1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Gomez-Pinto, I.
Marchan, V.
Gago, F.
Grandas, A.
Gonzalez, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
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
C4 H9 N O3
119.119
n
L-HOMOSERINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C10 H15 N5 O10 P2
427.201
n
2'-DEOXYGUANOSINE-3',5'-DIPHOSPHATE
DNA linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
N
1
N
C
N
2
N
O
N
3
N
C
N
4
N
H
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
N
N
9
S
C
N
10
N
C
N
11
N
O
N
12
N
C
N
13
N
O
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
O
N
22
N
P
N
23
N
O
N
24
N
O
N
25
N
O
N
26
N
C
N
27
R
C
N
28
N
O
N
29
S
C
N
30
N
O
N
31
N
C
N
32
R
C
Y
33
N
N
Y
34
N
C
Y
35
N
N
Y
36
N
C
Y
37
N
C
N
38
N
N
Y
39
N
N
Y
40
N
C
Y
41
N
N
Y
42
N
C
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
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
O
N
58
N
P
N
59
N
O
N
60
N
O
N
61
N
O
N
62
N
C
N
63
R
C
N
64
N
O
N
65
S
C
N
66
N
O
N
67
N
C
N
68
R
C
N
69
N
N
N
70
N
C
N
71
N
O
N
72
N
N
N
73
N
C
N
74
N
N
N
75
N
C
N
76
N
C
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
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
O
N
92
N
P
N
93
N
O
N
94
N
O
N
95
N
O
N
96
N
C
N
97
R
C
N
98
N
O
N
99
S
C
N
100
N
O
N
101
N
C
N
102
R
C
Y
103
N
N
Y
104
N
C
Y
105
N
N
Y
106
N
C
N
107
N
C
N
108
N
O
N
109
N
N
N
110
N
C
N
111
N
N
N
112
N
N
Y
113
N
C
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
O
N
129
N
P
N
130
N
O
N
131
N
O
N
132
N
O
N
133
N
C
N
134
R
C
N
135
N
O
N
136
S
C
N
137
N
O
N
138
N
C
N
139
R
C
N
140
N
N
N
141
N
C
N
142
N
O
N
143
N
N
N
144
N
C
N
145
N
O
N
146
N
C
N
147
N
C
N
148
N
C
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
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
N
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
O
N
169
N
O
N
170
N
C
N
171
N
O
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
N
H
N
179
N
H
N
180
N
H
N
181
N
N
N
182
S
C
N
183
N
C
N
184
N
O
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
C
N
189
N
N
N
190
N
O
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
P
N
207
N
O
N
208
N
O
N
209
N
O
N
210
N
P
N
211
N
O
N
212
N
O
N
213
N
O
N
214
N
O
N
215
N
C
N
216
R
C
N
217
N
O
N
218
S
C
N
219
N
O
N
220
N
C
N
221
R
C
Y
222
N
N
Y
223
N
C
Y
224
N
N
Y
225
N
C
N
226
N
C
N
227
N
O
N
228
N
N
N
229
N
C
N
230
N
N
N
231
N
N
Y
232
N
C
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
N
N
249
S
C
N
250
N
C
N
251
N
O
N
252
N
C
Y
253
N
C
Y
254
N
C
Y
255
N
C
Y
256
N
N
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
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
H
N
274
N
H
N
1
N
doub
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
doub
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
doub
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
Y
42
N
sing
Y
43
N
sing
Y
44
N
doub
N
45
N
sing
Y
46
N
sing
Y
47
N
sing
Y
48
N
doub
N
49
N
sing
Y
50
N
doub
N
51
N
sing
N
52
N
sing
Y
53
N
sing
Y
54
N
doub
N
55
N
sing
Y
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
doub
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
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
doub
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
doub
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
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
Y
115
N
sing
Y
116
N
sing
Y
117
N
doub
N
118
N
sing
Y
119
N
sing
N
120
N
sing
Y
121
N
doub
N
122
N
doub
N
123
N
sing
N
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
doub
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
doub
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
doub
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
doub
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
doub
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
sing
N
207
N
sing
N
208
N
doub
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
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
Y
236
N
sing
Y
237
N
sing
Y
238
N
doub
N
239
N
sing
Y
240
N
sing
N
241
N
sing
Y
242
N
doub
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
doub
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
doub
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
Y
263
N
doub
Y
264
N
sing
Y
265
N
sing
N
266
N
sing
Y
267
N
doub
Y
268
N
sing
Y
269
N
sing
N
270
N
sing
Y
271
N
sing
Y
272
N
doub
N
273
N
sing
Y
274
N
doub
N
275
N
sing
Y
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
GE
Chembiochem
1439-4227
4
40
49
10.1002/cbic.200390012
12512075
Solution structure and stability of tryptophan-containing nucleopeptide duplexes
2003
10.2210/pdb1j9n/pdb
pdb_00001j9n
There are chirality errors
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
1889.198
5'-D(*GP*CP*TP*AP*CP*(PGN))-3'
1
syn
polymer
1809.217
5'-D(*CP*GP*TP*AP*GP*C)-3'
1
syn
polymer
660.804
peptide ACE-LYS-TRP-LYS-HSE-ALA
1
syn
polymer
no
yes
(DG)(DC)(DT)(DA)(DC)(PGN)
GCTACG
A
polydeoxyribonucleotide
no
no
(DC)(DG)(DT)(DA)(DG)(DC)
CGTAGC
B
polydeoxyribonucleotide
no
yes
(ACE)KWK(HSE)A
XKWKSA
C
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
30.001
1
19
A
1
B
12
-3.916
A_DG1:DC12_B
1
-8.464
-0.108
0.517
0.082
7.462
1
19
A
2
B
11
-5.487
A_DC2:DG11_B
2
-17.154
-0.794
-0.170
-0.125
7.786
1
20
A
3
B
10
7.785
A_DT3:DA10_B
3
-13.154
0.526
0.144
-0.089
-0.625
1
20
A
4
B
9
-3.980
A_DA4:DT9_B
4
-0.822
-0.391
-0.169
-0.097
-2.701
1
19
A
5
B
8
-0.478
A_DC5:DG8_B
5
-6.364
-0.545
-0.044
0.053
6.471
1
19
A
6
B
7
-1.657
A_PGN6:DC7_B
6
-4.447
-0.551
-0.311
-0.096
3.548
31.474
A
A
1
2
8.550
B
B
12
11
3.704
4.622
-0.986
-0.705
AA_DG1DC2:DG11DC12_BB
1
0.523
-0.968
31.137
-2.261
1.927
2.913
37.124
A
A
2
3
16.470
B
B
11
10
3.101
10.356
0.903
-0.285
AA_DC2DT3:DA10DG11_BB
2
0.178
-0.283
35.698
-1.747
-1.397
1.767
40.262
A
A
3
4
49.202
B
B
10
9
3.275
30.191
-0.650
-0.566
AA_DT3DA4:DT9DA10_BB
3
1.819
-2.964
26.892
-4.039
1.138
3.035
27.520
A
A
4
5
12.100
B
B
9
8
3.247
5.710
0.361
-0.518
AA_DA4DC5:DG8DT9_BB
4
-2.192
4.645
26.845
-2.450
-1.282
1.918
27.007
A
A
5
6
40.385
B
B
8
7
3.041
17.400
0.018
-0.665
AA_DC5PGN6:DC7DG8_BB
5
0.872
-2.024
20.717
-5.246
0.154
atom_site
chem_comp_atom
chem_comp_bond
database_2
pdbx_nmr_software
pdbx_validate_torsion
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Data collection
Database references
Derived calculations
1
0
2003-01-21
1
1
2008-04-27
1
2
2011-07-13
2
0
2023-11-15
_atom_site.auth_atom_id
_atom_site.label_atom_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_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
RCSB
Y
RCSB
2001-05-28
REL
CHEMICALLY SYNTHESIZED
sample
all calculated structures submitted
10
10
2D NOESY
DQF-COSY
7
1
atm
278
K
7
1
atm
278
K
the structures are based on a total of 276 NOE-derived
distance constraints, and 33 dihedral angle restraints
molecular dynamics
matrix relaxation
1
2mM nucleopeptide, 25 mM phosphate buffer, 100 mM NaCl, 90% H2O, 10% D2O
90% H2O/10% D2O
2MM nucleopeptide, 25 mM phosphate buffer, 100 mM NaCl, 100% D2O
100% D2O
bruker
collection
XwinNMR
1.3
james, t.l.
iterative matrix relaxation
MARDIGRAS
5.2
guntert, P
structure solution
DYANA
1.5
kollman, p.
refinement
SANDER
5.0
600
Bruker
AMX
G
1
n
1
DG
1
A
C
2
n
2
DC
2
A
T
3
n
3
DT
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
PO2
6
n
6
PGN
6
A
C
7
n
1
DC
7
B
G
8
n
2
DG
8
B
T
9
n
3
DT
9
B
A
10
n
4
DA
10
B
G
11
n
5
DG
11
B
C
12
n
6
DC
12
B
ACE
13
n
1
ACE
12
C
LYS
13
n
2
LYS
13
C
TRP
14
n
3
TRP
14
C
LYS
15
n
4
LYS
15
C
HSE
16
n
5
HSE
16
C
ALA
17
n
6
ALA
17
C
author_defined_assembly
3
trimeric
A
PGN
6
2'-DEOXYGUANOSINE-3',5'-DIPHOSPHATE
A
PGN
6
DG
C
HSE
16
L-HOMOSERINE
C
HSE
5
SER
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
4
A
C4'
DG
1
WRONG HAND
4
C
CA
LYS
13
WRONG HAND
4
C
CA
LYS
15
WRONG HAND
6
C
CA
ALA
17
WRONG HAND
8
A
C4'
DC
5
WRONG HAND
9
C
CA
ALA
17
WRONG HAND
10
C
CA
TRP
14
WRONG HAND
1
A
DG
1
0.102
SIDE CHAIN
1
B
DA
10
0.078
SIDE CHAIN
1
B
DG
11
0.060
SIDE CHAIN
1
B
DC
12
0.096
SIDE CHAIN
2
B
DG
11
0.057
SIDE CHAIN
3
B
DA
10
0.081
SIDE CHAIN
3
B
DG
11
0.072
SIDE CHAIN
4
B
DC
7
0.063
SIDE CHAIN
4
B
DA
10
0.090
SIDE CHAIN
4
B
DG
11
0.095
SIDE CHAIN
5
B
DA
10
0.066
SIDE CHAIN
5
B
DG
11
0.058
SIDE CHAIN
5
B
DC
12
0.080
SIDE CHAIN
6
A
DG
1
0.075
SIDE CHAIN
6
B
DA
10
0.070
SIDE CHAIN
6
B
DG
11
0.070
SIDE CHAIN
6
B
DC
12
0.088
SIDE CHAIN
7
A
DG
1
0.073
SIDE CHAIN
7
B
DG
11
0.061
SIDE CHAIN
7
B
DC
12
0.096
SIDE CHAIN
8
B
DT
9
0.071
SIDE CHAIN
8
B
DA
10
0.080
SIDE CHAIN
8
B
DG
11
0.079
SIDE CHAIN
9
A
DG
1
0.067
SIDE CHAIN
9
B
DT
9
0.063
SIDE CHAIN
9
B
DA
10
0.107
SIDE CHAIN
9
B
DG
11
0.080
SIDE CHAIN
10
A
DG
1
0.090
SIDE CHAIN
10
B
DA
10
0.082
SIDE CHAIN
10
B
DG
11
0.060
SIDE CHAIN
10
B
DC
12
0.134
SIDE CHAIN
1
4.98
0.60
106.00
110.98
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
1
4.19
0.60
119.00
123.19
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
1
-6.09
0.60
122.90
116.81
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
1
7.33
1.20
119.70
127.03
A
A
A
C3'
O3'
P
DA
DA
DC
4
4
5
Y
1
6.68
0.30
108.30
114.98
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
2.95
0.30
108.30
111.25
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
2.64
0.30
108.30
110.94
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.13
0.60
106.00
110.13
B
B
B
O4'
C4'
C3'
DT
DT
DT
9
9
9
N
1
7.83
1.10
109.80
117.63
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
1
-7.78
1.00
110.10
102.32
B
B
B
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
1
-4.66
0.70
102.20
97.54
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
1
-7.62
0.80
105.90
98.28
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
1
7.00
0.60
119.00
126.00
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
1
-9.74
0.60
122.90
113.16
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
1
-4.49
0.60
118.60
114.11
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
1
-5.59
0.80
102.40
96.81
B
B
B
C3'
C2'
C1'
DG
DG
DG
11
11
11
N
1
5.09
0.30
108.30
113.39
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
2
4.09
0.60
106.00
110.09
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
2
2.29
0.30
108.30
110.59
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
2
4.76
0.60
119.00
123.76
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
2
-6.30
0.60
122.90
116.60
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
2
4.19
0.60
106.00
110.19
A
A
A
O4'
C4'
C3'
DA
DA
DA
4
4
4
N
2
5.91
0.30
108.30
114.21
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
2
5.59
0.30
108.30
113.89
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
2
4.30
0.30
108.30
112.60
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
2
-2.48
0.40
106.40
103.92
B
B
B
C8
N9
C4
DG
DG
DG
8
8
8
N
2
4.46
0.60
106.00
110.46
B
B
B
O4'
C4'
C3'
DT
DT
DT
9
9
9
N
2
9.02
1.10
109.80
118.82
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
2
-8.00
1.00
110.10
102.10
B
B
B
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
2
-5.67
0.70
102.20
96.53
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
2
-9.21
0.80
105.90
96.69
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
2
6.04
0.60
119.00
125.04
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
2
-8.66
0.60
122.90
114.24
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
2
-5.05
0.60
118.60
113.55
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
2
-5.19
0.80
102.40
97.21
B
B
B
C3'
C2'
C1'
DG
DG
DG
11
11
11
N
2
5.34
0.30
108.30
113.64
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
3
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
3
4.37
0.70
118.00
122.37
A
A
A
N3
C4
N4
DC
DC
DC
2
2
2
N
3
4.64
0.60
119.00
123.64
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
3
-6.35
0.60
122.90
116.55
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
3
7.28
1.20
119.70
126.98
A
A
A
C3'
O3'
P
DA
DA
DC
4
4
5
Y
3
6.93
0.30
108.30
115.23
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
3
2.81
0.30
108.30
111.11
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
3
3.41
0.30
108.30
111.71
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
3
6.15
0.60
106.00
112.15
B
B
B
O4'
C4'
C3'
DT
DT
DT
9
9
9
N
3
11.58
1.10
109.80
121.38
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
3
-9.20
1.00
110.10
100.90
B
B
B
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
3
-5.01
0.70
102.20
97.19
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
3
-5.86
0.80
105.90
100.04
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
3
6.99
0.60
119.00
125.99
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
3
-9.87
0.60
122.90
113.03
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
3
-3.95
0.60
118.60
114.65
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
3
4.68
0.30
108.30
112.98
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
4
9.52
1.10
109.80
119.32
A
A
A
C5'
C4'
O4'
DG
DG
DG
1
1
1
N
4
3.57
0.50
106.80
110.37
A
A
A
O4'
C1'
C2'
DG
DG
DG
1
1
1
N
4
6.73
0.30
108.30
115.03
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
4
3.63
0.60
106.00
109.63
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
4
4.60
0.70
118.00
122.60
A
A
A
N3
C4
N4
DC
DC
DC
2
2
2
N
4
4.67
0.60
119.00
123.67
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
4
-6.50
0.60
122.90
116.40
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
4
3.85
0.60
106.00
109.85
A
A
A
O4'
C4'
C3'
DA
DA
DA
4
4
4
N
4
6.32
0.30
108.30
114.62
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
4
3.79
0.30
108.30
112.09
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
4
3.65
0.30
108.30
111.95
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
4
5.34
0.60
106.00
111.34
B
B
B
O4'
C4'
C3'
DT
DT
DT
9
9
9
N
4
13.19
1.10
109.80
122.99
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
4
-8.60
1.00
110.10
101.50
B
B
B
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
4
-5.84
0.70
102.20
96.36
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
4
-9.00
0.80
105.90
96.90
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
4
2.53
0.30
108.30
110.83
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
4
6.64
0.60
119.00
125.64
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
4
-9.98
0.60
122.90
112.92
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
4
-4.39
0.60
118.60
114.21
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
4
-5.41
0.80
102.40
96.99
B
B
B
C3'
C2'
C1'
DG
DG
DG
11
11
11
N
4
5.18
0.30
108.30
113.48
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
5
2.04
0.30
108.30
110.34
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
5
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
5
4.50
0.70
118.00
122.50
A
A
A
N3
C4
N4
DC
DC
DC
2
2
2
N
5
7.79
1.20
119.70
127.49
A
A
A
C3'
O3'
P
DC
DC
DT
2
2
3
Y
5
5.54
0.60
119.00
124.54
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
5
-6.95
0.60
122.90
115.95
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
5
3.99
0.60
106.00
109.99
A
A
A
O4'
C4'
C3'
DA
DA
DA
4
4
4
N
5
5.74
0.30
108.30
114.04
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
5
2.14
0.30
108.30
110.44
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
5
3.67
0.60
118.90
122.57
B
B
B
N1
C2
O2
DC
DC
DC
7
7
7
N
5
3.75
0.30
108.30
112.05
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
5
5.69
0.60
106.00
111.69
B
B
B
O4'
C4'
C3'
DT
DT
DT
9
9
9
N
5
9.97
1.10
109.80
119.77
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
5
-8.79
1.00
110.10
101.31
B
B
B
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
5
-6.24
0.70
102.20
95.96
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
5
-7.49
0.80
105.90
98.41
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
5
6.31
0.60
119.00
125.31
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
5
-8.72
0.60
122.90
114.18
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
5
-4.59
0.60
118.60
114.01
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
5
-5.70
0.80
102.40
96.70
B
B
B
C3'
C2'
C1'
DG
DG
DG
11
11
11
N
5
4.98
0.30
108.30
113.28
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
6
3.94
0.60
106.00
109.94
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
6
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
6
4.31
0.60
119.00
123.31
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
6
-5.97
0.60
122.90
116.93
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
6
3.69
0.60
106.00
109.69
A
A
A
O4'
C4'
C3'
DA
DA
DA
4
4
4
N
6
7.01
0.30
108.30
115.31
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
6
2.83
0.30
108.30
111.13
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
6
2.73
0.30
108.30
111.03
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
6
6.02
0.60
106.00
112.02
B
B
B
O4'
C4'
C3'
DT
DT
DT
9
9
9
N
6
10.31
1.10
109.80
120.11
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
6
-9.94
1.00
110.10
100.16
B
B
B
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
6
-6.52
0.70
102.20
95.68
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
6
-8.15
0.80
105.90
97.75
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
6
6.48
0.60
119.00
125.48
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
6
-8.93
0.60
122.90
113.97
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
6
2.54
0.30
108.30
110.84
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
6
-4.56
0.60
118.60
114.04
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
6
-5.79
0.80
102.40
96.61
B
B
B
C3'
C2'
C1'
DG
DG
DG
11
11
11
N
6
4.14
0.30
108.30
112.44
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
7
4.24
0.60
106.00
110.24
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
7
7.61
1.20
119.70
127.31
A
A
A
C3'
O3'
P
DC
DC
DT
2
2
3
Y
7
4.56
0.60
119.00
123.56
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
7
-6.22
0.60
122.90
116.68
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
7
7.04
0.30
108.30
115.34
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
7
10.10
1.10
109.80
119.90
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
7
-4.84
0.70
102.20
97.36
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
7
-10.04
0.80
105.90
95.86
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
7
3.21
0.30
108.30
111.51
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
7
7.39
0.60
119.00
126.39
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
7
-9.76
0.60
122.90
113.14
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
7
-4.60
0.60
118.60
114.00
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
7
-5.96
0.80
102.40
96.44
B
B
B
C3'
C2'
C1'
DG
DG
DG
11
11
11
N
7
5.11
0.30
108.30
113.41
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
8
3.77
0.60
118.90
122.67
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
8
4.68
0.70
118.00
122.68
A
A
A
N3
C4
N4
DC
DC
DC
2
2
2
N
8
4.33
0.60
119.00
123.33
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
8
-5.88
0.60
122.90
117.02
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
8
9.73
1.10
109.80
119.53
A
A
A
C5'
C4'
O4'
DC
DC
DC
5
5
5
N
8
9.31
0.30
108.30
117.61
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
8
3.99
0.60
118.90
122.89
A
A
A
N1
C2
O2
DC
DC
DC
5
5
5
N
8
3.55
0.30
108.30
111.85
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
8
2.92
0.30
108.30
111.22
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
8
5.42
0.60
106.00
111.42
B
B
B
O4'
C4'
C3'
DT
DT
DT
9
9
9
N
8
8.25
1.20
115.70
123.95
B
B
B
C5'
C4'
C3'
DT
DT
DT
9
9
9
N
8
9.79
1.10
109.80
119.59
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
8
-6.52
1.00
110.10
103.58
B
B
B
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
8
4.02
0.60
119.00
123.02
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
8
-6.33
0.60
122.90
116.57
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
8
-4.69
0.60
118.60
113.91
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
8
-4.85
0.80
102.40
97.55
B
B
B
C3'
C2'
C1'
DG
DG
DG
11
11
11
N
8
5.09
0.30
108.30
113.39
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
9
4.84
0.60
106.00
110.84
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
9
5.55
0.60
119.00
124.55
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
9
-6.84
0.60
122.90
116.06
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
9
3.62
0.60
106.00
109.62
A
A
A
O4'
C4'
C3'
DA
DA
DA
4
4
4
N
9
7.25
0.30
108.30
115.55
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
9
7.23
1.20
119.70
126.93
A
A
A
C3'
O3'
P
DC
DC
PGN
5
5
6
Y
9
4.99
0.30
108.30
113.29
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
9
7.52
1.20
119.70
127.22
B
B
B
C3'
O3'
P
DC
DC
DG
7
7
8
Y
9
5.99
0.60
106.00
111.99
B
B
B
O4'
C4'
C3'
DT
DT
DT
9
9
9
N
9
7.80
1.10
109.80
117.60
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
9
-6.49
0.70
102.20
95.71
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
9
-9.35
0.80
105.90
96.55
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
9
6.17
0.60
119.00
125.17
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
9
-9.31
0.60
122.90
113.59
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
9
-4.27
0.60
118.60
114.33
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
9
5.45
0.30
108.30
113.75
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
10
4.26
0.60
106.00
110.26
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
10
3.79
0.60
119.00
122.79
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
10
-5.80
0.60
122.90
117.10
A
A
A
C6
C5
C7
DT
DT
DT
3
3
3
N
10
4.05
0.60
106.00
110.05
A
A
A
O4'
C4'
C3'
DA
DA
DA
4
4
4
N
10
6.50
0.30
108.30
114.80
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
10
4.15
0.30
108.30
112.45
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
10
3.27
0.30
108.30
111.57
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
10
8.90
1.10
109.80
118.70
B
B
B
C5'
C4'
O4'
DT
DT
DT
9
9
9
N
10
-8.00
0.80
105.90
97.90
B
B
B
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
10
1.83
0.30
108.30
110.13
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
10
6.06
0.60
119.00
125.06
B
B
B
C4
C5
C7
DT
DT
DT
9
9
9
N
10
-8.91
0.60
122.90
113.99
B
B
B
C6
C5
C7
DT
DT
DT
9
9
9
N
10
-4.09
0.60
118.60
114.51
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
10
6.11
0.30
108.30
114.41
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
C
TRP
14
29.86
-116.07
2
C
TRP
14
-146.18
-81.96
2
C
LYS
15
-161.40
107.05
3
C
TRP
14
-163.00
87.83
3
C
LYS
15
28.25
69.79
4
C
TRP
14
-162.11
75.15
4
C
LYS
15
30.57
71.02
5
C
LYS
15
-49.64
77.94
6
C
TRP
14
-59.19
176.93
7
C
TRP
14
-46.42
85.09
7
C
LYS
15
21.43
75.54
8
C
TRP
14
5.79
70.33
8
C
LYS
15
17.33
81.55
9
C
TRP
14
15.93
64.46
9
C
LYS
15
9.24
88.95
10
C
TRP
14
60.55
-100.99
10
C
LYS
15
-157.29
18.87
Solution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3*dGCATCG)-ALA]-[p5*dCGTAGC]
1
N
N
2
N
N
3
N
N
covale
1.623
both
A
DC
5
A
O3'
DC
5
1_555
A
PGN
6
A
P
PGN
6
1_555
covale
1.618
none
A
PGN
6
A
P1
PGN
6
1_555
C
HSE
16
C
O3
HSE
5
1_555
covale
1.340
both
C
ACE
12
C
C
ACE
1
1_555
C
LYS
13
C
N
LYS
2
1_555
covale
1.335
both
C
LYS
15
C
C
LYS
4
1_555
C
HSE
16
C
N
HSE
5
1_555
covale
1.339
both
C
HSE
16
C
C
HSE
5
1_555
C
ALA
17
C
N
ALA
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
12
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
12
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
12
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
11
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
11
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
11
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
10
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
10
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
9
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
9
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
PGN
6
A
N1
PGN
6
1_555
B
DC
7
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
PGN
6
A
N2
PGN
6
1_555
B
DC
7
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
PGN
6
A
O6
PGN
6
1_555
B
DC
7
B
N4
DC
1
1_555
DNA BINDING PROTEIN/DNA
COVALENTLY LINKED PEPTIDE-DNA COMPLEX, TRYPTOPHAN STACKING, DNA BINDING PROTEIN-DNA COMPLEX
1J9N
PDB
1
1J9N
1J9N
PDB
2
1J9N
1J9N
PDB
3
1J9N
1
6
1J9N
1
6
1J9N
A
1
1
6
7
12
1J9N
7
12
1J9N
B
2
1
6
12
17
1J9N
12
17
1J9N
C
3
1
6