RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY
BRUNGER
refinement
X-PLOR
T
1
n
1
DT
1
A
C
2
n
2
DC
2
A
C
3
n
3
DC
3
A
T
4
n
4
DT
4
A
C
5
n
5
DC
5
A
C
6
n
6
DC
6
A
T
7
n
7
DT
7
A
T
1
n
8
L
DT
1
A
n
9
L
2
A
n
10
L
3
A
n
11
L
4
A
T
5
n
12
L
DT
5
A
A
8
n
13
DA
8
A
G
9
n
14
DG
9
A
G
10
n
15
DG
10
A
A
11
n
16
DA
11
A
G
12
n
17
DG
12
A
G
13
n
18
DG
13
A
A
14
n
19
DA
14
A
T
6
n
20
L
DT
6
A
n
21
L
7
A
n
22
L
8
A
n
23
L
9
A
T
10
n
24
L
DT
10
A
T
15
n
25
DT
15
A
G
16
n
26
DG
16
A
G
17
n
27
DG
17
A
T
18
n
28
DT
18
A
G
19
n
29
DG
19
A
G
20
n
30
DG
20
A
T
21
n
31
DT
21
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
L
1
A
P
DT
5
A
P
DT
12
1
Y
L
1
A
OP1
DT
5
A
OP1
DT
12
1
Y
L
1
A
OP2
DT
5
A
OP2
DT
12
1
Y
L
1
A
P
DT
10
A
P
DT
24
1
Y
L
1
A
OP1
DT
10
A
OP1
DT
24
1
Y
L
1
A
OP2
DT
10
A
OP2
DT
24
1
Y
L
1
A
DT
2
A
DT
9
1
Y
L
1
A
DT
3
A
DT
10
1
Y
L
1
A
DT
4
A
DT
11
1
Y
L
1
A
DT
7
A
DT
21
1
Y
L
1
A
DT
8
A
DT
22
1
Y
L
1
A
DT
9
A
DT
23
1
Y
1
-5.92
0.80
105.90
99.98
A
A
A
O4'
C1'
C2'
DT
DT
DT
1
1
1
N
1
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
-4.24
0.70
102.20
97.96
A
A
A
C4'
C3'
C2'
DC
DC
DC
2
2
2
N
1
-5.06
0.80
105.90
100.84
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
1
4.25
0.60
118.90
123.15
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
1
-4.28
0.70
121.90
117.62
A
A
A
N3
C2
O2
DC
DC
DC
2
2
2
N
1
-7.14
0.70
108.00
100.86
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-7.63
1.00
110.10
102.47
A
A
A
C1'
O4'
C4'
DT
DT
DT
4
4
4
N
1
-6.88
0.80
105.90
99.02
A
A
A
O4'
C1'
C2'
DT
DT
DT
4
4
4
N
1
8.49
0.30
108.30
116.79
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
-3.83
0.60
122.30
118.47
A
A
A
N3
C2
O2
DT
DT
DT
4
4
4
N
1
3.99
0.60
118.90
122.89
A
A
A
N1
C2
O2
DC
DC
DC
5
5
5
N
1
-7.06
1.00
110.10
103.04
A
A
A
C1'
O4'
C4'
DT
DT
DT
7
7
7
N
1
-6.39
0.80
105.90
99.51
A
A
A
O4'
C1'
C2'
DT
DT
DT
7
7
7
N
1
4.48
0.30
108.30
112.78
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
L
L
L
1
-4.82
0.60
122.90
118.08
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
L
L
L
1
-3.91
0.60
122.90
118.99
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
1.89
0.30
108.30
110.19
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
-4.92
0.80
105.90
100.98
A
A
A
O4'
C1'
C2'
DG
DG
DG
10
10
10
N
1
3.22
0.30
108.30
111.52
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
4.64
0.30
108.30
112.94
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
1
-8.79
0.80
105.90
97.11
A
A
A
O4'
C1'
C2'
DG
DG
DG
13
13
13
N
1
4.89
0.30
108.30
113.19
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
6.91
0.30
108.30
115.21
A
A
A
O4'
C1'
N9
DA
DA
DA
14
14
14
N
L
L
L
1
-8.73
0.70
108.00
99.27
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
L
L
L
1
4.11
0.60
118.00
122.11
A
A
A
C4
C5
C6
DT
DT
DT
6
6
6
N
L
L
L
1
-3.75
0.60
122.90
119.15
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
L
L
L
1
-6.35
1.00
110.10
103.75
A
A
A
C1'
O4'
C4'
DT
DT
DT
10
10
10
N
L
L
L
1
-5.69
0.80
105.90
100.21
A
A
A
O4'
C1'
C2'
DT
DT
DT
10
10
10
N
L
L
L
1
3.18
0.30
108.30
111.48
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
-8.37
1.00
110.10
101.73
A
A
A
C1'
O4'
C4'
DT
DT
DT
15
15
15
N
1
-8.48
0.70
102.20
93.72
A
A
A
C4'
C3'
C2'
DT
DT
DT
15
15
15
N
1
5.72
0.30
108.30
114.02
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
3.95
0.60
114.60
118.55
A
A
A
N1
C2
N3
DT
DT
DT
15
15
15
N
1
-3.92
0.60
122.90
118.98
A
A
A
C6
C5
C7
DT
DT
DT
15
15
15
N
1
-5.14
0.80
105.90
100.76
A
A
A
O4'
C1'
C2'
DG
DG
DG
16
16
16
N
1
4.35
0.70
110.30
114.65
A
A
A
C1'
O4'
C4'
DG
DG
DG
17
17
17
N
1
-4.47
0.70
102.20
97.73
A
A
A
C4'
C3'
C2'
DT
DT
DT
18
18
18
N
1
-3.64
0.60
122.30
118.66
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
1
-5.84
0.60
122.90
117.06
A
A
A
C6
C5
C7
DT
DT
DT
18
18
18
N
1
-11.60
1.90
104.00
92.40
A
A
A
O3'
P
O5'
DG
DG
DG
19
20
20
Y
1
5.62
0.70
110.30
115.92
A
A
A
C1'
O4'
C4'
DG
DG
DG
20
20
20
N
1
-3.55
0.40
104.50
100.95
A
A
A
O4'
C4'
C3'
DT
DT
DT
21
21
21
N
1
-6.34
1.00
110.10
103.76
A
A
A
C1'
O4'
C4'
DT
DT
DT
21
21
21
N
1
-5.22
0.70
102.20
96.98
A
A
A
C4'
C3'
C2'
DT
DT
DT
21
21
21
N
1
-3.62
0.60
122.90
119.28
A
A
A
C6
C5
C7
DT
DT
DT
21
21
21
N
1
A
A
C3'
C2'
DT
DT
1
1
0.078
0.012
1.518
1.596
N
1
A
A
C2'
C1'
DT
DT
1
1
0.063
0.010
1.519
1.582
N
1
A
A
C5
C7
DT
DT
1
1
0.038
0.006
1.496
1.534
N
1
A
A
N1
C6
DC
DC
2
2
0.040
0.006
1.367
1.407
N
1
A
A
N1
C6
DC
DC
3
3
0.037
0.006
1.367
1.404
N
1
A
A
C5
C7
DT
DT
4
4
0.042
0.006
1.496
1.538
N
1
A
A
N1
C6
DC
DC
5
5
0.047
0.006
1.367
1.414
N
1
A
A
C5
C7
DT
DT
7
7
0.050
0.006
1.496
1.546
N
L
L
1
A
A
C5
C7
DT
DT
5
5
0.042
0.006
1.496
1.538
N
1
A
A
C2'
C1'
DA
DA
8
8
0.065
0.010
1.519
1.584
N
1
A
A
C4'
C3'
DG
DG
9
9
0.117
0.010
1.529
1.646
N
1
A
A
C3'
C2'
DG
DG
9
9
0.124
0.012
1.518
1.642
N
1
A
A
C2'
C1'
DG
DG
9
9
0.063
0.010
1.519
1.582
N
1
A
A
C4'
C3'
DA
DA
11
11
0.061
0.010
1.529
1.590
N
1
A
A
C3'
C2'
DA
DA
11
11
0.100
0.012
1.518
1.618
N
L
L
1
A
A
C3'
C2'
DT
DT
6
6
0.082
0.012
1.518
1.600
N
L
L
1
A
A
C2'
C1'
DT
DT
6
6
0.102
0.010
1.519
1.621
N
1
A
A
C3'
C2'
DT
DT
15
15
0.123
0.012
1.518
1.641
N
1
A
A
C2'
C1'
DT
DT
15
15
0.063
0.010
1.519
1.582
N
1
A
A
C2'
C1'
DG
DG
17
17
0.083
0.010
1.519
1.602
N
1
A
A
C3'
C2'
DT
DT
18
18
0.128
0.012
1.518
1.646
N
1
A
A
C2'
C1'
DT
DT
18
18
0.111
0.010
1.519
1.630
N
1
A
A
C5
C7
DT
DT
18
18
0.043
0.006
1.496
1.539
N
1
A
A
C2'
C1'
DG
DG
19
19
0.085
0.010
1.519
1.604
N
1
A
A
C3'
C2'
DG
DG
20
20
0.077
0.012
1.518
1.595
N
1
A
A
C2'
C1'
DG
DG
20
20
0.098
0.010
1.519
1.617
N
1
A
A
C4'
C3'
DT
DT
21
21
0.080
0.010
1.529
1.609
N
1
A
A
C5
C7
DT
DT
21
21
0.041
0.006
1.496
1.537
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES
1
N
N
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
A
DA
14
A
N1
DA
19
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
A
DA
14
A
N6
DA
19
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
13
A
N1
DG
18
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
13
A
O6
DG
18
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
13
A
N2
DG
18
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
A
DG
12
A
N1
DG
17
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
A
DG
12
A
O6
DG
17
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
A
DG
12
A
N2
DG
17
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
A
DA
11
A
N1
DA
16
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
A
DA
11
A
N6
DA
16
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
10
A
N1
DG
15
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
10
A
O6
DG
15
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
10
A
N2
DG
15
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
A
DG
9
A
N1
DG
14
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
A
DG
9
A
O6
DG
14
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
A
DG
9
A
N2
DG
14
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
A
DA
8
A
N1
DA
13
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
A
DA
8
A
N6
DA
13
1_555
hydrog
DT-DT MISPAIR
L
L
A
DT
1
A
N3
DT
8
1_555
A
DT
5
A
O4
DT
12
1_555
hydrog
REVERSED HOOGSTEEN
A
DA
8
A
N6
DA
13
1_555
A
DT
21
A
O2
DT
31
1_555
hydrog
REVERSED HOOGSTEEN
A
DA
8
A
N7
DA
13
1_555
A
DT
21
A
N3
DT
31
1_555
hydrog
TYPE_7_PAIR
A
DG
9
A
N7
DG
14
1_555
A
DG
20
A
N1
DG
30
1_555
hydrog
TYPE_7_PAIR
A
DG
9
A
O6
DG
14
1_555
A
DG
20
A
N2
DG
30
1_555
hydrog
TYPE_7_PAIR
A
DG
10
A
N7
DG
15
1_555
A
DG
19
A
N1
DG
29
1_555
hydrog
TYPE_7_PAIR
A
DG
10
A
O6
DG
15
1_555
A
DG
19
A
N2
DG
29
1_555
hydrog
REVERSED HOOGSTEEN
A
DA
11
A
N6
DA
16
1_555
A
DT
18
A
O2
DT
28
1_555
hydrog
REVERSED HOOGSTEEN
A
DA
11
A
N7
DA
16
1_555
A
DT
18
A
N3
DT
28
1_555
hydrog
TYPE_7_PAIR
A
DG
12
A
N7
DG
17
1_555
A
DG
17
A
N1
DG
27
1_555
hydrog
TYPE_7_PAIR
A
DG
12
A
O6
DG
17
1_555
A
DG
17
A
N2
DG
27
1_555
hydrog
TYPE_7_PAIR
A
DG
13
A
N7
DG
18
1_555
A
DG
16
A
N1
DG
26
1_555
hydrog
TYPE_7_PAIR
A
DG
13
A
O6
DG
18
1_555
A
DG
16
A
N2
DG
26
1_555
hydrog
REVERSED HOOGSTEEN
A
DA
14
A
N6
DA
19
1_555
A
DT
15
A
O2
DT
25
1_555
hydrog
REVERSED HOOGSTEEN
A
DA
14
A
N7
DA
19
1_555
A
DT
15
A
N3
DT
25
1_555
hydrog
TYPE_13_PAIR
L
L
A
DT
6
A
N3
DT
20
1_555
A
DT
10
A
O2
DT
24
1_555
hydrog
TYPE_13_PAIR
L
L
A
DT
6
A
O2
DT
20
1_555
A
DT
10
A
N3
DT
24
1_555
DNA
DNA, TRIPLEX
135D
PDB
1
135D
1
21
135D
1
21
135D
A
1
1
31
1
P 1