1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lin, C.H.
Patel, D.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
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C26 H27 N3 O8
509.508
4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER
DUOCARMYCIN A
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
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
Y
147
N
C
Y
148
N
C
Y
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
N
153
N
C
N
154
S
C
N
155
N
C
N
156
N
N
N
157
N
C
Y
158
N
C
Y
159
N
C
Y
160
N
C
Y
161
N
C
Y
162
N
C
Y
163
N
C
Y
164
N
C
Y
165
N
C
Y
166
N
N
N
167
N
O
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
O
N
172
N
C
N
173
N
O
N
174
N
O
N
175
N
O
N
176
N
C
N
177
N
C
N
178
N
O
N
179
N
O
N
180
N
C
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
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
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
N
205
N
H
N
206
N
H
N
207
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
doub
Y
158
N
doub
Y
159
N
sing
Y
160
N
sing
Y
161
N
doub
N
162
N
sing
Y
163
N
sing
N
164
N
sing
Y
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
doub
Y
180
N
doub
Y
181
N
sing
Y
182
N
sing
N
183
N
sing
Y
184
N
doub
Y
185
N
sing
Y
186
N
sing
N
187
N
sing
Y
188
N
doub
N
189
N
sing
Y
190
N
sing
N
191
N
sing
Y
192
N
doub
N
193
N
sing
Y
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
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
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
doub
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
248
162
179
10.1006/jmbi.1995.0209
7731041
Solution structure of the covalent duocarmycin A-DNA duplex complex.
1995
10.2210/pdb107d/pdb
pdb_0000107d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2039.359
DNA (5'-D(*CP*CP*TP*TP*TP*TP*C)-3')
1
syn
polymer
2195.487
DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3')
1
syn
polymer
CHEMICALLY SYNTHESIZED
509.508
4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER
1
syn
non-polymer
DEOXYRIBONUCLEIC ACID
DEOXYRIBONUCLEIC ACID
no
no
(DC)(DC)(DT)(DT)(DT)(DT)(DC)
CCTTTTC
A
polydeoxyribonucleotide
no
no
(DG)(DA)(DA)(DA)(DA)(DG)(DG)
GAAAAGG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
3.839
1
19
A
1
B
14
-0.998
A_DC1:DG14_B
1
-3.256
0.473
-0.285
-0.264
-1.193
1
19
A
2
B
13
-2.815
A_DC2:DG13_B
2
-6.733
0.466
-0.032
-0.220
2.465
1
20
A
3
B
12
-9.859
A_DT3:DA12_B
3
-14.247
-0.679
-0.275
0.151
7.883
1
20
A
4
B
11
6.447
A_DT4:DA11_B
4
-27.323
-0.233
-0.064
-0.117
-3.567
1
20
A
5
B
10
7.911
A_DT5:DA10_B
5
-26.784
-0.126
-0.100
-0.207
-4.502
1
20
A
6
B
9
-4.255
A_DT6:DA9_B
6
-6.098
0.217
0.212
-0.131
5.168
1
19
A
7
B
8
-0.701
A_DC7:DG8_B
7
-10.630
0.738
-0.343
-0.307
3.569
37.417
A
A
1
2
-1.446
B
B
14
13
3.455
-0.926
-1.346
-0.311
AA_DC1DC2:DG13DG14_BB
1
-3.521
5.497
37.246
-0.354
1.601
3.243
31.573
A
A
2
3
-1.450
B
B
13
12
3.278
-0.783
0.360
1.543
AA_DC2DT3:DA12DG13_BB
2
6.643
-12.297
30.874
2.983
0.582
2.841
33.878
A
A
3
4
3.588
B
B
12
11
2.871
2.089
0.726
-0.148
AA_DT3DT4:DA11DA12_BB
3
-0.712
1.222
33.808
-0.548
-1.347
3.283
43.317
A
A
4
5
-4.675
B
B
11
10
3.313
-3.434
0.440
0.652
AA_DT4DT5:DA10DA11_BB
4
6.797
-9.252
42.674
1.223
0.077
3.160
33.642
A
A
5
6
1.362
B
B
10
9
3.157
0.788
-0.207
-0.127
AA_DT5DT6:DA9DA10_BB
5
-1.785
3.085
33.587
-0.344
0.076
2.984
41.194
A
A
6
7
-0.786
B
B
9
8
2.847
-0.551
1.084
0.046
AA_DT6DC7:DG8DA9_BB
6
6.945
-9.914
40.626
0.119
-0.868
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
chem_comp_atom
chem_comp_bond
entity
pdbx_entity_src_syn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Data collection
Source and taxonomy
Structure summary
1
0
1995-05-08
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
1
4
2024-03-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_entity.details
Y
BNL
1995-01-17
REL
DUO
4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER
CHEMICALLY SYNTHESIZED
sample
CHEMICALLY SYNTHESIZED
sample
DUOCARMYCIN A WAS PROVIDED BY KYOWA HAKKO KOGYO CO., JAPAN.
4
TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE 2-D NMR DATA. ONE INITIAL VELOCITY SEED WAS USED FOR EACH STARTING STRUCTURE WHICH YIELDS TWO DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER WITH TWO INITIAL VELOCITIES USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS TO GENERATE THE FINAL FOUR STRUCTURES. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.0 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 40, 80, 120 AND 160 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1-MODEL4 R(1/6) FACTOR 0.042-0.045 BOND (ANG) 0.009-0.010 ANGLES (DEG) 3.078-3.780 IMPROPERS (DEG) 0.310-0.321. THE STRUCTURE HAS APPROXIMATE TWO-FOLD SYMMETRY RELATING THE TWO STRANDS OF THE DNA WITH THE SYMMETRY AXIS PERPENDICULAR TO THE HELICAL AXIS. THE TRANSFORMATION MATRIX WAS CALCULATED FOR THE AVERAGED STRUCTURE OF THE FOUR MODELS.
MOLECULAR DYNAMICS, MATRIX RELAXATION
BRUNGER
refinement
X-PLOR
DUO
15
3
DUO
DUO
15
B
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
T
3
n
3
DT
3
A
T
4
n
4
DT
4
A
T
5
n
5
DT
5
A
T
6
n
6
DT
6
A
C
7
n
7
DC
7
A
G
8
n
1
DG
8
B
A
9
n
2
DA
9
B
A
10
n
3
DA
10
B
A
11
n
4
DA
11
B
A
12
n
5
DA
12
B
G
13
n
6
DG
13
B
G
14
n
7
DG
14
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
1
B
B
N3
C10
DA
DUO
12
15
1.41
2
B
B
N3
C10
DA
DUO
12
15
1.41
3
B
B
N3
C10
DA
DUO
12
15
1.41
4
B
B
N3
C10
DA
DUO
12
15
1.40
1
-5.54
0.80
105.90
100.36
A
A
A
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
1
9.35
0.30
108.30
117.65
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.95
0.60
118.90
122.85
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
1
5.10
0.30
108.30
113.40
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
-3.66
0.60
122.90
119.24
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
1
8.54
1.10
109.80
118.34
A
A
A
C5'
C4'
O4'
DT
DT
DT
4
4
4
N
1
-3.65
0.60
122.30
118.65
A
A
A
N3
C2
O2
DT
DT
DT
4
4
4
N
1
-3.95
0.60
122.90
118.95
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
1
-3.79
0.60
122.90
119.11
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
-3.96
0.60
122.90
118.94
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
1
1.85
0.30
108.30
110.15
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
5.17
0.30
108.30
113.47
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
-5.18
0.80
105.90
100.72
B
B
B
O4'
C1'
C2'
DA
DA
DA
12
12
12
N
1
5.89
0.30
108.30
114.19
B
B
B
O4'
C1'
N9
DA
DA
DA
12
12
12
N
1
8.46
1.20
119.70
128.16
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
1
5.95
0.30
108.30
114.25
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
2
-5.16
0.80
105.90
100.74
A
A
A
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
2
4.40
0.30
108.30
112.70
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
2
3.77
0.60
106.00
109.77
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
2
4.24
0.60
118.90
123.14
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
2
7.54
1.20
119.70
127.24
A
A
A
C3'
O3'
P
DT
DT
DT
3
3
4
Y
2
-3.72
0.60
122.90
119.18
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
2
3.82
0.30
108.30
112.12
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
2
5.75
0.30
108.30
114.05
B
B
B
O4'
C1'
N9
DA
DA
DA
12
12
12
N
2
8.07
1.20
119.70
127.77
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
2
4.35
0.30
108.30
112.65
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
3
-5.27
0.80
105.90
100.63
A
A
A
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
3
9.94
0.30
108.30
118.24
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
3
3.63
0.60
118.90
122.53
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
3
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
3
7.43
1.10
109.80
117.23
A
A
A
C5'
C4'
O4'
DT
DT
DT
4
4
4
N
3
-3.94
0.60
122.90
118.96
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
3
1.85
0.30
108.30
110.15
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
3
3.09
0.30
108.30
111.39
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
3
-6.43
0.80
105.90
99.47
B
B
B
O4'
C1'
C2'
DA
DA
DA
12
12
12
N
3
6.13
0.30
108.30
114.43
B
B
B
O4'
C1'
N9
DA
DA
DA
12
12
12
N
3
8.97
1.20
119.70
128.67
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
3
5.35
0.30
108.30
113.65
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
4
-4.94
0.80
105.90
100.96
A
A
A
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
4
4.46
0.30
108.30
112.76
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
4
3.69
0.60
106.00
109.69
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
4
4.18
0.60
118.90
123.08
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
4
7.89
1.20
119.70
127.59
A
A
A
C3'
O3'
P
DT
DT
DT
3
3
4
Y
4
-3.77
0.60
122.90
119.13
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
4
3.83
0.60
118.90
122.73
A
A
A
N1
C2
O2
DC
DC
DC
7
7
7
N
4
8.16
1.20
119.70
127.86
B
B
B
C3'
O3'
P
DG
DG
DA
8
8
9
Y
4
6.23
0.30
108.30
114.53
B
B
B
O4'
C1'
N9
DA
DA
DA
9
9
9
N
4
7.79
1.20
119.70
127.49
B
B
B
C3'
O3'
P
DA
DA
DA
9
9
10
Y
4
6.20
0.30
108.30
114.50
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
4
-4.32
0.70
102.20
97.88
B
B
B
C4'
C3'
C2'
DA
DA
DA
12
12
12
N
4
-5.81
0.80
105.90
100.09
B
B
B
O4'
C1'
C2'
DA
DA
DA
12
12
12
N
4
2.24
0.30
108.30
110.54
B
B
B
O4'
C1'
N9
DA
DA
DA
12
12
12
N
4
7.92
1.20
119.70
127.62
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
4
4.10
0.30
108.30
112.40
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
A
A
C5
C7
DT
DT
5
5
0.041
0.006
1.496
1.537
N
2
A
A
C5
C7
DT
DT
3
3
0.038
0.006
1.496
1.534
N
2
A
A
C5
C7
DT
DT
4
4
0.037
0.006
1.496
1.533
N
2
A
A
C5
C7
DT
DT
5
5
0.048
0.006
1.496
1.544
N
2
A
A
C5
C7
DT
DT
6
6
0.036
0.006
1.496
1.532
N
4
A
A
C5
C7
DT
DT
3
3
0.040
0.006
1.496
1.536
N
4
A
A
C5
C7
DT
DT
5
5
0.039
0.006
1.496
1.535
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX
1
N
N
2
N
N
3
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
14
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
14
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
14
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
13
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
13
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
13
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
12
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
12
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
11
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
11
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
10
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
10
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
9
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
9
B
N6
DA
2
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
DG
8
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
8
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
8
B
N2
DG
1
1_555
DNA
DNA, DOUBLE HELIX
107D
PDB
1
107D
107D
PDB
2
107D
1
7
107D
1
7
107D
A
1
1
7
8
14
107D
8
14
107D
B
2
1
7
BINDING SITE FOR RESIDUE DUO B 15
B
DUO
15
Software
9
A
DT
4
A
DT
4
9
1_555
A
DT
5
A
DT
5
9
1_555
A
DT
6
A
DT
6
9
1_555
A
DC
7
A
DC
7
9
1_555
B
DA
10
B
DA
3
9
1_555
B
DA
11
B
DA
4
9
1_555
B
DA
12
B
DA
5
9
1_555
B
DG
13
B
DG
6
9
1_555
B
DG
14
B
DG
7
9
1_555
1
P 1