1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Gochin, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C7 H14 O4
162.184
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose
4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE; 2-deoxy-4-O-methyl-alpha-D-fucopyranose; 2,6-dideoxy-4-O-methyl-alpha-D-galactose; 2,6-dideoxy-4-O-methyl-D-galactose; 2,6-dideoxy-4-O-methyl-galactose
D-saccharide, alpha linking
C8 H14 O5
190.194
4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose
4-O-ACETYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE; 4-O-acetyl-2,6-dideoxy-beta-D-galactose; 4-O-acetyl-2,6-dideoxy-D-galactose; 4-O-acetyl-2,6-dideoxy-galactose
D-saccharide, beta linking
Co 2
58.933
COBALT (II) ION
non-polymer
C21 H24 O9
420.410
(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
None
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
C6 H12 O4
148.157
beta-D-Olivopyranose
beta-D-Olivose; 2,6-dideoxy-beta-D-arabino-hexopyranose; 2,6-dideoxy-beta-D-glucopyranose; 2,6-dideoxy-beta-D-mannopyranose; 2-deoxy-beta-D-quinovopyranose; 2-deoxy-beta-D-rhamnoopyranose; D-Olivose; Olivose; 2,6-DIDEOXY-BETA-D-GLUCOSE; 2,6-DIDEOXY-BETA-D-MANNOSE
D-saccharide, beta 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
C9 H16 O5
204.220
n
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose
4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE; 3-C-methyl-4-O-acetyl-alpha-L-Olivose; 3-C-methyl-4-O-acetyl-L-Olivose; 3-C-methyl-4-O-acetyl-Olivose
L-saccharide, alpha linking
N
1
N
O
N
2
S
C
N
3
N
C
N
4
R
C
N
5
N
O
N
6
R
C
N
7
N
O
N
8
N
C
N
9
R
C
N
10
N
O
N
11
N
C
N
12
N
H
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
O
N
27
R
C
N
28
N
C
N
29
R
C
N
30
N
O
N
31
R
C
N
32
N
O
N
33
N
C
N
34
N
C
N
35
N
O
N
36
R
C
N
37
N
O
N
38
N
C
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
CO
N
54
N
C
N
55
N
O
N
56
S
C
N
57
R
C
N
58
N
C
Y
59
N
C
Y
60
N
C
Y
61
N
C
Y
62
N
C
N
63
N
O
Y
64
N
C
N
65
N
O
N
66
S
C
N
67
N
O
Y
68
N
C
N
69
N
C
N
70
N
O
N
71
S
C
N
72
N
O
N
73
R
C
N
74
N
O
Y
75
N
C
N
76
N
C
Y
77
N
C
Y
78
N
C
Y
79
N
C
N
80
N
C
N
81
N
O
N
82
N
O
N
83
N
C
N
84
N
H
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
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
Y
120
N
N
Y
121
N
C
Y
122
N
N
Y
123
N
C
Y
124
N
C
N
125
N
N
Y
126
N
N
Y
127
N
C
Y
128
N
N
Y
129
N
C
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
O
N
145
N
P
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
N
C
N
155
R
C
N
156
N
N
N
157
N
C
N
158
N
O
N
159
N
N
N
160
N
C
N
161
N
N
N
162
N
C
N
163
N
C
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
R
C
N
179
N
C
N
180
R
C
N
181
S
C
N
182
R
C
N
183
N
C
N
184
N
O
N
185
N
O
N
186
N
O
N
187
N
O
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
O
N
201
N
P
N
202
N
O
N
203
N
O
N
204
N
O
N
205
N
C
N
206
R
C
N
207
N
O
N
208
S
C
N
209
N
O
N
210
N
C
N
211
R
C
Y
212
N
N
Y
213
N
C
Y
214
N
N
Y
215
N
C
N
216
N
C
N
217
N
O
N
218
N
N
N
219
N
C
N
220
N
N
N
221
N
N
Y
222
N
C
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
O
N
238
N
P
N
239
N
O
N
240
N
O
N
241
N
O
N
242
N
C
N
243
R
C
N
244
N
O
N
245
S
C
N
246
N
O
N
247
N
C
N
248
R
C
N
249
N
N
N
250
N
C
N
251
N
O
N
252
N
N
N
253
N
C
N
254
N
O
N
255
N
C
N
256
N
C
N
257
N
C
N
258
N
H
N
259
N
H
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
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
O
N
274
R
C
N
275
N
C
N
276
S
C
N
277
N
O
N
278
N
C
N
279
S
C
N
280
N
O
N
281
N
C
N
282
N
C
N
283
N
O
N
284
S
C
N
285
N
O
N
286
N
C
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
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
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
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
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
N
41
N
sing
N
42
N
sing
N
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
doub
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
Y
65
N
doub
Y
66
N
sing
N
67
N
sing
Y
68
N
sing
N
69
N
sing
N
70
N
sing
Y
71
N
doub
N
72
N
sing
Y
73
N
sing
N
74
N
sing
N
75
N
sing
Y
76
N
doub
Y
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
Y
83
N
doub
Y
84
N
sing
N
85
N
sing
N
86
N
doub
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
Y
96
N
doub
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
N
101
N
sing
N
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
doub
N
112
N
sing
N
113
N
sing
N
114
N
sing
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
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
Y
132
N
sing
Y
133
N
sing
Y
134
N
doub
N
135
N
sing
Y
136
N
sing
Y
137
N
sing
Y
138
N
doub
N
139
N
sing
Y
140
N
doub
N
141
N
sing
N
142
N
sing
Y
143
N
sing
Y
144
N
doub
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
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
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
doub
N
173
N
sing
N
174
N
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
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
sing
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
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
doub
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
Y
227
N
sing
Y
228
N
sing
Y
229
N
doub
N
230
N
sing
Y
231
N
sing
N
232
N
sing
Y
233
N
doub
N
234
N
doub
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
doub
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
doub
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
N
266
N
sing
N
267
N
sing
N
268
N
doub
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
doub
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
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
doub
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
UK
Structure Fold.Des.
FODEFH
1263
0969-2126
8
441
452
10.1016/S0969-2126(00)00124-6
10801486
A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance.
2000
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
121
9276
9285
10.1021/ja9904540
Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints
1999
10.2210/pdb1eki/pdb
pdb_00001eki
DA A 8 HAS WRONG CHIRALITY AT ATOM C3'
DA B 18 HAS WRONG CHIRALITY AT ATOM C3'
CPH A 33 HAS WRONG CHIRALITY AT ATOM C1'
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
TWO MOLECULES OF THE DRUG CHROMOMYCIN A3 (1GL-2GL-DXB-DDA-DDA-1AR, CHAINS C, AND D) ARE BOUND IN THE MINOR GROOVE
2426.617
DNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3')
2
syn
polymer
334.363
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose
2
man
branched
464.504
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose
2
man
branched
58.933
COBALT (II) ION
1
syn
non-polymer
420.410
(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
2
syn
non-polymer
no
no
(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DA)
TTGGCCAA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
3.476
1
20
A
1
B
18
8.528
A_DT1:DA18_B
1
-24.133
0.142
-0.228
-0.108
-3.134
1
20
A
2
B
17
-5.318
A_DT2:DA17_B
2
-18.262
-0.011
-0.267
-0.050
-5.234
1
19
A
3
B
16
5.134
A_DG3:DC16_B
3
-9.137
-0.111
-0.011
-0.037
-1.693
1
19
A
4
B
15
-4.561
A_DG4:DC15_B
4
-22.407
0.073
0.630
-0.289
3.870
1
19
A
5
B
14
-4.124
A_DC5:DG14_B
5
-19.872
-0.080
0.508
-0.240
4.498
1
19
A
6
B
13
11.361
A_DC6:DG13_B
6
-12.092
0.885
-0.185
-0.100
5.335
1
20
A
7
B
12
-5.143
A_DA7:DT12_B
7
-16.053
0.099
-0.179
-0.036
0.591
1
20
A
8
B
11
9.683
A_DA8:DT11_B
8
-24.079
-0.225
-0.135
-0.107
3.060
33.718
A
A
1
2
14.293
B
B
18
17
3.337
8.197
-0.206
-0.600
AA_DT1DT2:DA17DA18_BB
1
3.607
-6.290
32.541
-2.362
0.939
2.918
37.609
A
A
2
3
21.048
B
B
17
16
3.342
13.289
0.783
-0.510
AA_DT2DG3:DC16DA17_BB
2
-2.112
3.345
35.201
-2.506
-1.487
3.023
26.945
A
A
3
4
8.081
B
B
16
15
3.253
3.753
1.314
-1.645
AA_DG3DG4:DC15DC16_BB
3
0.547
-1.177
26.681
-4.456
-2.686
2.617
29.046
A
A
4
5
5.126
B
B
15
14
2.846
2.567
-0.059
-2.499
AA_DG4DC5:DG14DC15_BB
4
0.591
-1.180
28.928
-5.455
0.226
3.164
28.127
A
A
5
6
4.355
B
B
14
13
3.282
2.115
-0.992
-1.589
AA_DC5DC6:DG13DG14_BB
5
-0.224
0.462
28.048
-3.758
1.989
3.071
35.636
A
A
6
7
20.314
B
B
13
12
3.353
12.190
-1.208
-0.070
AA_DC6DA7:DT12DG13_BB
6
1.927
-3.211
33.496
-1.910
2.257
2.989
32.545
A
A
7
8
13.545
B
B
12
11
3.274
7.504
0.201
-0.655
AA_DA7DA8:DT11DT12_BB
7
-4.305
7.770
31.404
-2.446
-1.092
atom_site
chem_comp
database_PDB_caveat
entity
pdbx_branch_scheme
pdbx_chem_comp_identifier
pdbx_entity_branch
pdbx_entity_branch_descriptor
pdbx_entity_branch_link
pdbx_entity_branch_list
pdbx_entity_nonpoly
pdbx_nmr_software
pdbx_nonpoly_scheme
pdbx_struct_assembly_gen
pdbx_struct_conn_angle
pdbx_unobs_or_zero_occ_atoms
pdbx_validate_close_contact
struct_asym
struct_conn
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Version format compliance
Advisory
Advisory
Atomic model
Data collection
Derived calculations
Structure summary
Data collection
Database references
Structure summary
1
0
2000-03-20
1
1
2008-04-27
1
2
2011-07-13
1
3
2011-12-28
2
0
2020-07-29
2
1
2024-05-01
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.type_symbol
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.type
_pdbx_nmr_software.name
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.value
_pdbx_validate_close_contact.auth_asym_id_1
_pdbx_validate_close_contact.auth_asym_id_2
_pdbx_validate_close_contact.auth_atom_id_1
_pdbx_validate_close_contact.auth_atom_id_2
_pdbx_validate_close_contact.auth_comp_id_1
_pdbx_validate_close_contact.auth_comp_id_2
_pdbx_validate_close_contact.auth_seq_id_1
_pdbx_validate_close_contact.auth_seq_id_2
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
A
2GL
32
n
C
2GL
1
A
1GL
31
n
C
1GL
2
B
2GL
22
n
D
2GL
1
B
1GL
21
n
D
1GL
2
B
DDA
26
n
E
DDA
1
B
DDA
25
n
E
DDA
2
B
ERI
24
n
E
ERI
3
B
DDA
36
n
F
DDA
1
B
DDA
35
n
F
DDA
2
B
ERI
34
n
F
ERI
3
a-D-2-deoxy-Fucp4OMe
DOlib
b-D-Olivopyranose
b-D-2,6-deoxy-Glcp
Oli
Family of 6 structures
RCSB
Y
RCSB
2000-03-08
REL
oligosaccharide
oligosaccharide
WURCS=2.0/2,2,1/[ad112m-1b_1-5_4*OCC/3=O][ad112m-1a_1-5_4*OC]/1-2/a3-b1
2
PDB2Glycan
1.1.0
WURCS
[][b-D-2-deoxy-Fucp4Ac]{[(3+1)][a-D-2-deoxy-Fucp4Me]{}}
2
PDB-CARE
LINUCS
WURCS=2.0/2,3,2/[ad122m-1b_1-5][ad611m-1a_1-5_3*C_4*OCC/3=O]/1-1-2/a3-b1_b3-c1
3
PDB2Glycan
1.1.0
WURCS
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2,6-deoxy-Glcp]{[(3+1)][a-L-2,6-deoxy-Glcp4Ac]{}}}
3
PDB-CARE
LINUCS
C1
O3
1GL
2GL
2
1
2
O1
HO3
sing
C1
O3
DDA
DDA
2
1
3
O1
HO3
sing
C1
O3
ERI
DDA
3
2
3
O1
HO3
sing
n
n
n
n
n
CO
COBALT (II) ION
CPH
(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
This structure was determined using standard 2D homonuclear techniques as well as 2D 13C-1H heteronuclear correlation
average structure
1
1
2D NOESY
13C-1H HMQC
110mM
6
1
atm
298
K
molecular dynamics, isolated spin-pair approximation for NOE's; pseudocontact shift refinement
simulated annealing
1
minimized average structure
2mM DNA-drug complex, 25 degrees C, in buffer (100mM NaCl, 10mM Na borate), final PH 6.
90% H2O/10% D2O
DeLaglio and Bax
processing
NMRPipe
1.7
Kneller and Goddard
data analysis
Sparky
3.0
Brunger (modified Gochin and Tu)
refinement
X-PLOR
3.0, 3.851
Biosym
data analysis
Felix
2.1
500
GE
OMEGA
CO
41
4
CO
CO
41
A
CPH
33
5
CPH
CPH
33
A
CPH
23
5
CPH
CPH
23
B
DT
1
n
1
DT
1
A
DT
2
n
2
DT
2
A
DG
3
n
3
DG
3
A
DG
4
n
4
DG
4
A
DC
5
n
5
DC
5
A
DC
6
n
6
DC
6
A
DA
7
n
7
DA
7
A
DA
8
n
8
DA
8
A
DT
11
n
1
DT
11
B
DT
12
n
2
DT
12
B
DG
13
n
3
DG
13
B
DG
14
n
4
DG
14
B
DC
15
n
5
DC
15
B
DC
16
n
6
DC
16
B
DA
17
n
7
DA
17
B
DA
18
n
8
DA
18
B
author_defined_assembly
2
dimeric
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
O1
CPH
1_555
102.5
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
C9
CPH
1_555
35.6
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
C9
CPH
1_555
83.5
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
C1
CPH
1_555
85.3
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
C1
CPH
1_555
22.9
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
C1
CPH
1_555
61.2
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
120.4
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
115.3
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
155.1
A
CPH
33
H
C1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
138.1
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
127.9
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
88.0
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
97.9
A
CPH
33
H
C1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
86.6
B
CPH
23
I
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
98.9
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
151.5
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
90.9
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
172.6
A
CPH
33
H
C1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
112.8
B
CPH
23
I
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
32.3
B
CPH
23
I
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
77.0
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C1
CPH
1_555
146.1
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C1
CPH
1_555
91.8
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C1
CPH
1_555
118.8
A
CPH
33
H
C1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C1
CPH
1_555
98.1
B
CPH
23
I
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C1
CPH
1_555
78.7
B
CPH
23
I
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C1
CPH
1_555
20.9
B
CPH
23
I
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C1
CPH
1_555
56.3
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
A
O6
CPH
33
H
O6
CPH
1
1
N
1
A
O2
CPH
33
H
O2
CPH
1
1
N
1
B
O6
CPH
23
I
O6
CPH
1
1
N
1
B
O2
CPH
23
I
O2
CPH
1
1
N
1
A
C3'
DA
8
WRONG HAND
1
B
C3'
DA
18
WRONG HAND
1
A
C1'
CPH
33
PLANAR
1
D
B
O1
C6
2GL
CPH
1
23
1.41
1
C
A
O1
C6
2GL
CPH
1
33
1.42
1
E
B
O1
C2
DDA
CPH
1
23
1.42
1
F
A
O1
C2
DDA
CPH
1
33
1.45
1
A
B
O2
H21
DC
DG
6
13
1.59
1
A
DT
2
0.096
SIDE CHAIN
1
A
DA
7
0.078
SIDE CHAIN
1
B
DT
12
0.097
SIDE CHAIN
1
B
DG
14
0.057
SIDE CHAIN
1
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
-3.62
0.60
122.90
119.28
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
1
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
1
-9.86
0.70
102.20
92.34
A
A
A
C4'
C3'
C2'
DG
DG
DG
3
3
3
N
1
17.59
1.20
119.70
137.29
A
A
A
C3'
O3'
P
DG
DG
DG
3
3
4
Y
1
18.06
1.60
120.90
138.96
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
1
5.25
0.70
119.90
125.15
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
1
9.64
1.20
119.70
129.34
A
A
A
C3'
O3'
P
DG
DG
DC
4
4
5
Y
1
-4.66
0.70
102.20
97.54
A
A
A
C4'
C3'
C2'
DC
DC
DC
5
5
5
N
1
3.18
0.30
108.30
111.48
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
10.98
1.60
120.90
131.88
A
A
A
P
O5'
C5'
DA
DA
DA
7
7
7
N
1
16.14
1.20
119.70
135.84
A
A
A
C3'
O3'
P
DA
DA
DA
7
7
8
Y
1
2.67
0.30
108.30
110.97
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
-3.71
0.60
122.90
119.19
B
B
B
C6
C5
C7
DT
DT
DT
11
11
11
N
1
2.88
0.30
108.30
111.18
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
1
9.89
1.60
120.90
130.79
B
B
B
P
O5'
C5'
DG
DG
DG
13
13
13
N
1
-9.84
0.70
102.20
92.36
B
B
B
C4'
C3'
C2'
DG
DG
DG
13
13
13
N
1
17.27
1.20
119.70
136.97
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
1
17.59
1.60
120.90
138.49
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
1
5.63
0.70
119.90
125.53
B
B
B
N3
C2
N2
DG
DG
DG
14
14
14
N
1
8.61
1.20
119.70
128.31
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
1
-5.28
0.70
102.20
96.92
B
B
B
C4'
C3'
C2'
DC
DC
DC
15
15
15
N
1
3.28
0.30
108.30
111.58
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
2.26
0.30
108.30
110.56
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
16.08
1.20
119.70
135.78
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
minimized average
AVERAGE SOLUTION STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
5
N
N
5
N
N
covale
1.455
both
sing
C
2GL
1
C
O3
2GL
1_555
C
1GL
2
C
C1
1GL
1_555
covale
1.453
both
sing
D
2GL
1
D
O3
2GL
1_555
D
1GL
2
D
C1
1GL
1_555
covale
1.422
both
sing
E
DDA
1
E
O3
DDA
1_555
E
DDA
2
E
C1
DDA
1_555
covale
1.433
both
sing
E
DDA
2
E
O3
DDA
1_555
E
ERI
3
E
C1
ERI
1_555
covale
1.425
both
sing
F
DDA
1
F
O3
DDA
1_555
F
DDA
2
F
C1
DDA
1_555
covale
1.440
both
sing
F
DDA
2
F
O3
DDA
1_555
F
ERI
3
F
C1
ERI
1_555
metalc
1.902
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
metalc
1.931
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
metalc
2.408
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
metalc
2.754
A
CPH
33
H
C1
CPH
1_555
A
CO
41
G
CO
CO
1_555
metalc
1.912
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
metalc
1.863
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
metalc
2.570
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
metalc
2.765
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C1
CPH
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
DA
18
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
DA
18
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
17
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
17
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
16
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
16
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
16
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
15
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
15
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
15
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
14
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
14
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
14
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
13
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
13
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
12
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
12
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
11
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
11
B
O4
DT
1
1_555
DNA
drug bound in the minor groove of DNA, DNA
1EKI
PDB
1
1EKI
1
8
1EKI
1
8
1EKI
A
1
1
8
11
18
1EKI
11
18
1EKI
B
1
1
8
1
P 1