0.035373
0.000000
0.000000
0.000000
0.035373
0.000000
0.000000
0.000000
0.018598
0.00000
0.00000
0.00000
Hu, G.G.
Shui, X.
Leng, F.
Priebe, W.
Chaires, J.B.
Williams, L.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
28.270
28.270
53.770
C62 H66 N2 O20 2
1159.189
4-METHYLBENZYL-N-BIS[DAUNOMYCIN]
WP631
non-polymer
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
H2 O
18.015
WATER
non-polymer
Y
1
N
C
Y
2
N
C
Y
3
N
C
Y
4
N
C
N
5
N
O
Y
6
N
C
N
7
N
C
N
8
N
O
Y
9
N
C
Y
10
N
C
N
11
N
O
Y
12
N
C
N
13
S
C
N
14
N
O
N
15
N
C
N
16
S
C
N
17
N
O
N
18
N
C
N
19
N
O
N
20
N
C
N
21
N
C
Y
22
N
C
Y
23
N
C
N
24
N
O
Y
25
N
C
N
26
N
C
N
27
N
O
Y
28
N
C
N
29
N
C
N
30
R
C
N
31
N
C
N
32
S
C
N
33
N
N
N
34
S
C
N
35
N
O
N
36
S
C
N
37
N
O
N
38
N
C
N
39
N
C
Y
40
N
C
Y
41
N
C
Y
42
N
C
Y
43
N
C
Y
44
N
C
Y
45
N
C
Y
46
N
C
N
47
N
O
Y
48
N
C
N
49
N
C
N
50
N
O
Y
51
N
C
Y
52
N
C
N
53
N
O
Y
54
N
C
N
55
S
C
N
56
N
O
N
57
N
C
N
58
S
C
N
59
N
O
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
Y
64
N
C
Y
65
N
C
N
66
N
O
Y
67
N
C
N
68
N
C
N
69
N
O
Y
70
N
C
N
71
N
C
N
72
R
C
N
73
N
C
N
74
S
C
N
75
N
N
N
76
S
C
N
77
N
O
N
78
S
C
N
79
N
O
N
80
N
C
N
81
N
C
Y
82
N
C
Y
83
N
C
Y
84
N
C
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
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
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
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
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
O
N
152
N
P
N
153
N
O
N
154
N
O
N
155
N
O
N
156
N
C
N
157
R
C
N
158
N
O
N
159
S
C
N
160
N
O
N
161
N
C
N
162
R
C
Y
163
N
N
Y
164
N
C
Y
165
N
N
Y
166
N
C
Y
167
N
C
N
168
N
N
Y
169
N
N
Y
170
N
C
Y
171
N
N
Y
172
N
C
N
173
N
H
N
174
N
H
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
O
N
188
N
P
N
189
N
O
N
190
N
O
N
191
N
O
N
192
N
C
N
193
R
C
N
194
N
O
N
195
S
C
N
196
N
O
N
197
N
C
N
198
R
C
N
199
N
N
N
200
N
C
N
201
N
O
N
202
N
N
N
203
N
C
N
204
N
N
N
205
N
C
N
206
N
C
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
O
N
222
N
P
N
223
N
O
N
224
N
O
N
225
N
O
N
226
N
C
N
227
R
C
N
228
N
O
N
229
S
C
N
230
N
O
N
231
N
C
N
232
R
C
Y
233
N
N
Y
234
N
C
Y
235
N
N
Y
236
N
C
N
237
N
C
N
238
N
O
N
239
N
N
N
240
N
C
N
241
N
N
N
242
N
N
Y
243
N
C
N
244
N
H
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
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
O
N
259
N
P
N
260
N
O
N
261
N
O
N
262
N
O
N
263
N
C
N
264
R
C
N
265
N
O
N
266
S
C
N
267
N
O
N
268
N
C
N
269
R
C
N
270
N
N
N
271
N
C
N
272
N
O
N
273
N
N
N
274
N
C
N
275
N
O
N
276
N
C
N
277
N
C
N
278
N
C
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
O
N
295
N
H
N
296
N
H
Y
1
N
doub
Y
2
N
sing
N
3
N
sing
Y
4
N
sing
N
5
N
sing
Y
6
N
doub
N
7
N
sing
N
8
N
sing
Y
9
N
sing
N
10
N
sing
N
11
N
sing
Y
12
N
doub
N
13
N
doub
N
14
N
sing
Y
15
N
sing
Y
16
N
doub
N
17
N
sing
Y
18
N
doub
N
19
N
sing
N
20
N
sing
Y
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
Y
41
N
doub
N
42
N
sing
Y
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
doub
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
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
Y
76
N
doub
Y
77
N
sing
Y
78
N
sing
N
79
N
sing
Y
80
N
doub
N
81
N
sing
Y
82
N
doub
Y
83
N
sing
N
84
N
sing
Y
85
N
sing
N
86
N
sing
Y
87
N
doub
N
88
N
sing
N
89
N
sing
Y
90
N
sing
N
91
N
sing
N
92
N
sing
Y
93
N
doub
N
94
N
doub
N
95
N
sing
Y
96
N
sing
Y
97
N
doub
N
98
N
sing
Y
99
N
doub
N
100
N
sing
N
101
N
sing
Y
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
Y
122
N
doub
N
123
N
sing
Y
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
doub
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
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
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
Y
157
N
doub
Y
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
doub
N
164
N
sing
N
165
N
sing
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
Y
184
N
sing
Y
185
N
sing
Y
186
N
doub
N
187
N
sing
Y
188
N
sing
Y
189
N
sing
Y
190
N
doub
N
191
N
sing
Y
192
N
doub
N
193
N
sing
N
194
N
sing
Y
195
N
sing
Y
196
N
doub
N
197
N
sing
Y
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
doub
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
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
doub
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
doub
N
237
N
sing
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
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
Y
257
N
sing
Y
258
N
sing
Y
259
N
doub
N
260
N
sing
Y
261
N
sing
N
262
N
sing
Y
263
N
doub
N
264
N
doub
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
doub
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
doub
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
doub
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
doub
N
303
N
sing
N
304
N
sing
N
305
N
doub
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
36
5940
5946
10.1021/bi9705218
9166763
Structure of a DNA-bisdaunomycin complex.
1997
10.2210/pdb1agl/pdb
pdb_00001agl
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
294.00
1
AREA DETECTOR
1996-05-01
SDMS
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.0
ROTATING ANODE
RIGAKU RU200
1809.217
DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
1
syn
polymer
1159.189
4-METHYLBENZYL-N-BIS[DAUNOMYCIN]
1
syn
non-polymer
18.015
water
8
nat
water
no
no
(DC)(DG)(DA)(DT)(DC)(DG)
CGATCG
A
polydeoxyribonucleotide
n
n
n
n
n
n
1
2.84
56.74
VAPOR DIFFUSION, SITTING DROP
6.50
pH 6.50, VAPOR DIFFUSION, SITTING DROP
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
SPERMINE_HCL
1
WATER
2
MPD
2
7.237
1
19
A
1
A
6
-0.918
A_DC1:DG6_A
1
1.710
0.410
-0.099
-0.367
-20.524
1
19
A
2
A
5
-0.778
A_DG2:DC5_A
2
2.722
-0.610
-0.312
-0.530
-2.211
1
20
A
3
A
4
4.199
A_DA3:DT4_A
3
-5.817
-0.184
0.214
-0.211
2.211
1
20
A
4
A
3
4.199
A_DT4:DA3_A
4
-5.817
0.184
0.214
-0.211
20.524
1
19
A
5
A
2
-0.778
A_DC5:DG2_A
5
2.722
0.610
-0.312
-0.530
-7.237
1
19
A
6
A
1
-0.918
A_DG6:DC1_A
6
1.709
-0.410
-0.099
-0.367
7.190
31.554
A
A
1
2
-1.909
A
A
6
5
7.184
-1.036
0.884
1.325
AA_DC1DG2:DC5DG6_AA
1
3.211
-5.916
31.378
2.860
-0.312
3.254
36.213
A
A
2
3
4.661
A
A
5
4
3.036
2.873
-0.777
1.720
AA_DG2DA3:DT4DC5_AA
2
-7.839
12.719
35.269
2.373
0.176
3.413
29.976
A
A
3
4
-3.724
A
A
4
3
3.382
-1.925
0.000
-0.596
AA_DA3DT4:DA3DT4_AA
3
0.000
0.000
29.915
-0.741
0.000
3.254
36.213
A
A
4
5
4.661
A
A
3
2
3.036
2.873
0.777
1.720
AA_DT4DC5:DG2DA3_AA
4
7.839
-12.719
35.269
2.373
-0.176
7.190
31.554
A
A
5
6
-1.909
A
A
2
1
7.184
-1.036
-0.884
1.325
AA_DC5DG6:DC1DG2_AA
5
-3.211
5.916
31.378
2.860
0.312
chem_comp_atom
chem_comp_bond
database_2
pdbx_unobs_or_zero_occ_atoms
struct_conn
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Advisory
Data collection
Database references
Derived calculations
Refinement description
1
0
1997-04-29
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
1
4
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1997-03-25
REL
BDA
4-METHYLBENZYL-N-BIS[DAUNOMYCIN]
HOH
water
152D
DDF045
PDB
experimental model
BDA
7
2
BDA
BDA
7
A
HOH
8
3
HOH
HOH
8
A
HOH
9
3
HOH
HOH
9
A
HOH
10
3
HOH
HOH
10
A
HOH
11
3
HOH
HOH
11
A
HOH
12
3
HOH
HOH
12
A
HOH
13
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
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
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_665
-y+1,-x+1,-z+1/2
crystal symmetry operation
28.2700000000
28.2700000000
26.8850000000
1
3.83
0.60
118.90
122.73
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
2.15
0.30
108.30
110.45
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-4.47
0.60
122.30
117.83
A
A
A
N3
C2
O2
DT
DT
DT
4
4
4
N
1
-4.27
0.60
122.90
118.63
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
1
4.34
0.60
118.90
123.24
A
A
A
N1
C2
O2
DC
DC
DC
5
5
5
N
1
-4.26
0.70
121.90
117.64
A
A
A
N3
C2
O2
DC
DC
DC
5
5
5
N
PARDNA.PRO
TOPDNA.PRO
0.3140000
0.1990000
0.1990000
2.200
10.000
1061
10.000
97.400
RANDOM
1
3.000
MOLECULAR REPLACEMENT
DDF045
TR
isotropic
TR
isotropic
2.200
10.000
8
170
42
120
0
0.014
3.10
0.2850000
2.30
111
82.80
fix
fix
1.800
12.000
1AGL
11192
2058
0.000
0.0700000
1
5.5000
6.760
93.000
refinement
X-PLOR
data collection
ADSC
STRUCTURE OF A DNA-BISDAUNOMYCIN COMPLEX
1
N
N
2
N
N
3
N
N
covale
1.355
none
A
BDA
7
B
C9A
BDA
1_555
A
BDA
7
B
C9A
BDA
8_665
covale
1.360
none
A
BDA
7
B
C9B
BDA
1_555
A
BDA
7
B
C9B
BDA
8_665
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
6
A
N1
DG
6
8_665
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
6
A
O6
DG
6
8_665
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
6
A
N2
DG
6
8_665
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
DC
5
A
N3
DC
5
8_665
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
DC
5
A
O2
DC
5
8_665
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
A
DC
5
A
N4
DC
5
8_665
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
4
A
N3
DT
4
8_665
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
4
A
O4
DT
4
8_665
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
A
DA
3
A
N1
DA
3
8_665
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
A
DA
3
A
N6
DA
3
8_665
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
2
A
N1
DG
2
8_665
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
2
A
O6
DG
2
8_665
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
2
A
N2
DG
2
8_665
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
1
A
N3
DC
1
8_665
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
1
A
O2
DC
1
8_665
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
1
A
N4
DC
1
8_665
DNA
RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA
1AGL
PDB
1
1AGL
1
6
1AGL
1
6
1AGL
A
1
1
6
BINDING SITE FOR RESIDUE BDA A 7
A
BDA
7
Software
8
A
DC
1
A
DC
1
8
8_665
A
DG
2
A
DG
2
8
8_665
A
DA
3
A
DA
3
8
8_665
A
DT
4
A
DT
4
8
8_665
A
DT
4
A
DT
4
8
1_555
A
DC
5
A
DC
5
8
1_555
A
DG
6
A
DG
6
8
1_555
A
HOH
11
C
HOH
8
1_555
92
P 41 21 2