1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Gyi, J.I.
Lane, A.N.
Conn, G.L.
Brown, T.
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
US
Biochemistry
BICHAW
0033
0006-2960
37
73
10.1021/bi9719713
9425027
Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes.
1998
US
Biochemistry
BICHAW
0033
0006-2960
35
12538
Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA.RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes
1996
10.2210/pdb1axp/pdb
pdb_00001axp
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3127.082
DNA (D(GAAGAGAAGC)(DOT)D(GCTTCTCTTC))
1
syn
polymer
2961.940
DNA (D(GAAGAGAAGC)(DOT)D(GCTTCTCTTC))
1
syn
polymer
DR10.DY10
DR10.DY10
no
no
(DG)(DA)(DA)(DG)(DA)(DG)(DA)(DA)(DG)(DC)
GAAGAGAAGC
A
polydeoxyribonucleotide
no
no
(DG)(DC)(DT)(DT)(DC)(DT)(DC)(DT)(DT)(DC)
GCTTCTCTTC
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
8.951
1
19
A
1
B
10
-3.160
A_DG1:DC10_B
1
-11.160
-0.385
0.399
-0.124
4.635
1
20
A
2
B
9
-3.128
A_DA2:DT9_B
2
-15.631
-0.198
0.342
-0.106
6.464
1
20
A
3
B
8
-3.633
A_DA3:DT8_B
3
-15.260
-0.188
0.529
-0.137
3.664
1
19
A
4
B
7
-4.232
A_DG4:DC7_B
4
-14.344
-0.372
0.498
-0.192
6.365
1
20
A
5
B
6
-3.791
A_DA5:DT6_B
5
-13.574
-0.209
0.602
-0.153
6.249
1
19
A
6
B
5
-4.352
A_DG6:DC5_B
6
-14.140
-0.375
0.531
-0.191
6.104
1
20
A
7
B
4
-4.106
A_DA7:DT4_B
7
-16.075
-0.197
0.483
-0.131
6.985
1
20
A
8
B
3
-4.797
A_DA8:DT3_B
8
-17.467
-0.208
0.646
-0.172
0.297
1
19
A
9
B
2
-4.061
A_DG9:DC2_B
9
-17.747
-0.348
0.520
-0.198
-9.051
1
19
A
10
B
1
-3.521
A_DC10:DG1_B
10
-12.361
0.667
0.615
-0.244
3.139
37.933
A
A
1
2
0.464
B
B
10
9
3.147
0.302
-0.047
-1.017
AA_DG1DA2:DT9DC10_BB
1
-0.326
0.501
37.930
-1.602
0.032
2.998
34.916
A
A
2
3
-1.894
B
B
9
8
2.968
-1.136
0.001
-1.058
AA_DA2DA3:DT8DT9_BB
2
-1.339
2.233
34.873
-1.606
-0.186
3.055
33.753
A
A
3
4
1.269
B
B
8
7
3.083
0.737
0.049
-1.216
AA_DA3DG4:DC7DT8_BB
3
-0.664
1.143
33.739
-2.206
-0.185
3.005
36.493
A
A
4
5
-2.619
B
B
7
6
2.961
-1.640
0.098
-1.114
AA_DG4DA5:DT6DC7_BB
4
-0.401
0.641
36.455
-1.572
-0.207
3.053
33.604
A
A
5
6
-0.684
B
B
6
5
3.039
-0.395
0.027
-1.306
AA_DA5DG6:DC5DT6_BB
5
-0.076
0.132
33.602
-2.199
-0.059
3.032
35.601
A
A
6
7
-0.163
B
B
5
4
3.029
-0.099
-0.089
-1.102
AA_DG6DA7:DT4DC5_BB
6
0.063
-0.103
35.600
-1.789
0.154
3.011
35.348
A
A
7
8
-2.625
B
B
4
3
2.972
-1.593
-0.003
-1.007
AA_DA7DA8:DT3DT4_BB
7
-1.296
2.136
35.290
-1.444
-0.171
3.179
34.822
A
A
8
9
0.201
B
B
3
2
3.183
0.120
0.048
-1.143
AA_DA8DG9:DC2DT3_BB
8
0.488
-0.815
34.819
-1.927
-0.008
3.381
41.509
A
A
9
10
-1.219
B
B
2
1
3.361
-0.863
-0.039
-1.018
AA_DG9DC10:DG1DC2_BB
9
-0.897
1.266
41.491
-1.342
-0.043
database_2
pdbx_database_status
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
Other
1
0
1998-04-22
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
_pdbx_nmr_software.name
Y
BNL
1997-10-17
REL
REL
THE ASSIGNMENTS, NOES AND COUPLING CONSTANTS DETERMINED FROM 2D HOMONUCLEAR NMR EXPERIMENTS USING UNLABELLED SAMPLE.
LOWEST POTENTIAL ENERGY AND MINIMAL VIOLATIONS AND ACCEPTABLE STEREOCHEMISTRY
32
6
NOESY
COSY
7.0
303
K
DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, DEOXYRIBOSE PSEUDOROTATIONAL PHASE ANGLES AND AMPLITUDES CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING CONSTANTS BY A LEAST SQUARES/GRID-SEARCH METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). INTERNUCLEOTIDE DISTANCE CONSTRAINTS CALCULATED FROM NOE BUILD-UP CURVES. STRUCTURES CALCULATED BY SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN AMBER FORCEFIELD AND A DISTANCE DEPENDENT DIELECTRIC CONSTANT.
simulated annealing
MOLECULAR SIMULATIONS INC.
refinement
Discover
95.0
structure solution
Felix
95.0
structure solution
NUCFIT
structure solution
pfit
structure solution
DISCOVER 95.0 (INSIGHT II)
II)
500
Varian
UNITY
600
Varian
UNITYPLUS
G
1
n
1
DG
1
A
A
2
n
2
DA
2
A
A
3
n
3
DA
3
A
G
4
n
4
DG
4
A
A
5
n
5
DA
5
A
G
6
n
6
DG
6
A
A
7
n
7
DA
7
A
A
8
n
8
DA
8
A
G
9
n
9
DG
9
A
C
10
n
10
DC
10
A
G
1
n
1
DG
1
B
C
2
n
2
DC
2
B
T
3
n
3
DT
3
B
T
4
n
4
DT
4
B
C
5
n
5
DC
5
B
T
6
n
6
DT
6
B
C
7
n
7
DC
7
B
T
8
n
8
DT
8
B
T
9
n
9
DT
9
B
C
10
n
10
DC
10
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
3
A
DG
1
0.080
SIDE CHAIN
4
B
DG
1
0.050
SIDE CHAIN
4
B
DT
3
0.069
SIDE CHAIN
5
B
DG
1
0.051
SIDE CHAIN
5
B
DT
9
0.062
SIDE CHAIN
1
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
1.98
0.30
108.30
110.28
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
2.98
0.30
108.30
111.28
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
1.99
0.30
108.30
110.29
B
B
B
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
1.98
0.30
108.30
110.28
B
B
B
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
1.97
0.30
108.30
110.27
B
B
B
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
2.17
0.30
108.30
110.47
B
B
B
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
2.20
0.30
108.30
110.50
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.44
0.30
108.30
110.74
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
2.14
0.30
108.30
110.44
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
2.61
0.30
108.30
110.91
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
2.35
0.30
108.30
110.65
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
2
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
2
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
2
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
2
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
2
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
2
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
2
1.98
0.30
108.30
110.28
B
B
B
O4'
C1'
N9
DG
DG
DG
1
1
1
N
2
2.01
0.30
108.30
110.31
B
B
B
O4'
C1'
N1
DT
DT
DT
3
3
3
N
2
2.35
0.30
108.30
110.65
B
B
B
O4'
C1'
N1
DT
DT
DT
4
4
4
N
2
2.64
0.30
108.30
110.94
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
1.86
0.30
108.30
110.16
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
2
2.15
0.30
108.30
110.45
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
2
2.61
0.30
108.30
110.91
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
2
2.37
0.30
108.30
110.67
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
3
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
3
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
3
3.07
0.30
108.30
111.37
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
3
1.86
0.30
108.30
110.16
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
3
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
3
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
3
3.46
0.30
108.30
111.76
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
3
2.84
0.30
108.30
111.14
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
3
2.09
0.30
108.30
110.39
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
1.92
0.30
108.30
110.22
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
3
2.04
0.30
108.30
110.34
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
4
2.15
0.30
108.30
110.45
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
4
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
4
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
4
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
4
2.62
0.30
108.30
110.92
B
B
B
O4'
C1'
N1
DC
DC
DC
2
2
2
N
4
2.63
0.30
108.30
110.93
B
B
B
O4'
C1'
N1
DT
DT
DT
4
4
4
N
4
1.88
0.30
108.30
110.18
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
4
2.67
0.30
108.30
110.97
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
4
2.15
0.30
108.30
110.45
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
4
1.82
0.30
108.30
110.12
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
4
2.63
0.30
108.30
110.93
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
5
1.83
0.30
108.30
110.13
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
5
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
5
1.84
0.30
108.30
110.14
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
5
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
5
1.84
0.30
108.30
110.14
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
5
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
5
2.99
0.30
108.30
111.29
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
5
2.13
0.30
108.30
110.43
B
B
B
O4'
C1'
N1
DC
DC
DC
2
2
2
N
5
1.80
0.30
108.30
110.10
B
B
B
O4'
C1'
N1
DT
DT
DT
3
3
3
N
5
2.10
0.30
108.30
110.40
B
B
B
O4'
C1'
N1
DT
DT
DT
4
4
4
N
5
2.82
0.30
108.30
111.12
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
5
2.58
0.30
108.30
110.88
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
5
2.84
0.30
108.30
111.14
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
5
2.63
0.30
108.30
110.93
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
6
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
6
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
6
1.93
0.30
108.30
110.23
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
6
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
6
1.80
0.30
108.30
110.10
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
6
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
6
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
6
2.10
0.30
108.30
110.40
B
B
B
O4'
C1'
N1
DC
DC
DC
2
2
2
N
6
1.84
0.30
108.30
110.14
B
B
B
O4'
C1'
N1
DT
DT
DT
3
3
3
N
6
2.15
0.30
108.30
110.45
B
B
B
O4'
C1'
N1
DT
DT
DT
4
4
4
N
6
2.72
0.30
108.30
111.02
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
6
2.24
0.30
108.30
110.54
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
6
2.47
0.30
108.30
110.77
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
6
2.14
0.30
108.30
110.44
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
6
2.61
0.30
108.30
110.91
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
6
2.32
0.30
108.30
110.62
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
refinement
AMBER
DNA DUPLEX CONTAINING A PURINE-RICH STRAND, NMR, 6 STRUCTURES
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
10
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
10
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
10
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
DT
9
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
DT
9
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
8
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
8
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
7
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
7
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
7
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
6
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
6
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
5
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
5
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
5
B
N4
DC
5
1_555
hydrog
DA-DT PAIR
A
DA
7
A
N6
DA
7
1_555
B
DT
3
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
4
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
4
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
3
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
3
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
DC
2
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
DC
2
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
DC
2
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
1
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
1
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
1
B
N2
DG
1
1_555
DNA
DNA DUPLEX, PURINE/PYRIMIDINE-RICH STRANDS, B-FORM, DEOXYRIBONUCLEIC ACID, DNA
1AXP
PDB
1
1AXP
1AXP
PDB
2
1AXP
1
10
1AXP
1
10
1AXP
A
1
1
10
1
10
1AXP
1
10
1AXP
B
2
1
10
1
P 1