1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Denisov, A.
Bekiroglu, S.
Maltseva, T.
Sandstrom, A.
Altmann, K.-H.
Egli, M.
Chattopadhyaya, 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
C12 H19 N2 O7 P
334.262
n
6'-ALPHA-METHYL CARBOCYCLIC THYMIDINE 5'-MONOPHOSPHATE
DNA linking
US
J.Biomol.Struct.Dyn.
JBSDD6
0646
0739-1102
16
547
568
10052613
The solution conformation of a carbocyclic analog of the Dickerson-Drew dodecamer: comparison with its own X-ray structure and that of the NMR structure of the native counterpart.
1998
10.2210/pdb1dau/pdb
pdb_00001dau
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3687.500
DNA (5'-D(*CP*GP*CP*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3')
2
syn
polymer
no
yes
(DC)(DG)(DC)(DG)(DA)(DA)(T32)(T32)(DC)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
6.703
1
19
A
1
B
24
5.498
A_DC1:DG24_B
1
-28.705
-0.078
-0.617
-0.057
5.641
1
19
A
2
B
23
-1.123
A_DG2:DC23_B
2
-1.098
-0.167
0.474
0.010
-0.118
1
19
A
3
B
22
-2.077
A_DC3:DG22_B
3
-7.451
0.862
0.201
-0.187
10.393
1
19
A
4
B
21
0.092
A_DG4:DC21_B
4
5.457
-0.116
0.180
0.064
-11.665
1
20
A
5
B
20
-2.333
A_DA5:T3220_B
5
-3.588
0.679
-1.003
-0.046
-2.625
1
20
A
6
B
19
-0.194
A_DA6:T3219_B
6
1.878
0.445
-0.717
0.044
2.630
1
20
A
7
B
18
-0.188
A_T327:DA18_B
7
1.901
-0.444
-0.718
0.044
11.663
1
20
A
8
B
17
-2.338
A_T328:DA17_B
8
-3.600
-0.679
-1.003
-0.046
-10.397
1
19
A
9
B
16
0.085
A_DC9:DG16_B
9
5.477
0.117
0.181
0.064
0.125
1
19
A
10
B
15
-2.073
A_DG10:DC15_B
10
-7.440
-0.863
0.202
-0.187
-5.636
1
19
A
11
B
14
-1.116
A_DC11:DG14_B
11
-1.097
0.167
0.474
0.010
-6.694
1
19
A
12
B
13
5.484
A_DG12:DC13_B
12
-28.714
0.079
-0.617
-0.057
3.178
38.423
A
A
1
2
19.962
B
B
24
23
3.437
12.691
-0.336
-0.032
AA_DC1DG2:DC23DG24_BB
1
-11.921
18.751
34.385
-1.744
-1.083
3.350
40.788
A
A
2
3
5.763
B
B
23
22
3.443
4.009
0.065
-0.820
AA_DG2DC3:DG22DC23_BB
2
1.761
-2.532
40.563
-1.636
0.109
2.972
24.847
A
A
3
4
0.185
B
B
22
21
3.003
0.080
0.428
-1.045
AA_DC3DG4:DC21DG22_BB
3
-1.376
3.199
24.809
-2.450
-1.373
3.513
42.023
A
A
4
5
12.818
B
B
21
20
3.979
9.054
-0.109
-1.273
AA_DG4DA5:T3220DC21_BB
4
9.365
-13.259
40.041
-2.879
1.294
3.132
28.789
A
A
5
6
1.248
B
B
20
19
3.202
0.620
0.432
-0.963
AA_DA5DA6:T3219T3220_BB
5
-2.505
5.045
28.676
-2.072
-1.413
3.150
24.917
A
A
6
7
4.561
B
B
19
18
3.286
1.966
0.000
-1.622
AA_DA6T327:DA18T3219_BB
6
0.010
-0.024
24.841
-4.340
0.002
3.133
28.784
A
A
7
8
1.262
B
B
18
17
3.202
0.627
-0.432
-0.963
AA_T327T328:DA17DA18_BB
7
2.498
-5.031
28.671
-2.073
1.412
3.513
42.031
A
A
8
9
12.827
B
B
17
16
3.980
9.061
0.109
-1.273
AA_T328DC9:DG16DA17_BB
8
-9.368
13.261
40.046
-2.879
-1.294
2.971
24.840
A
A
9
10
0.163
B
B
16
15
3.002
0.070
-0.427
-1.045
AA_DC9DG10:DC15DG16_BB
9
1.370
-3.186
24.803
-2.449
1.371
3.351
40.787
A
A
10
11
5.758
B
B
15
14
3.443
4.006
-0.065
-0.820
AA_DG10DC11:DG14DC15_BB
10
-1.748
2.513
40.562
-1.636
-0.108
3.178
38.428
A
A
11
12
19.963
B
B
14
13
3.437
12.694
0.335
-0.032
AA_DC11DG12:DC13DG14_BB
11
11.915
-18.738
34.392
-1.744
1.082
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
1
0
1998-05-27
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
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
MINIMIZED AVERAGE STRUCTURE
Y
BNL
1998-01-21
REL
LOWEST ENERGY, BEST AGREEMENT WITH NOE VOLUMES
9
1
NOESY
DQF-COSY
7.0
293
K
REFINEMENT DETAILS CAN BE FOUND IN THE PAPER.
RESTRAINED MD
PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
refinement
Amber
4.1
structure solution
AURELIA
structure solution
Amber
structure solution
MARDIGRAS
600
Bruker
DRX 600
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
DC
3
n
3
DC
3
A
DG
4
n
4
DG
4
A
DA
5
n
5
DA
5
A
DA
6
n
6
DA
6
A
T32
7
n
7
T32
7
A
T32
8
n
8
T32
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
DC
13
n
1
DC
13
B
DG
14
n
2
DG
14
B
DC
15
n
3
DC
15
B
DG
16
n
4
DG
16
B
DA
17
n
5
DA
17
B
DA
18
n
6
DA
18
B
T32
19
n
7
T32
19
B
T32
20
n
8
T32
20
B
DC
21
n
9
DC
21
B
DG
22
n
10
DG
22
B
DC
23
n
11
DC
23
B
DG
24
n
12
DG
24
B
author_defined_assembly
2
dimeric
A
T32
7
A
T32
7
DT
A
T32
8
A
T32
8
DT
B
T32
19
B
T32
7
DT
B
T32
20
B
T32
8
DT
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
1
4.13
0.30
108.30
112.43
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
4.03
0.60
106.00
110.03
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
4.08
0.30
108.30
112.38
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
1.83
0.30
108.30
110.13
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
3.76
0.60
106.00
109.76
A
A
A
O4'
C4'
C3'
DC
DC
DC
9
9
9
N
1
5.13
0.30
108.30
113.43
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
6.33
0.60
106.00
112.33
A
A
A
O4'
C4'
C3'
DC
DC
DC
11
11
11
N
1
4.12
0.30
108.30
112.42
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
4.04
0.60
106.00
110.04
B
B
B
O4'
C4'
C3'
DC
DC
DC
15
15
15
N
1
4.12
0.30
108.30
112.42
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
1.83
0.30
108.30
110.13
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
3.76
0.60
106.00
109.76
B
B
B
O4'
C4'
C3'
DC
DC
DC
21
21
21
N
1
5.17
0.30
108.30
113.47
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
6.35
0.60
106.00
112.35
B
B
B
O4'
C4'
C3'
DC
DC
DC
23
23
23
N
refinement
AMBER
Analog of dickerson-drew DNA dodecamer with 6'-alpha-methyl carbocyclic thymidines, NMR, minimized average structure
1
N
N
1
N
N
covale
1.616
both
A
DA
6
A
O3'
DA
6
1_555
A
T32
7
A
P
T32
7
1_555
covale
1.611
one
A
T32
7
A
O3'
T32
7
1_555
A
T32
8
A
P
T32
8
1_555
covale
1.621
one
A
T32
8
A
O3'
T32
8
1_555
A
DC
9
A
P
DC
9
1_555
covale
1.617
both
B
DA
18
B
O3'
DA
6
1_555
B
T32
19
B
P
T32
7
1_555
covale
1.612
one
B
T32
19
B
O3'
T32
7
1_555
B
T32
20
B
P
T32
8
1_555
covale
1.620
one
B
T32
20
B
O3'
T32
8
1_555
B
DC
21
B
P
DC
9
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
24
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
24
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
24
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
23
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
23
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
23
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
22
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
21
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
21
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
21
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
T32
20
B
N3
T32
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
T32
20
B
O4
T32
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
T32
19
B
N3
T32
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
T32
19
B
O4
T32
7
1_555
hydrog
DA-T32 PAIR
A
DA
6
A
N1
DA
6
1_555
B
T32
20
B
N3
T32
8
1_555
hydrog
WATSON-CRICK
A
T32
7
A
N3
T32
7
1_555
B
DA
18
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
T32
7
A
O4
T32
7
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
T32
8
A
N3
T32
8
1_555
B
DA
17
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
T32
8
A
O4
T32
8
1_555
B
DA
17
B
N6
DA
5
1_555
hydrog
T32-DA PAIR
A
T32
8
A
N3
T32
8
1_555
B
DA
18
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
16
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
13
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
13
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
13
B
N4
DC
1
1_555
DNA
DNA, CARBOCYCLIC, DODECAMER, DEOXYRIBONUCLEIC ACID, MINIMIZED AVERAGE STRUCTURE
1DAU
PDB
1
1DAU
1
12
1DAU
1
12
1DAU
A
1
1
12
13
24
1DAU
13
24
1DAU
B
1
1
12
1
P 1