0.038023
0.021952
0.000000
0.000000
0.043905
0.000000
0.000000
0.000000
0.009999
0.00000
0.00000
0.00000
Egli, M.
Williams, L.D.
Frederick, C.A.
Rich, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
26.300
26.300
100.010
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-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
C39 H49 N O16
787.803
NOGALAMYCIN
non-polymer
N
1
N
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
N
22
N
H
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
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
N
C
N
49
R
C
Y
50
N
N
Y
51
N
C
Y
52
N
N
Y
53
N
C
Y
54
N
C
N
55
N
N
Y
56
N
N
Y
57
N
C
Y
58
N
N
Y
59
N
C
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
H
N
72
N
H
N
73
N
H
N
74
N
O
N
75
N
P
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
O
N
82
S
C
N
83
N
O
N
84
N
C
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
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
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
N
C
N
122
R
C
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
C
N
128
N
O
N
129
N
C
N
130
N
C
N
131
N
C
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
O
N
148
N
H
N
149
N
H
Y
150
N
C
Y
151
N
C
Y
152
N
C
Y
153
N
C
N
154
N
C
Y
155
N
C
N
156
S
C
N
157
N
C
N
158
S
C
N
159
R
C
Y
160
N
C
N
161
N
C
N
162
N
C
N
163
N
C
N
164
N
C
Y
165
N
C
Y
166
N
C
Y
167
N
C
Y
168
N
C
Y
169
N
C
Y
170
N
C
N
171
N
C
N
172
N
C
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
C
N
178
N
C
N
179
S
C
N
180
S
C
N
181
R
C
N
182
R
C
N
183
R
C
N
184
R
C
N
185
R
C
N
186
R
C
N
187
S
C
N
188
S
C
N
189
N
N
N
190
N
O
N
191
N
O
N
192
N
O
N
193
N
O
N
194
N
O
N
195
N
O
N
196
N
O
N
197
N
O
N
198
N
O
N
199
N
O
N
200
N
O
N
201
N
O
N
202
N
O
N
203
N
O
N
204
N
O
N
205
N
O
N
206
N
H
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
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
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
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
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
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
doub
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
doub
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
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
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
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
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
sing
Y
67
N
sing
Y
68
N
doub
N
69
N
sing
Y
70
N
doub
N
71
N
sing
N
72
N
sing
Y
73
N
sing
Y
74
N
doub
N
75
N
sing
Y
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
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
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
doub
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
sing
N
139
N
sing
N
140
N
sing
N
141
N
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
Y
155
N
doub
Y
156
N
sing
N
157
N
sing
Y
158
N
sing
N
159
N
sing
Y
160
N
doub
N
161
N
sing
Y
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
Y
167
N
doub
Y
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
Y
183
N
sing
Y
184
N
doub
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
doub
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
Y
198
N
doub
Y
199
N
sing
Y
200
N
doub
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
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
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
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
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
30
1364
1372
10.1021/bi00219a029
1991116
DNA-nogalamycin interactions.
1991
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
87
2225
2229
Structure of Nogalamycin Bound to a DNA Hexamer
1990
10.2210/pdb1d17/pdb
pdb_00001d17
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
300.00
1
DIFFRACTOMETER
RIGAKU AFC-5
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
1837.271
DNA (5'-D(*(5CM)P*GP*TP*AP*(5CM)P*G)-3')
1
syn
polymer
787.803
NOGALAMYCIN
1
syn
non-polymer
18.015
water
39
nat
water
no
yes
(5CM)(DG)(DT)(DA)(5CM)(DG)
CGTACG
A
polydeoxyribonucleotide
n
n
n
n
n
n
2.72
54.73
VAPOR DIFFUSION, SITTING DROP
6.00
pH 6.00, VAPOR DIFFUSION, SITTING DROP
ROOM TEMPERATURE
WATER
1
MPD
1
METHANOL
1
NA CACODYLATE
1
MGCL2
1
SPERMINE
1
WATER
2
MPD
2
12.620
1
19
A
1
A
6
-0.820
A_5CM1:DG6_A
1
-6.336
0.647
0.046
-0.449
-25.238
1
19
A
2
A
5
-2.501
A_DG2:5CM5_A
2
-0.324
-0.803
-0.580
-0.525
-11.447
1
20
A
3
A
4
1.196
A_DT3:DA4_A
3
-6.537
-0.317
0.279
-0.219
11.447
1
20
A
4
A
3
1.196
A_DA4:DT3_A
4
-6.537
0.317
0.279
-0.219
25.238
1
19
A
5
A
2
-2.501
A_5CM5:DG2_A
5
-0.324
0.803
-0.580
-0.525
-12.620
1
19
A
6
A
1
-0.820
A_DG6:5CM1_A
6
-6.336
-0.647
0.046
-0.449
7.313
27.366
A
A
1
2
5.119
A
A
6
5
7.377
2.402
0.392
0.454
AA_5CM1DG2:5CM5DG6_AA
1
5.671
-12.086
26.677
-0.395
2.370
3.150
28.865
A
A
2
3
-4.657
A
A
5
4
3.041
-2.296
-0.816
-0.148
AA_DG2DT3:DA45CM5_AA
2
-7.055
14.306
27.915
0.196
0.124
2.729
42.085
A
A
3
4
0.453
A
A
4
3
2.736
0.325
0.000
-0.894
AA_DT3DA4:DT3DA4_AA
3
0.000
0.000
42.084
-1.273
0.000
3.150
28.865
A
A
4
5
-4.657
A
A
3
2
3.041
-2.296
0.816
-0.148
AA_DA45CM5:DG2DT3_AA
4
7.055
-14.306
27.915
0.196
-0.124
7.313
27.366
A
A
5
6
5.119
A
A
2
1
7.377
2.402
-0.392
0.454
AA_5CM5DG6:5CM1DG2_AA
5
-5.671
12.086
26.677
-0.395
-2.370
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Derived calculations
Data collection
Database references
Derived calculations
1
0
1991-07-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2011-08-24
1
4
2024-02-07
_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
BNL
1990-08-08
REL
NGM
NOGALAMYCIN
HOH
water
NGM
7
2
NGM
NGM
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
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
43
3
HOH
HOH
43
A
HOH
44
3
HOH
HOH
44
A
HOH
45
3
HOH
HOH
45
A
HOH
46
3
HOH
HOH
46
A
5CM
1
n
1
5CM
1
A
DG
2
n
2
DG
2
A
DT
3
n
3
DT
3
A
DA
4
n
4
DA
4
A
5CM
5
n
5
5CM
5
A
DG
6
n
6
DG
6
A
author_defined_assembly
2
dimeric
A
5CM
1
A
5CM
1
DC
A
5CM
5
A
5CM
5
DC
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
11_655
-x+y+1,y,-z+1/2
crystal symmetry operation
26.3000000000
0.0000000000
50.0050000000
1
A
DT
3
0.133
SIDE CHAIN
1
A
DA
4
0.055
SIDE CHAIN
1
8.97
1.20
119.70
128.67
A
A
A
C3'
O3'
P
5CM
5CM
DG
1
1
2
Y
1
6.63
1.10
109.80
116.43
A
A
A
C5'
C4'
O4'
DG
DG
DG
2
2
2
N
1
-9.23
1.00
110.10
100.87
A
A
A
C1'
O4'
C4'
DG
DG
DG
2
2
2
N
1
-5.51
0.80
105.90
100.39
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
1
7.08
0.30
108.30
115.38
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
7.64
0.30
108.30
115.94
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
-4.26
0.70
108.00
103.74
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
-3.25
0.50
103.90
100.65
A
A
A
C5
N7
C8
DA
DA
DA
4
4
4
N
1
3.80
0.50
113.80
117.60
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
-2.49
0.40
105.80
103.31
A
A
A
C8
N9
C4
DA
DA
DA
4
4
4
N
1
4.01
0.30
108.30
112.31
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
-2.48
0.40
106.40
103.92
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
1
2.60
0.40
105.40
108.00
A
A
A
N9
C4
C5
DG
DG
DG
6
6
6
N
1
-4.34
0.60
119.90
115.56
A
A
A
N1
C6
O6
DG
DG
DG
6
6
6
N
1
A
A
C5
C7
DT
DT
3
3
0.054
0.006
1.496
1.550
N
1
A
A
N9
C4
DA
DA
4
4
-0.037
0.006
1.374
1.337
N
0.206
0.206
2.000
809
1
2.000
TR
isotropic
TR
isotropic
2.000
39
217
56
122
0
fix
fix
refinement
X-PLOR
DNA-NOGALAMYCIN INTERACTIONS
1
N
N
2
N
N
3
N
N
covale
1.656
both
A
5CM
1
A
O3'
5CM
1
1_555
A
DG
2
A
P
DG
2
1_555
covale
1.620
both
A
DA
4
A
O3'
DA
4
1_555
A
5CM
5
A
P
5CM
5
1_555
covale
1.643
both
A
5CM
5
A
O3'
5CM
5
1_555
A
DG
6
A
P
DG
6
1_555
hydrog
WATSON-CRICK
A
5CM
1
A
N3
5CM
1
1_555
A
DG
6
A
N1
DG
6
11_655
hydrog
WATSON-CRICK
A
5CM
1
A
N4
5CM
1
1_555
A
DG
6
A
O6
DG
6
11_655
hydrog
WATSON-CRICK
A
5CM
1
A
O2
5CM
1
1_555
A
DG
6
A
N2
DG
6
11_655
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
5CM
5
A
N3
5CM
5
11_655
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
5CM
5
A
O2
5CM
5
11_655
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
A
5CM
5
A
N4
5CM
5
11_655
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
A
DA
4
A
N1
DA
4
11_655
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
A
DA
4
A
N6
DA
4
11_655
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
A
DT
3
A
N3
DT
3
11_655
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
A
DT
3
A
O4
DT
3
11_655
hydrog
WATSON-CRICK
A
5CM
5
A
N3
5CM
5
1_555
A
DG
2
A
N1
DG
2
11_655
hydrog
WATSON-CRICK
A
5CM
5
A
N4
5CM
5
1_555
A
DG
2
A
O6
DG
2
11_655
hydrog
WATSON-CRICK
A
5CM
5
A
O2
5CM
5
1_555
A
DG
2
A
N2
DG
2
11_655
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
5CM
1
A
N3
5CM
1
11_655
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
5CM
1
A
O2
5CM
1
11_655
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
5CM
1
A
N4
5CM
1
11_655
DNA
RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA
1D17
PDB
1
1D17
1
6
1D17
1
6
1D17
A
1
1
6
BINDING SITE FOR RESIDUE NGM A 7
A
NGM
7
Software
14
A
5CM
1
A
5CM
1
14
1_555
A
DG
2
A
DG
2
14
1_555
A
DG
2
A
DG
2
14
9_655
A
DT
3
A
DT
3
14
1_555
A
DT
3
A
DT
3
14
5_564
A
DA
4
A
DA
4
14
1_555
A
5CM
5
A
5CM
5
14
11_655
A
DG
6
A
DG
6
14
11_655
A
HOH
35
C
HOH
14
1_555
A
HOH
38
C
HOH
14
5_564
A
HOH
41
C
HOH
14
1_555
A
HOH
42
C
HOH
14
1_555
A
HOH
44
C
HOH
14
1_555
A
HOH
46
C
HOH
14
1_555
178
P 61 2 2