0.019467
0.000000
0.008586
0.000000
0.016106
0.000000
0.000000
0.000000
0.043648
0.00000
0.00000
0.00000
Shinomiya, M.
Chu, W.
Carlson, R.G.
Weaver, R.F.
Takusagawa, F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
113.80
90.00
51.370
62.090
25.040
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
C5 H11 N O2
117.146
D-VALINE
D-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
n
N-METHYLVALINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C16 H12 N2 O4
296.277
2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
PHENOXAZINE
non-polymer
C3 H7 N O2
89.093
n
SARCOSINE
peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
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
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
N
N
145
R
C
N
146
N
C
N
147
N
C
N
148
N
C
N
149
N
C
N
150
N
O
N
151
N
O
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
O
N
164
N
H
N
165
N
H
N
166
N
N
N
167
N
C
N
168
S
C
N
169
N
C
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
O
N
174
N
O
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
N
N
189
S
C
N
190
N
C
N
191
N
O
N
192
N
C
N
193
N
C
N
194
N
C
N
195
N
O
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
Y
205
N
C
N
206
N
C
N
207
N
O
Y
208
N
C
N
209
N
N
Y
210
N
C
N
211
N
O
Y
212
N
C
Y
213
N
O
Y
214
N
C
Y
215
N
C
Y
216
N
C
Y
217
N
C
N
218
N
C
N
219
N
O
Y
220
N
N
Y
221
N
C
Y
222
N
C
Y
223
N
C
Y
224
N
C
N
225
N
C
N
226
N
C
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
N
N
240
N
C
N
241
N
C
N
242
N
O
N
243
N
C
N
244
N
O
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
N
N
253
S
C
N
254
N
C
N
255
N
O
N
256
R
C
N
257
N
O
N
258
N
C
N
259
N
O
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
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
N
41
N
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
Y
209
N
doub
Y
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
Y
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
doub
Y
218
N
sing
Y
219
N
doub
N
220
N
sing
Y
221
N
sing
Y
222
N
sing
Y
223
N
doub
Y
224
N
sing
N
225
N
sing
Y
226
N
sing
N
227
N
sing
Y
228
N
doub
N
229
N
sing
N
230
N
sing
Y
231
N
sing
N
232
N
doub
N
233
N
sing
Y
234
N
doub
Y
235
N
sing
Y
236
N
sing
Y
237
N
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
doub
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
doub
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
225
445
10.1016/0022-2836(92)90931-9
1593629
Crystal Structure of the 2:1 Complex between D(Gaagcttc) and the Anticancer Drug Actinomycin D.
1992
US
Biochemistry
BICHAW
0033
0006-2960
34
8481
10.1021/BI00026A032
7541244
Structural, Physical, and Biological Characteristics of RNA.DNA Binding Agent N8- Actinomycin D.
1995
10.2210/pdb2d55/pdb
pdb_00002d55
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
DIFFRACTOMETER
SINGLE WAVELENGTH
M
x-ray
1
1.0
ROTATING ANODE
2426.617
DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
2
syn
polymer
1259.447
ACTINOMYCIN D
1
nat
polymer
18.015
water
104
nat
water
no
no
(DG)(DA)(DA)(DG)(DC)(DT)(DT)(DC)
GAAGCTTC
A,B
polydeoxyribonucleotide
no
yes
T(DVA)P(SAR)(MVA)(PXZ)T(DVA)P(SAR)(MVA)
TVPGVXTVPGV
C
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
1890
STREPTOMYCES ANTIBIOTICUS
3.76
67.32
7.00
PH 7.00, VAPOR DIFFUSION, TEMPERATURE 277.00K
WATER
1
MPD
1
MGCL2
1
NA CACODYLATE
1
SPERMINE_HCL
1
WATER
2
MPD
2
-2.350
1
19
A
1
B
16
-3.646
A_DG1:DC16_B
1
-11.398
0.100
0.023
-0.184
0.233
1
20
A
2
B
15
0.546
A_DA2:DT15_B
2
-6.485
-0.612
-0.009
-0.237
6.269
1
20
A
3
B
14
-3.485
A_DA3:DT14_B
3
-9.123
-0.141
0.338
-0.216
-1.337
1
19
A
4
B
13
-5.172
A_DG4:DC13_B
4
4.018
-0.253
0.106
-0.178
-0.192
1
19
A
5
B
12
-0.692
A_DC5:DG12_B
5
1.943
0.046
0.410
-0.203
28.108
1
20
A
6
B
11
0.141
A_DT6:DA11_B
6
-5.693
-0.043
-0.656
-0.010
4.577
1
20
A
7
B
10
-11.068
A_DT7:DA10_B
7
-5.254
0.253
-0.962
-0.357
-9.243
1
19
A
8
B
9
-3.324
A_DC8:DG9_B
8
4.635
0.265
0.541
-0.193
2.495
26.624
A
A
1
2
18.870
B
B
16
15
3.268
8.530
-0.494
-1.743
AA_DG1DA2:DT15DC16_BB
1
2.397
-5.302
25.132
-5.812
1.642
3.046
44.053
A
A
2
3
2.873
B
B
15
14
2.982
2.154
-0.337
1.180
AA_DA2DA3:DT14DT15_BB
2
-2.071
2.763
43.957
1.387
0.269
2.788
34.401
A
A
3
4
31.489
B
B
14
13
3.565
17.757
-0.459
-0.616
AA_DA3DG4:DC13DT14_BB
3
-2.286
4.054
29.496
-3.954
0.401
6.223
5.209
A
A
4
5
-19.398
B
B
13
12
7.131
-1.697
-0.539
-0.165
AA_DG4DC5:DG12DC13_BB
4
1.672
-19.111
4.633
23.517
30.884
2.490
38.919
A
A
5
6
-5.517
B
B
12
11
2.683
-3.634
0.457
2.355
AA_DC5DT6:DA11DG12_BB
5
9.836
-14.933
37.533
3.890
0.276
4.247
44.772
A
A
6
7
6.265
B
B
11
10
4.233
4.764
-2.038
0.690
AA_DT6DT7:DA10DA11_BB
6
0.773
-1.017
44.524
0.342
2.767
1.539
26.939
A
A
7
8
51.723
B
B
10
9
4.110
21.047
2.074
-1.531
AA_DT7DC8:DG9DA10_BB
7
1.947
-4.786
16.798
-9.066
-3.917
atom_site
chem_comp_atom
chem_comp_bond
database_2
pdbx_validate_polymer_linkage
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Other
Advisory
Atomic model
Data collection
Database references
Derived calculations
1
0
1995-10-15
1
1
2011-06-14
1
2
2011-07-13
1
3
2011-07-27
1
4
2012-12-12
2
0
2023-11-15
_atom_site.auth_atom_id
_atom_site.label_atom_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr2_label_atom_id
1995-10-15
SPRSDE
CRYSTAL STRUCTURE OF ACTINOMYCIN Z3
CRYSTAL STRUCTURE OF N8-ACTINOMYCIN D COMPLEXED WITH D(GAAGCTTC)2
CRYSTAL STRUCTURE OF 7-AMINOACTINOMYCIN D COMPLEXED WITH NON-COMPLEMENTARY DNA
CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CGATCGATCG)2
CRYSTAL STRUCTURE OF ACTINOMYCIN D
SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (AAGCGCTT)2
CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2
SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2
SOLUTION STRUCTURE OF ACTNIOMYCIN D COMPLEXED WITH MISMATCHED DNA (GTCACCGAC)
CRYSTAL STRUCTURE OF F8-ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2
SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GATGCTTC)2
CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (ATGCTGCAT)2
CRYSTAL STRUCTURE OF 7-AMINO-ACTINOMYCIN D COMPLEXED WITH A NON-COMPLEMENTARY DNA (TTAGT)2
SOLUTIOM STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CCGTTTTGTGG)2
CRYSTAL STRUCTURE OF ACTINOMYCIN X2
BNL
Y
NDB
1995-05-01
REL
REL
HOH
water
ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE
ACTINOMYCIN FAMILY.
HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)
Antibiotic
ACTINOMYCIN D CONSISTS OF TWO PENTAMER
RINGS LINKED BY THE CHROMOPHORE (PXZ)
Actinomycin D
Polypeptide
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
HOH
2027
3
HOH
HOH
2027
A
HOH
2028
3
HOH
HOH
2028
A
HOH
2029
3
HOH
HOH
2029
A
HOH
2030
3
HOH
HOH
2030
A
HOH
2031
3
HOH
HOH
2031
A
HOH
2032
3
HOH
HOH
2032
A
HOH
2033
3
HOH
HOH
2033
A
HOH
2034
3
HOH
HOH
2034
A
HOH
2035
3
HOH
HOH
2035
A
HOH
2036
3
HOH
HOH
2036
A
HOH
2037
3
HOH
HOH
2037
A
HOH
2038
3
HOH
HOH
2038
A
HOH
2039
3
HOH
HOH
2039
A
HOH
2040
3
HOH
HOH
2040
A
HOH
2041
3
HOH
HOH
2041
A
HOH
2042
3
HOH
HOH
2042
A
HOH
2043
3
HOH
HOH
2043
A
HOH
2044
3
HOH
HOH
2044
A
HOH
2045
3
HOH
HOH
2045
A
HOH
2046
3
HOH
HOH
2046
A
HOH
2047
3
HOH
HOH
2047
A
HOH
2048
3
HOH
HOH
2048
A
HOH
2001
3
HOH
HOH
2001
B
HOH
2002
3
HOH
HOH
2002
B
HOH
2003
3
HOH
HOH
2003
B
HOH
2004
3
HOH
HOH
2004
B
HOH
2005
3
HOH
HOH
2005
B
HOH
2006
3
HOH
HOH
2006
B
HOH
2007
3
HOH
HOH
2007
B
HOH
2008
3
HOH
HOH
2008
B
HOH
2009
3
HOH
HOH
2009
B
HOH
2010
3
HOH
HOH
2010
B
HOH
2011
3
HOH
HOH
2011
B
HOH
2012
3
HOH
HOH
2012
B
HOH
2013
3
HOH
HOH
2013
B
HOH
2014
3
HOH
HOH
2014
B
HOH
2015
3
HOH
HOH
2015
B
HOH
2016
3
HOH
HOH
2016
B
HOH
2017
3
HOH
HOH
2017
B
HOH
2018
3
HOH
HOH
2018
B
HOH
2019
3
HOH
HOH
2019
B
HOH
2020
3
HOH
HOH
2020
B
HOH
2021
3
HOH
HOH
2021
B
HOH
2022
3
HOH
HOH
2022
B
HOH
2023
3
HOH
HOH
2023
B
HOH
2024
3
HOH
HOH
2024
B
HOH
2025
3
HOH
HOH
2025
B
HOH
2026
3
HOH
HOH
2026
B
HOH
2027
3
HOH
HOH
2027
B
HOH
2028
3
HOH
HOH
2028
B
HOH
2029
3
HOH
HOH
2029
B
HOH
2030
3
HOH
HOH
2030
B
HOH
2031
3
HOH
HOH
2031
B
HOH
2032
3
HOH
HOH
2032
B
HOH
2033
3
HOH
HOH
2033
B
HOH
2034
3
HOH
HOH
2034
B
HOH
2035
3
HOH
HOH
2035
B
HOH
2036
3
HOH
HOH
2036
B
HOH
2037
3
HOH
HOH
2037
B
HOH
2038
3
HOH
HOH
2038
B
HOH
2039
3
HOH
HOH
2039
B
HOH
2040
3
HOH
HOH
2040
B
HOH
2041
3
HOH
HOH
2041
B
HOH
2042
3
HOH
HOH
2042
B
HOH
2043
3
HOH
HOH
2043
B
HOH
2044
3
HOH
HOH
2044
B
HOH
2045
3
HOH
HOH
2045
B
HOH
2046
3
HOH
HOH
2046
B
HOH
2047
3
HOH
HOH
2047
B
HOH
2048
3
HOH
HOH
2048
B
HOH
2049
3
HOH
HOH
2049
B
HOH
2050
3
HOH
HOH
2050
B
HOH
2051
3
HOH
HOH
2051
B
HOH
2052
3
HOH
HOH
2052
B
HOH
2053
3
HOH
HOH
2053
B
HOH
2054
3
HOH
HOH
2054
B
HOH
2055
3
HOH
HOH
2055
B
HOH
2001
3
HOH
HOH
2001
C
DG
1
n
1
DG
1
A
DA
2
n
2
DA
2
A
DA
3
n
3
DA
3
A
DG
4
n
4
DG
4
A
DC
5
n
5
DC
5
A
DT
6
n
6
DT
6
A
DT
7
n
7
DT
7
A
DC
8
n
8
DC
8
A
DG
9
n
1
DG
9
B
DA
10
n
2
DA
10
B
DA
11
n
3
DA
11
B
DG
12
n
4
DG
12
B
DC
13
n
5
DC
13
B
DT
14
n
6
DT
14
B
DT
15
n
7
DT
15
B
DC
16
n
8
DC
16
B
THR
1
n
1
THR
1
C
DVA
2
n
2
DVA
2
C
PRO
3
n
3
PRO
3
C
SAR
4
n
4
SAR
4
C
MVA
5
n
5
MVA
5
C
PXZ
6
n
6
PXZ
6
C
THR
7
n
7
THR
7
C
DVA
8
n
8
DVA
8
C
PRO
9
n
9
PRO
9
C
SAR
10
n
10
SAR
10
C
MVA
11
n
11
MVA
11
C
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
1
B
O5'
DG
9
B
O5'
DG
1
1
Y
1
A
A
O
H2
HOH
HOH
2040
2041
1.57
1
A
DG
1
0.091
SIDE CHAIN
1
A
DA
2
0.105
SIDE CHAIN
1
A
DA
3
0.097
SIDE CHAIN
1
A
DG
4
0.082
SIDE CHAIN
1
A
DT
7
0.156
SIDE CHAIN
1
A
DC
8
0.071
SIDE CHAIN
1
B
DG
9
0.074
SIDE CHAIN
1
B
DA
10
0.079
SIDE CHAIN
1
B
DG
12
0.082
SIDE CHAIN
1
B
DT
14
0.172
SIDE CHAIN
1
B
DC
16
0.072
SIDE CHAIN
1
-8.66
1.00
110.10
101.44
A
A
A
C1'
O4'
C4'
DG
DG
DG
1
1
1
N
1
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
10.24
1.20
119.70
129.94
A
A
A
C3'
O3'
P
DG
DG
DA
1
1
2
Y
1
-11.22
1.00
110.10
98.88
A
A
A
C1'
O4'
C4'
DA
DA
DA
2
2
2
N
1
-5.40
0.70
102.20
96.80
A
A
A
C4'
C3'
C2'
DA
DA
DA
2
2
2
N
1
-7.57
0.80
105.90
98.33
A
A
A
O4'
C1'
C2'
DA
DA
DA
2
2
2
N
1
18.46
1.40
114.30
132.76
A
A
A
N9
C1'
C2'
DA
DA
DA
2
2
2
N
1
7.92
1.20
119.70
127.62
A
A
A
C3'
O3'
P
DA
DA
DA
2
2
3
Y
1
7.77
1.10
109.80
117.57
A
A
A
C5'
C4'
O4'
DA
DA
DA
3
3
3
N
1
9.20
1.20
119.70
128.90
A
A
A
C3'
O3'
P
DA
DA
DG
3
3
4
Y
1
14.82
1.60
120.90
135.72
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
1
-5.11
0.70
102.20
97.09
A
A
A
C4'
C3'
C2'
DG
DG
DG
4
4
4
N
1
-5.90
0.80
105.90
100.00
A
A
A
O4'
C1'
C2'
DG
DG
DG
4
4
4
N
1
5.92
0.30
108.30
114.22
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-5.14
0.70
102.20
97.06
A
A
A
C4'
C3'
C2'
DC
DC
DC
5
5
5
N
1
13.08
1.60
120.90
133.98
A
A
A
P
O5'
C5'
DT
DT
DT
6
6
6
N
1
-5.78
0.80
105.90
100.12
A
A
A
O4'
C1'
C2'
DT
DT
DT
6
6
6
N
1
9.51
0.30
108.30
117.81
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
-3.25
0.50
121.30
118.05
A
A
A
C6
N1
C2
DT
DT
DT
6
6
6
N
1
-3.81
0.60
115.20
111.39
A
A
A
N3
C4
C5
DT
DT
DT
6
6
6
N
1
4.12
0.60
118.00
122.12
A
A
A
C4
C5
C6
DT
DT
DT
6
6
6
N
1
-4.59
0.60
122.30
117.71
A
A
A
N3
C2
O2
DT
DT
DT
6
6
6
N
1
-4.80
0.60
122.90
118.10
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
1
11.16
1.20
119.70
130.86
A
A
A
C3'
O3'
P
DT
DT
DT
6
6
7
Y
1
5.11
0.30
108.30
113.41
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
12.71
1.20
119.70
132.41
A
A
A
C3'
O3'
P
DT
DT
DC
7
7
8
Y
1
-6.68
0.70
102.20
95.52
A
A
A
C4'
C3'
C2'
DC
DC
DC
8
8
8
N
1
7.73
0.30
108.30
116.03
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
4.46
0.60
118.90
123.36
A
A
A
N1
C2
O2
DC
DC
DC
8
8
8
N
1
-3.89
0.40
104.50
100.61
B
B
B
O4'
C4'
C3'
DG
DG
DG
9
9
9
N
1
-11.27
1.00
110.10
98.83
B
B
B
C1'
O4'
C4'
DG
DG
DG
9
9
9
N
1
6.45
0.30
108.30
114.75
B
B
B
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
12.36
1.90
104.00
116.36
B
B
B
O3'
P
O5'
DG
DA
DA
9
10
10
Y
1
5.70
0.60
118.60
124.30
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
1
-6.89
0.80
123.70
116.81
B
B
B
C5
C6
N6
DA
DA
DA
10
10
10
N
1
8.51
1.20
119.70
128.21
B
B
B
C3'
O3'
P
DA
DA
DA
10
10
11
Y
1
15.93
1.60
120.90
136.83
B
B
B
P
O5'
C5'
DA
DA
DA
11
11
11
N
1
12.32
2.00
112.30
124.62
B
B
B
C4'
C3'
O3'
DA
DA
DA
11
11
11
N
1
11.58
0.30
108.30
119.88
B
B
B
O4'
C1'
N9
DA
DA
DA
11
11
11
N
1
11.08
1.20
119.70
130.78
B
B
B
C3'
O3'
P
DA
DA
DG
11
11
12
Y
1
11.64
1.60
120.90
132.54
B
B
B
P
O5'
C5'
DG
DG
DG
12
12
12
N
1
7.32
0.30
108.30
115.62
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
12.76
2.00
112.30
125.06
B
B
B
C4'
C3'
O3'
DC
DC
DC
13
13
13
N
1
-8.57
0.80
105.90
97.33
B
B
B
O4'
C1'
C2'
DC
DC
DC
13
13
13
N
1
9.39
0.30
108.30
117.69
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
5.30
0.60
118.90
124.20
B
B
B
N1
C2
O2
DC
DC
DC
13
13
13
N
1
-5.13
0.70
121.90
116.77
B
B
B
N3
C2
O2
DC
DC
DC
13
13
13
N
1
17.11
1.20
119.70
136.81
B
B
B
C3'
O3'
P
DC
DC
DT
13
13
14
Y
1
6.75
1.10
109.80
116.55
B
B
B
C5'
C4'
O4'
DT
DT
DT
14
14
14
N
1
10.57
1.40
114.30
124.87
B
B
B
N1
C1'
C2'
DT
DT
DT
14
14
14
N
1
5.38
0.30
108.30
113.68
B
B
B
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
10.66
1.60
120.90
131.56
B
B
B
P
O5'
C5'
DC
DC
DC
16
16
16
N
1
3.19
0.30
108.30
111.49
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
A
A
P
O5'
DA
DA
2
2
0.066
0.010
1.593
1.659
N
1
A
A
C5'
C4'
DA
DA
3
3
0.064
0.007
1.512
1.576
N
1
A
A
C5'
C4'
DG
DG
4
4
0.051
0.007
1.512
1.563
N
1
A
A
C6
N1
DG
DG
4
4
-0.042
0.007
1.391
1.349
N
1
A
A
P
O5'
DT
DT
6
6
0.064
0.010
1.593
1.657
N
1
A
A
C5'
C4'
DT
DT
6
6
0.052
0.007
1.512
1.564
N
1
A
A
C5'
C4'
DT
DT
7
7
0.060
0.007
1.512
1.572
N
1
A
A
C5
C7
DT
DT
7
7
0.038
0.006
1.496
1.534
N
1
B
B
P
O5'
DA
DA
11
11
0.076
0.010
1.593
1.669
N
1
B
B
C5'
C4'
DA
DA
11
11
0.045
0.007
1.512
1.557
N
1
B
B
P
O5'
DG
DG
12
12
0.076
0.010
1.593
1.669
N
1
B
B
C5'
C4'
DG
DG
12
12
0.049
0.007
1.512
1.561
N
1
B
B
O3'
P
DC
DT
13
14
0.078
0.012
1.607
1.685
Y
0.190
0.190
3.00
7.00
1360
1
3.00
7.00
104
515
0
321
90
0.019
4.80
refinement
X-PLOR
Structural, physical and biological characteristics of RNA.DNA binding agent N8-actinomycin D
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
covale
1.347
both
C
THR
1
C
C
THR
1
1_555
C
DVA
2
C
N
DVA
2
1_555
covale
1.387
one
C
THR
1
C
OG1
THR
1
1_555
C
MVA
5
C
C
MVA
5
1_555
covale
1.337
one
C
THR
1
C
N
THR
1
1_555
C
PXZ
6
C
C0
PXZ
6
1_555
covale
1.343
both
C
DVA
2
C
C
DVA
2
1_555
C
PRO
3
C
N
PRO
3
1_555
covale
1.342
both
C
PRO
3
C
C
PRO
3
1_555
C
SAR
4
C
N
SAR
4
1_555
covale
1.350
both
C
SAR
4
C
C
SAR
4
1_555
C
MVA
5
C
N
MVA
5
1_555
covale
1.343
one
C
PXZ
6
C
C0'
PXZ
6
1_555
C
THR
7
C
N
THR
7
1_555
covale
1.335
both
C
THR
7
C
C
THR
7
1_555
C
DVA
8
C
N
DVA
8
1_555
covale
1.398
one
C
THR
7
C
OG1
THR
7
1_555
C
MVA
11
C
C
MVA
11
1_555
covale
1.348
both
C
DVA
8
C
C
DVA
8
1_555
C
PRO
9
C
N
PRO
9
1_555
covale
1.368
both
C
PRO
9
C
C
PRO
9
1_555
C
SAR
10
C
N
SAR
10
1_555
covale
1.371
both
C
SAR
10
C
C
SAR
10
1_555
C
MVA
11
C
N
MVA
11
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
16
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
16
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
16
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
DT
15
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
DT
15
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
14
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
14
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
13
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
13
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
13
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
12
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
12
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
12
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
11
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
11
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
10
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
10
B
N6
DA
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
9
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
9
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
9
B
N2
DG
1
1_555
DNA/ANTIBIOTIC
ACTINOMYCIN D, DACTINOMYCIN, ANTIBIOTIC, ANTI CANCER, ANTITUMOR, CHROMOPHORE, DEPSIPEPTIDE, DNA-ANTIBIOTIC COMPLEX
C
DVA
2
C
DVA
2
1
C
PRO
3
C
PRO
3
29.13
C
PRO
3
C
PRO
3
1
C
SAR
4
C
SAR
4
-1.57
C
DVA
8
C
DVA
8
1
C
PRO
9
C
PRO
9
19.32
C
PRO
9
C
PRO
9
1
C
SAR
10
C
SAR
10
-18.31
2D55
PDB
1
2D55
NOR00228
NOR
2
NOR00228
1
8
2D55
1
8
2D55
A
1
1
8
9
16
2D55
9
16
2D55
B
1
1
8
1
11
2D55
1
11
NOR00228
C
2
1
11
BINDING SITE FOR CHAIN C OF ACTINOMYCIN D
Software
11
A
DG
4
A
DG
4
11
1_555
A
DC
5
A
DC
5
11
1_555
A
DT
6
A
DT
6
11
1_555
A
DT
7
A
DT
7
11
1_555
A
HOH
2009
D
HOH
11
1_555
B
DA
11
B
DA
3
11
1_555
B
DG
12
B
DG
4
11
1_555
B
DC
13
B
DC
5
11
1_555
B
DT
14
B
DT
6
11
1_555
B
DT
15
B
DT
7
11
1_555
C
HOH
2001
F
HOH
11
1_555
5
C 1 2 1