0.10
0.421
4.039
-2.933
A
P
DA
1
ATOM
A
P
DA
1
1
1.00
1
P
0.16
0.818
5.069
-3.901
A
OP1
DA
1
ATOM
A
OP1
DA
1
1
1.00
1
O
0.12
0.311
4.338
-1.509
A
OP2
DA
1
ATOM
A
OP2
DA
1
1
1.00
1
O
0.11
1.400
2.800
-2.997
A
O5'
DA
1
ATOM
A
O5'
DA
1
1
1.00
1
O
0.13
1.801
2.311
-4.251
A
C5'
DA
1
ATOM
A
C5'
DA
1
1
1.00
1
C
0.08
2.995
1.329
-4.062
A
C4'
DA
1
ATOM
A
C4'
DA
1
1
1.00
1
C
0.08
4.119
2.107
-3.636
A
O4'
DA
1
ATOM
A
O4'
DA
1
1
1.00
1
O
0.07
2.825
0.234
-2.994
A
C3'
DA
1
ATOM
A
C3'
DA
1
1
1.00
1
C
0.09
3.486
-0.903
-3.541
A
O3'
DA
1
ATOM
A
O3'
DA
1
1
1.00
1
O
0.09
3.512
0.802
-1.757
A
C2'
DA
1
ATOM
A
C2'
DA
1
1
1.00
1
C
0.09
4.621
1.636
-2.392
A
C1'
DA
1
ATOM
A
C1'
DA
1
1
1.00
1
C
0.08
5.017
2.794
-1.636
A
N9
DA
1
ATOM
A
N9
DA
1
1
1.00
1
N
0.10
4.355
3.964
-1.571
A
C8
DA
1
ATOM
A
C8
DA
1
1
1.00
1
C
0.10
4.943
4.873
-0.817
A
N7
DA
1
ATOM
A
N7
DA
1
1
1.00
1
N
0.08
6.031
4.196
-0.300
A
C5
DA
1
ATOM
A
C5
DA
1
1
1.00
1
C
0.07
7.094
4.570
0.542
A
C6
DA
1
ATOM
A
C6
DA
1
1
1.00
1
C
0.08
7.194
5.794
1.058
A
N6
DA
1
ATOM
A
N6
DA
1
1
1.00
1
N
0.09
8.004
3.701
0.819
A
N1
DA
1
ATOM
A
N1
DA
1
1
1.00
1
N
0.10
7.926
2.564
0.285
A
C2
DA
1
ATOM
A
C2
DA
1
1
1.00
1
C
0.10
6.983
2.026
-0.522
A
N3
DA
1
ATOM
A
N3
DA
1
1
1.00
1
N
0.07
6.068
2.946
-0.788
A
C4
DA
1
ATOM
A
C4
DA
1
1
1.00
1
C
0.09
14.944
9.099
5.933
B
P
DA
2
ATOM
B
P
DA
1
1
1.00
1
P
0.15
15.269
9.154
4.483
B
OP1
DA
2
ATOM
B
OP1
DA
1
1
1.00
1
O
0.13
15.672
9.976
6.862
B
OP2
DA
2
ATOM
B
OP2
DA
1
1
1.00
1
O
0.10
13.348
9.362
5.980
B
O5'
DA
2
ATOM
B
O5'
DA
1
1
1.00
1
O
0.12
12.696
9.433
7.234
B
C5'
DA
2
ATOM
B
C5'
DA
1
1
1.00
1
C
0.10
11.318
9.990
7.024
B
C4'
DA
2
ATOM
B
C4'
DA
1
1
1.00
1
C
0.11
11.421
11.354
6.614
B
O4'
DA
2
ATOM
B
O4'
DA
1
1
1.00
1
O
0.10
10.430
9.273
5.987
B
C3'
DA
2
ATOM
B
C3'
DA
1
1
1.00
1
C
0.08
9.132
9.324
6.513
B
O3'
DA
2
ATOM
B
O3'
DA
1
1
1.00
1
O
0.09
10.633
10.186
4.785
B
C2'
DA
2
ATOM
B
C2'
DA
1
1
1.00
1
C
0.09
10.804
11.562
5.401
B
C1'
DA
2
ATOM
B
C1'
DA
1
1
1.00
1
C
0.09
11.568
12.473
4.612
B
N9
DA
2
ATOM
B
N9
DA
1
1
1.00
1
N
0.15
12.900
12.477
4.536
B
C8
DA
2
ATOM
B
C8
DA
1
1
1.00
1
C
0.12
13.380
13.505
3.788
B
N7
DA
2
ATOM
B
N7
DA
1
1
1.00
1
N
0.10
12.238
14.069
3.280
B
C5
DA
2
ATOM
B
C5
DA
1
1
1.00
1
C
0.12
12.104
15.166
2.454
B
C6
DA
2
ATOM
B
C6
DA
1
1
1.00
1
C
0.14
13.096
15.851
1.925
B
N6
DA
2
ATOM
B
N6
DA
1
1
1.00
1
N
0.11
10.788
15.546
2.175
B
N1
DA
2
ATOM
B
N1
DA
1
1
1.00
1
N
0.13
9.927
14.827
2.742
B
C2
DA
2
ATOM
B
C2
DA
1
1
1.00
1
C
0.11
9.928
13.794
3.511
B
N3
DA
2
ATOM
B
N3
DA
1
1
1.00
1
N
0.10
11.185
13.473
3.789
B
C4
DA
2
ATOM
B
C4
DA
1
1
1.00
1
C
0.17
0.000
0.000
-0.975
A
O
HOH
4
HETATM
C
O
HOH
2
0.33
1
O
0.18
11.665
6.734
3.904
A
O
HOH
5
HETATM
C
O
HOH
2
0.33
1
O
0.19
0.000
0.000
3.307
A
O
HOH
6
HETATM
C
O
HOH
2
0.33
1
O
0.11
0.890
2.325
0.214
A
O
HOH
7
HETATM
C
O
HOH
2
1.00
1
O
0.10
9.230
7.154
2.752
A
O
HOH
8
HETATM
C
O
HOH
2
1.00
1
O
0.22
0.020
5.012
3.134
A
O
HOH
9
HETATM
C
O
HOH
2
1.00
1
O
0.13
10.807
4.273
0.669
A
O
HOH
10
HETATM
C
O
HOH
2
1.00
1
O
0.14
-0.877
2.489
2.321
A
O
HOH
11
HETATM
C
O
HOH
2
1.00
1
O
0.21
11.664
6.735
-0.303
A
O
HOH
12
HETATM
C
O
HOH
2
0.33
1
O
0.17
0.146
6.831
1.878
A
O
HOH
13
HETATM
C
O
HOH
2
1.00
1
O
0.24
1.701
5.931
0.657
A
O
HOH
14
HETATM
C
O
HOH
2
1.00
1
O
0.28
-1.182
6.653
9.847
A
O
HOH
15
HETATM
C
O
HOH
2
1.00
1
O
0.29
11.619
1.752
9.559
B
O
HOH
9
HETATM
D
O
HOH
2
1.00
1
O
0.042867
0.024749
0.000000
0.000000
0.049498
0.000000
0.000000
0.000000
0.103306
0.00000
0.00000
0.00000
Gao, Y.G.
Robinson, H.
Guan, Y.
Liaw, Y.C.
van Boom, J.H.
van der Marel, G.A.
Wang, A.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
23.328
23.328
9.680
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
N
C
N
12
R
C
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
O
N
38
N
H
N
39
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
US
J.Biomol.Struct.Dyn.
JBSDD6
0646
0739-1102
16
69
76
9745896
Molecular structure of two crystal forms of cyclic triadenylic acid at 1A resolution.
1998
10.2210/pdb1o56/pdb
pdb_00001o56
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298.00
1
IMAGE PLATE
1997-12-29
RIGAKU
SINGLE WAVELENGTH
M
x-ray
1
1.0
ROTATING ANODE
RIGAKU RU200
894.663
DNA (5'-CD(*AP*AP*AP*)-3')
2
syn
polymer
18.015
water
13
nat
water
no
no
(DA)(DA)(DA)
AAA
A,B
polydeoxyribonucleotide
n
n
n
1
1.41
42.0000
VAPOR DIFFUSION, HANGING DROP
4.50
pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K
298.00
MPD
1
GLYCINE
1
MGCL2
1
MPD
2
software
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Refinement description
Data collection
Database references
1
0
2003-08-26
1
1
2008-04-26
1
2
2011-07-13
1
3
2011-11-16
1
4
2017-10-04
1
5
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
2003-08-26
SPRSDE
SEQUENCE
The crystallized entity is 5'-CD(*AP*AP*AP)-3', however,
each of the two independent molecules sits on the
crystallographic 3-fold axis. Remark 350 provides the way
to create cyclic D(*Ap*Ap*Ap) molecule.
RCSB
Y
RCSB
2003-08-20
REL
HOH
water
Synthetic
sample
HOH
3
2
HOH
HOH
4
A
HOH
4
2
HOH
HOH
5
A
HOH
5
2
HOH
HOH
6
A
HOH
6
2
HOH
HOH
7
A
HOH
7
2
HOH
HOH
8
A
HOH
8
2
HOH
HOH
9
A
HOH
10
2
HOH
HOH
10
A
HOH
11
2
HOH
HOH
11
A
HOH
12
2
HOH
HOH
12
A
HOH
13
2
HOH
HOH
13
A
HOH
14
2
HOH
HOH
14
A
HOH
15
2
HOH
HOH
15
A
HOH
9
2
HOH
HOH
9
B
A
1
n
1
DA
1
A
n
2
2
A
n
3
3
A
A
2
n
1
DA
2
B
n
2
3
B
n
3
4
B
0.109
author_defined_assembly
3
trimeric
author_defined_assembly
3
trimeric
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_555
-y,x-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_555
-x+y,-x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_655
-y+1,x-y,z
crystal symmetry operation
23.3280000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_665
-x+y+1,-x+1,z
crystal symmetry operation
11.6640000000
20.2026406195
0.0000000000
1
A
HOH
4
C
HOH
1
A
HOH
5
C
HOH
1
A
HOH
6
C
HOH
1
A
HOH
12
C
HOH
1
A
DA
2
A
DA
2
1
Y
1
A
DA
3
A
DA
3
1
Y
1
B
DA
3
B
DA
2
1
Y
1
B
DA
4
B
DA
3
1
Y
1
A
A
O
O
HOH
HOH
13
14
2.17
1
1.80
0.30
108.30
110.10
B
B
B
O4'
C1'
N9
DA
DA
DA
2
2
2
N
1
-5.06
0.60
118.60
113.54
B
B
B
C6
N1
C2
DA
DA
DA
2
2
2
N
1
7.39
0.50
129.30
136.69
B
B
B
N1
C2
N3
DA
DA
DA
2
2
2
N
1
4.01
0.50
117.00
121.01
B
B
B
C4
C5
C6
DA
DA
DA
2
2
2
N
1
4.38
0.40
105.80
110.18
B
B
B
N9
C4
C5
DA
DA
DA
2
2
2
N
1
A
A
C5'
C4'
DA
DA
1
1
0.045
0.007
1.512
1.557
N
1
A
A
N1
C2
DA
DA
1
1
-0.080
0.009
1.339
1.259
N
1
A
A
C6
N1
DA
DA
1
1
-0.063
0.007
1.351
1.288
N
1
B
B
N1
C2
DA
DA
2
2
-0.082
0.009
1.339
1.257
N
1
B
B
C4
C5
DA
DA
2
2
-0.070
0.007
1.383
1.313
N
1
B
B
C6
N1
DA
DA
2
2
0.047
0.007
1.351
1.398
N
1
B
B
N7
C8
DA
DA
2
2
0.048
0.007
1.311
1.359
N
1
B
B
P
O3'
DA
DA
2
2
1.59
1_555
3_665
1
A
A
P
O3'
DA
DA
1
1
1.61
1_555
2_555
1
A
A
O
O
HOH
HOH
13
15
2.17
1_555
1_554
0.109
0.900
10.000
3059
3059
1
3.000
0.900
10.000
13
55
0
42
0
0.032
0.900
10.000
1O56
3059
3.000
1
phasing
SHELXS
refinement
SHELXL-97
MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION
1
N
N
1
N
N
2
N
N
2
N
N
DNA
CYCLIC TRINUCLEOTIDE, DNA
1O56
PDB
1
1O56
1
3
1O56
1
3
1O56
A
1
1
3
2
4
1O56
2
4
1O56
B
1
1
3
143
P 3