0.025397
0.014663
0.000000
0.000000
0.029326
0.000000
0.000000
0.000000
0.012542
0.00000
0.00000
0.00000
Cuesta-Seijo, J.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
39.374
39.374
79.734
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
Cl -1
35.453
CHLORIDE ION
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
C3 H7 N O3
105.093
D-SERINE
D-peptide linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
n
N-METHYLVALINE
L-peptide linking
C5 H11 N O2 S
149.211
N,S-DIMETHYLCYSTEINE
L-peptide linking
C4 H9 N O2 S
135.185
N-METHYLCYSTEINE
L-peptide linking
C9 H6 N2 O2
174.156
2-CARBOXYQUINOXALINE
non-polymer
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
CL
N
15
N
O
N
16
N
P
N
17
N
O
N
18
N
O
N
19
N
O
N
20
N
C
N
21
R
C
N
22
N
O
N
23
S
C
N
24
N
O
N
25
N
C
N
26
R
C
Y
27
N
N
Y
28
N
C
Y
29
N
N
Y
30
N
C
Y
31
N
C
N
32
N
N
Y
33
N
N
Y
34
N
C
Y
35
N
N
Y
36
N
C
N
37
N
H
N
38
N
H
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
O
N
52
N
P
N
53
N
O
N
54
N
O
N
55
N
O
N
56
N
C
N
57
R
C
N
58
N
O
N
59
S
C
N
60
N
O
N
61
N
C
N
62
R
C
N
63
N
N
N
64
N
C
N
65
N
O
N
66
N
N
N
67
N
C
N
68
N
N
N
69
N
C
N
70
N
C
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
O
N
86
N
P
N
87
N
O
N
88
N
O
N
89
N
O
N
90
N
C
N
91
R
C
N
92
N
O
N
93
S
C
N
94
N
O
N
95
N
C
N
96
R
C
Y
97
N
N
Y
98
N
C
Y
99
N
N
Y
100
N
C
N
101
N
C
N
102
N
O
N
103
N
N
N
104
N
C
N
105
N
N
N
106
N
N
Y
107
N
C
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
N
N
123
R
C
N
124
N
C
N
125
N
O
N
126
N
O
N
127
N
C
N
128
N
O
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
O
N
137
N
P
N
138
N
O
N
139
N
O
N
140
N
O
N
141
N
C
N
142
R
C
N
143
N
O
N
144
S
C
N
145
N
O
N
146
N
C
N
147
R
C
N
148
N
N
N
149
N
C
N
150
N
O
N
151
N
N
N
152
N
C
N
153
N
O
N
154
N
C
N
155
N
C
N
156
N
C
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
H
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
O
N
173
N
H
N
174
N
H
N
175
N
N
N
176
N
C
N
177
S
C
N
178
N
C
N
179
N
C
N
180
N
C
N
181
N
C
N
182
N
O
N
183
N
O
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
N
N
198
R
C
N
199
N
C
N
200
N
S
N
201
N
C
N
202
N
C
N
203
N
C
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
N
N
218
R
C
N
219
N
C
N
220
N
S
N
221
N
C
N
222
N
C
N
223
N
O
N
224
N
O
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
Y
234
N
N
Y
235
N
C
Y
236
N
C
Y
237
N
N
Y
238
N
C
Y
239
N
C
Y
240
N
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
N
244
N
C
N
245
N
O
N
246
N
O
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
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
doub
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
doub
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
Y
36
N
sing
Y
37
N
sing
Y
38
N
doub
N
39
N
sing
Y
40
N
sing
Y
41
N
sing
Y
42
N
doub
N
43
N
sing
Y
44
N
doub
N
45
N
sing
N
46
N
sing
Y
47
N
sing
Y
48
N
doub
N
49
N
sing
Y
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
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
N
76
N
doub
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
doub
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
doub
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
N
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
Y
109
N
sing
Y
110
N
sing
Y
111
N
doub
N
112
N
sing
Y
113
N
sing
N
114
N
sing
Y
115
N
doub
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
doub
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
doub
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
doub
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
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
doub
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
doub
N
168
N
sing
N
169
N
sing
N
170
N
doub
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
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
doub
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
sing
N
213
N
sing
N
214
N
doub
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
doub
N
231
N
sing
N
232
N
sing
Y
233
N
doub
Y
234
N
sing
Y
235
N
sing
N
236
N
sing
Y
237
N
doub
N
238
N
sing
Y
239
N
sing
Y
240
N
doub
Y
241
N
sing
N
242
N
sing
Y
243
N
sing
N
244
N
sing
Y
245
N
doub
N
246
N
sing
Y
247
N
sing
N
248
N
sing
Y
249
N
doub
N
250
N
doub
N
251
N
sing
N
252
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
61
442
10.1107/S090744490500137X
15805599
Structures of Complexes between Echinomycin and Duplex DNA.
2005
10.2210/pdb1pfe/pdb
pdb_00001pfe
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2002-11-19
MARRESEARCH
TRIANGULAR MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
0.8162
1.0
X11
EMBL/DESY, HAMBURG
0.8162
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
2427.605
5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'
1
syn
polymer
809.008
ECHINOMYCIN
1
nat
polymer
35.453
CHLORIDE ION
1
syn
non-polymer
174.156
2-CARBOXYQUINOXALINE
2
syn
non-polymer
18.015
water
80
nat
water
QUINOMYCIN A
no
no
(DG)(DC)(DG)(DT)(DA)(DC)(DG)(DC)
GCGTACGC
A
polydeoxyribonucleotide
no
yes
(DSN)A(N2C)(MVA)(DSN)A(NCY)(MVA)
SAXVSAXV
B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
y
y
n
n
n
y
y
n
sample
67293
STREPTOMYCES ECHINATUS
1
3.51
64.98
4.5
LI2SO4, MGCL2, METHANOL, NAAC, SPERMINE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Li2SO4
1
MgCl2
1
Methanol
1
NaAc
1
Spermine
1
H2O
1
MgCl2
2
4.097
A
1
A
8
66.359
A_DG1:DC8_A
1
-4.685
0.445
-0.388
-3.489
4.097
A
1
A
8
66.359
A_DG1:DC8_A
2
-4.685
0.445
-0.388
-3.489
-23.917
1
19
A
2
A
7
-1.666
A_DC2:DG7_A
3
6.552
0.376
0.312
-0.127
23.129
1
19
A
3
A
6
-0.062
A_DG3:DC6_A
4
7.146
-0.350
0.358
-0.080
0.747
3
23
A
4
A
5
-67.135
A_DT4:DA5_A
5
9.053
-0.567
0.189
3.640
-0.747
3
23
A
5
A
4
67.135
A_DA5:DT4_A
6
-9.053
0.567
-0.189
-3.640
-23.129
1
19
A
6
A
3
-0.062
A_DC6:DG3_A
7
7.146
0.350
0.358
-0.080
23.917
1
19
A
7
A
2
-1.666
A_DG7:DC2_A
8
6.552
-0.376
0.312
-0.127
1.749
-4.899
A
A
2
3
-27.621
A
A
7
6
2.432
2.248
0.152
0.809
AA_DC2DG3:DC6DG7_AA
1
-1.150
-14.134
-4.199
-21.547
-4.403
7.090
66.045
A
A
3
4
7.533
A
A
6
5
7.183
8.186
0.307
-0.059
AA_DG3DT4:DA5DC6_AA
2
-5.488
5.050
65.388
-0.779
-0.767
0.000
180.000
A
A
4
5
39.003
A
A
5
4
0.000
78.005
2.940
-5.003
AA_DT4DA5:DT4DA5_AA
3
-151.053
75.527
180.000
-2.501
-1.470
-0.307
-174.517
A
A
5
6
-46.401
A
A
4
3
-0.222
91.904
3.695
6.164
AA_DA5DC6:DG3DT4_AA
4
-143.188
-72.294
-112.324
-3.042
1.917
1.749
-4.899
A
A
6
7
-27.621
A
A
3
2
2.432
2.248
-0.152
0.809
AA_DC6DG7:DC2DG3_AA
5
1.150
14.134
-4.199
-21.547
4.403
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
pdbx_initial_refinement_model
pdbx_validate_polymer_linkage
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Other
Advisory
Data collection
Database references
Derived calculations
Refinement description
1
0
2004-06-08
1
1
2011-06-14
1
2
2011-07-13
1
3
2011-07-27
1
4
2012-12-12
1
5
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
SOLUTION STRUCTURE OF D(GACGTC) COMPLEXED WITH TRIOSTIN A
SOLUTION STRUCTURE OF D(ACACGTGT) COMPLEXED WITH QUINOMYCIN UK-6305
CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A
CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632
CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632
CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP C21
CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P42212
SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN A AT POSITIONS 4 AND 8
CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P41212
RCSB
Y
RCSB
2003-05-26
REL
REL
CL
CHLORIDE ION
QUI
2-CARBOXYQUINOXALINE
HOH
water
THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER
OF THE QUINOXALINE CLASS OF ANTIBIOTICS.
HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE
SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI.
TROSTIN A - (GCGTACGC)2 COMPLEX
Other
experimental model
Antibiotic
ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE.
BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND
THE C- TERMINI, AND A THIOACETAL BOND BETWEEN
RESIDUES 3 AND 7.
THE TWO QUINOXALINE CHROMOPHORES ARE LINKED
TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
Echinomycin
Cyclic depsipeptide
CL
20
3
CL
CL
20
A
QUI
0
4
QUI
QUI
0
B
QUI
9
4
QUI
QUI
9
B
HOH
2001
5
HOH
HOH
2001
A
HOH
2002
5
HOH
HOH
2002
A
HOH
2003
5
HOH
HOH
2003
A
HOH
2004
5
HOH
HOH
2004
A
HOH
2005
5
HOH
HOH
2005
A
HOH
2006
5
HOH
HOH
2006
A
HOH
2007
5
HOH
HOH
2007
A
HOH
2008
5
HOH
HOH
2008
A
HOH
2009
5
HOH
HOH
2009
A
HOH
2010
5
HOH
HOH
2010
A
HOH
2011
5
HOH
HOH
2011
A
HOH
2012
5
HOH
HOH
2012
A
HOH
2013
5
HOH
HOH
2013
A
HOH
2014
5
HOH
HOH
2014
A
HOH
2015
5
HOH
HOH
2015
A
HOH
2016
5
HOH
HOH
2016
A
HOH
2017
5
HOH
HOH
2017
A
HOH
2018
5
HOH
HOH
2018
A
HOH
2019
5
HOH
HOH
2019
A
HOH
2020
5
HOH
HOH
2020
A
HOH
2021
5
HOH
HOH
2021
A
HOH
2022
5
HOH
HOH
2022
A
HOH
2023
5
HOH
HOH
2023
A
HOH
2024
5
HOH
HOH
2024
A
HOH
2025
5
HOH
HOH
2025
A
HOH
2026
5
HOH
HOH
2026
A
HOH
2027
5
HOH
HOH
2027
A
HOH
2028
5
HOH
HOH
2028
A
HOH
2029
5
HOH
HOH
2029
A
HOH
2030
5
HOH
HOH
2030
A
HOH
2031
5
HOH
HOH
2031
A
HOH
2032
5
HOH
HOH
2032
A
HOH
2033
5
HOH
HOH
2033
A
HOH
2034
5
HOH
HOH
2034
A
HOH
2035
5
HOH
HOH
2035
A
HOH
2036
5
HOH
HOH
2036
A
HOH
2037
5
HOH
HOH
2037
A
HOH
2038
5
HOH
HOH
2038
A
HOH
2039
5
HOH
HOH
2039
A
HOH
2040
5
HOH
HOH
2040
A
HOH
2041
5
HOH
HOH
2041
A
HOH
2042
5
HOH
HOH
2042
A
HOH
2043
5
HOH
HOH
2043
A
HOH
2044
5
HOH
HOH
2044
A
HOH
2045
5
HOH
HOH
2045
A
HOH
2046
5
HOH
HOH
2046
A
HOH
2047
5
HOH
HOH
2047
A
HOH
2048
5
HOH
HOH
2048
A
HOH
2049
5
HOH
HOH
2049
A
HOH
2050
5
HOH
HOH
2050
A
HOH
2051
5
HOH
HOH
2051
A
HOH
2052
5
HOH
HOH
2052
A
HOH
2053
5
HOH
HOH
2053
A
HOH
2054
5
HOH
HOH
2054
A
HOH
2055
5
HOH
HOH
2055
A
HOH
2056
5
HOH
HOH
2056
A
HOH
2057
5
HOH
HOH
2057
A
HOH
2058
5
HOH
HOH
2058
A
HOH
2059
5
HOH
HOH
2059
A
HOH
2060
5
HOH
HOH
2060
A
HOH
2061
5
HOH
HOH
2061
A
HOH
2062
5
HOH
HOH
2062
A
HOH
2063
5
HOH
HOH
2063
A
HOH
2064
5
HOH
HOH
2064
A
HOH
2065
5
HOH
HOH
2065
A
HOH
2066
5
HOH
HOH
2066
A
HOH
2067
5
HOH
HOH
2067
A
HOH
2068
5
HOH
HOH
2068
A
HOH
2069
5
HOH
HOH
2069
A
HOH
2070
5
HOH
HOH
2070
A
HOH
2001
5
HOH
HOH
2001
B
HOH
2002
5
HOH
HOH
2002
B
HOH
2003
5
HOH
HOH
2003
B
HOH
2004
5
HOH
HOH
2004
B
HOH
2005
5
HOH
HOH
2005
B
HOH
2006
5
HOH
HOH
2006
B
HOH
2007
5
HOH
HOH
2007
B
HOH
2008
5
HOH
HOH
2008
B
HOH
2009
5
HOH
HOH
2009
B
HOH
2010
5
HOH
HOH
2010
B
DG
1
n
1
DG
1
A
DC
2
n
2
DC
2
A
DG
3
n
3
DG
3
A
DT
4
n
4
DT
4
A
DA
5
n
5
DA
5
A
DC
6
n
6
DC
6
A
DG
7
n
7
DG
7
A
DC
8
n
8
DC
8
A
DSN
1
n
1
DSN
1
B
ALA
2
n
2
ALA
2
B
N2C
3
y
3
N2C
3
B
NCY
3
y
3
NCY
3
B
MVA
4
n
4
MVA
4
B
DSN
5
n
5
DSN
5
B
ALA
6
n
6
ALA
6
B
NCY
7
y
7
NCY
7
B
N2C
7
y
7
N2C
7
B
MVA
8
n
8
MVA
8
B
0.146
0.138
0.146
0.160
0.168
478
3.000
software_defined_assembly
PISA
4
tetrameric
730
-6.4
3960
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
-0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
9_555
-x,-x+y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
HOH
2002
F
HOH
1
A
HOH
2013
F
HOH
1
A
HOH
2019
F
HOH
1
A
HOH
2024
F
HOH
1
B
CD
N2C
3
B
CD
N2C
3
1
Y
1
B
CD
NCY
7
B
CD
NCY
7
1
Y
1
-8.66
0.70
108.00
99.34
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
9.38
1.10
109.80
119.18
A
A
A
C5'
C4'
O4'
DC
DC
DC
2
2
2
B
B
N
1
-5.50
0.70
108.00
102.50
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
6.91
0.30
108.30
115.21
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-6.34
0.70
108.00
101.66
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
-6.71
1.00
110.10
103.39
A
A
A
C1'
O4'
C4'
DA
DA
DA
5
5
5
N
1
-5.74
0.70
108.00
102.26
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
6.22
0.30
108.30
114.52
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
-5.18
0.70
108.00
102.82
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
-3.28
0.40
121.90
118.62
A
A
A
N3
C4
C5
DC
DC
DC
8
8
8
N
1
4.77
0.60
118.90
123.67
A
A
A
N1
C2
O2
DC
DC
DC
8
8
8
N
1
A
A
C2'
C1'
DG
DG
1
1
-0.077
0.010
1.518
1.441
A
N
1
A
A
O4'
C1'
DG
DG
1
1
0.111
0.011
1.420
1.531
N
1
A
A
O4'
C1'
DC
DC
2
2
0.086
0.011
1.420
1.506
N
1
A
A
C2'
C1'
DG
DG
3
3
0.078
0.010
1.519
1.597
N
1
A
A
O4'
C1'
DG
DG
3
3
-0.086
0.012
1.418
1.332
N
1
A
A
O4'
C1'
DT
DT
4
4
0.079
0.011
1.420
1.499
N
1
A
A
C2'
C1'
DG
DG
7
7
0.076
0.010
1.519
1.595
N
1
A
A
O4'
C1'
DG
DG
7
7
-0.079
0.012
1.418
1.339
N
1
A
A
O4'
C1'
DC
DC
8
8
0.085
0.011
1.420
1.505
N
THE SKELETON OF ECHINOMYCIN IS NEARLY SYMMETRIC (NOT MODELLED TO DO SO), THE BRIDGE IS NOT. BOTH POSSIBLE ORIENTATIONS OF BINDING WERE OBSERVED, BUT SKELETON POSITIONS NEARLY OVERLAP, SO ONLY THE BRIDGE WAS MODELLED AS DISORDERED/MICROHETEROGENEITY.
0.168
0.146
0.146
1.10
21.00
2979
478
15164
2074
3.000
97.2
THIN SHELLS
1
FREE R
0.000
MOLECULAR REPLACEMENT
TROSTIN A - (GCGTACGC)2 COMPLEX
TARGETS FOR ECHINOMYCIN BUILT FROM THE CSD
STANDARD SHELX FOR THE DNA, ENGH & HUBER FOR THE STANDARD PROTEIN PARTS OF ECHINOMYCIN, BUILT FROM THE CSD FOR THE REST
7
149.00
303.00
1.10
21.00
80
332
25
161
66
0.022
0.036
0.172
0.068
0.059
0.041
1.2
95.7
1.100
21.000
1PFE
15164
0.000
0.04900
1
30.0100
14.910
97.2
0.24200
1.10
1.20
11.480
1
13.05
95.7
phasing
EPMR
refinement
SHELXL-97
data reduction
DENZO
data scaling
SCALEPACK
Echinomycin-(gcgtacgc)2 complex
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
5
N
N
The second part of the biological assembly is generated by: -x, -x+y, -z
covale
1.345
both
B
QUI
0
D
C
QUI
1_555
B
DSN
1
B
N
DSN
1
1_555
covale
1.352
both
B
DSN
1
B
C
DSN
1
1_555
B
ALA
2
B
N
ALA
2
1_555
covale
1.325
one
B
DSN
1
B
OG
DSN
1
1_555
B
MVA
8
B
C
MVA
8
1_555
covale
1.355
both
A
B
ALA
2
B
C
ALA
2
1_555
B
N2C
3
B
N
N2C
3
1_555
covale
1.355
both
B
B
ALA
2
B
C
ALA
2
1_555
B
NCY
3
B
N
NCY
3
1_555
covale
1.338
both
B
B
NCY
3
B
C
NCY
3
1_555
B
MVA
4
B
N
MVA
4
1_555
covale
1.338
both
A
B
N2C
3
B
C
N2C
3
1_555
B
MVA
4
B
N
MVA
4
1_555
covale
1.796
both
A
A
B
N2C
3
B
CB
N2C
3
1_555
B
NCY
7
B
SG
NCY
7
1_555
covale
1.814
both
B
B
B
NCY
3
B
SG
NCY
3
1_555
B
N2C
7
B
CB
N2C
7
1_555
covale
1.326
one
B
MVA
4
B
C
MVA
4
1_555
B
DSN
5
B
OG
DSN
5
1_555
covale
1.317
both
B
DSN
5
B
C
DSN
5
1_555
B
ALA
6
B
N
ALA
6
1_555
covale
1.365
both
B
DSN
5
B
N
DSN
5
1_555
B
QUI
9
E
C
QUI
1_555
covale
1.354
both
A
B
ALA
6
B
C
ALA
6
1_555
B
NCY
7
B
N
NCY
7
1_555
covale
1.354
both
B
B
ALA
6
B
C
ALA
6
1_555
B
N2C
7
B
N
N2C
7
1_555
covale
1.323
both
A
B
NCY
7
B
C
NCY
7
1_555
B
MVA
8
B
N
MVA
8
1_555
covale
1.323
both
B
B
N2C
7
B
C
N2C
7
1_555
B
MVA
8
B
N
MVA
8
1_555
hydrog
DG-DC PAIR
A
DG
1
A
O6
DG
1
1_555
A
DC
8
A
N4
DC
8
9_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
7
A
N1
DG
7
9_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
7
A
O6
DG
7
9_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
7
A
N2
DG
7
9_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
A
DC
6
A
N3
DC
6
9_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
A
DC
6
A
O2
DC
6
9_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
A
DC
6
A
N4
DC
6
9_555
hydrog
HOOGSTEEN
A
DT
4
A
N3
DT
4
1_555
A
DA
5
A
N7
DA
5
9_555
hydrog
HOOGSTEEN
A
DT
4
A
O4
DT
4
1_555
A
DA
5
A
N6
DA
5
9_555
hydrog
HOOGSTEEN
A
DA
5
A
N6
DA
5
1_555
A
DT
4
A
O4
DT
4
9_555
hydrog
HOOGSTEEN
A
DA
5
A
N7
DA
5
1_555
A
DT
4
A
N3
DT
4
9_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
A
DG
3
A
N1
DG
3
9_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
A
DG
3
A
O6
DG
3
9_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
A
DG
3
A
N2
DG
3
9_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
A
DC
2
A
N3
DC
2
9_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
A
DC
2
A
O2
DC
2
9_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
A
DC
2
A
N4
DC
2
9_555
hydrog
DC-DG PAIR
A
DC
8
A
N4
DC
8
1_555
A
DG
1
A
O6
DG
1
9_555
DNA/ANTIBIOTIC
BISINTERCALATOR, HOOGSTEEN BASEPAIR, DEPSIPEPTIDE, QUINOXALINE, THIOACETAL, ANTIBIOTIC, ANTITUMOR, DNA-ANTIBIOTIC COMPLEX
1PFE
PDB
1
1PFE
NOR01126
NOR
2
NOR01126
1
8
1PFE
1
8
1PFE
A
1
1
8
1
8
1PFE
1
8
NOR01126
B
2
1
8
2
NCY
microheterogeneity
N2C
3
1PFE
B
NOR01126
NOR
3
3
2
N2C
microheterogeneity
NCY
7
1PFE
B
NOR01126
NOR
7
7
BINDING SITE FOR RESIDUE CL A 20
A
CL
20
Software
1
BINDING SITE FOR CHAIN B OF ECHINOMYCIN
Software
16
A
HOH
2069
F
HOH
1
1_555
A
DG
1
A
DG
1
16
1_555
A
DC
2
A
DC
2
16
1_555
A
DG
3
A
DG
3
16
1_555
A
DT
4
A
DT
4
16
1_555
A
DA
5
A
DA
5
16
1_555
A
DC
6
A
DC
6
16
1_555
A
DG
7
A
DG
7
16
1_555
A
DC
8
A
DC
8
16
1_555
B
HOH
2001
G
HOH
16
1_555
B
HOH
2002
G
HOH
16
1_555
B
HOH
2003
G
HOH
16
1_555
B
HOH
2005
G
HOH
16
1_555
B
HOH
2006
G
HOH
16
1_555
B
HOH
2007
G
HOH
16
1_555
B
HOH
2009
G
HOH
16
1_555
B
HOH
2010
G
HOH
16
1_555
182
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