0.028622
0.016525
0.000000
0.000000
0.033050
0.000000
0.000000
0.000000
0.027935
0.00000
0.00000
0.00000
Menchise, V.
De Simone, G.
Tedeschi, T.
Corradini, R.
Sforza, S.
Marchelli, R.
Capasso, D.
Saviano, M.
Pedone, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
3
90.00
90.00
120.00
34.94
34.94
35.80
C15 H24 N8 O3
364.403
2-AMINOETHYLLYSINE-CARBONYLMETHYLENE-ADENINE
L-peptide linking
C11 H16 N7 O3 1
294.290
2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
peptide-like
C14 H24 N6 O4
340.378
2-AMINOETHYLLYSINE-CARBONYLMETHYLENE-CYTOSINE
L-peptide linking
C10 H16 N5 O4 1
270.265
2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
peptide-like
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
C11 H16 N7 O4 1
310.289
2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
peptide-like
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
H2 N
16.023
AMINO GROUP
non-polymer
C15 H25 N5 O5
355.390
2-AMINOETHYLLYSINE-CARBONYLMETHYLENE-THYMINE
L-peptide linking
C11 H17 N4 O5 1
285.276
2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE
peptide-like
N
1
N
C
N
2
N
C
N
3
N
O
N
4
R
C
N
5
N
C
N
6
N
O
N
7
N
O
N
8
N
N
N
9
N
C
N
10
N
C
N
11
N
N
Y
12
N
N
Y
13
N
C
Y
14
N
N
Y
15
N
C
Y
16
N
C
N
17
N
N
Y
18
N
N
Y
19
N
C
Y
20
N
N
Y
21
N
C
N
22
N
C
N
23
N
C
N
24
N
C
N
25
N
C
N
26
N
N
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
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
C
N
52
N
C
N
53
N
O
N
54
N
C
N
55
N
C
N
56
N
O
N
57
N
O
N
58
N
N
N
59
N
C
N
60
N
C
N
61
N
N
Y
62
N
N
Y
63
N
C
Y
64
N
N
Y
65
N
C
Y
66
N
C
N
67
N
N
Y
68
N
N
Y
69
N
C
Y
70
N
N
Y
71
N
C
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
H
N
86
N
H
N
87
N
H
N
88
N
C
N
89
N
C
N
90
N
O
N
91
R
C
N
92
N
C
N
93
N
O
N
94
N
O
N
95
N
N
N
96
N
C
N
97
N
C
N
98
N
N
N
99
N
N
N
100
N
C
N
101
N
N
N
102
N
C
N
103
N
C
N
104
N
C
N
105
N
O
N
106
N
N
N
107
N
C
N
108
N
C
N
109
N
C
N
110
N
C
N
111
N
N
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
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
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
C
N
137
N
C
N
138
N
O
N
139
N
C
N
140
N
C
N
141
N
O
N
142
N
O
N
143
N
N
N
144
N
C
N
145
N
C
N
146
N
N
N
147
N
N
N
148
N
C
N
149
N
N
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
N
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
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
O
N
172
N
P
N
173
N
O
N
174
N
O
N
175
N
O
N
176
N
C
N
177
R
C
N
178
N
O
N
179
S
C
N
180
N
O
N
181
N
C
N
182
R
C
Y
183
N
N
Y
184
N
C
Y
185
N
N
Y
186
N
C
Y
187
N
C
N
188
N
N
Y
189
N
N
Y
190
N
C
Y
191
N
N
Y
192
N
C
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
O
N
208
N
P
N
209
N
O
N
210
N
O
N
211
N
O
N
212
N
C
N
213
R
C
N
214
N
O
N
215
S
C
N
216
N
O
N
217
N
C
N
218
R
C
N
219
N
N
N
220
N
C
N
221
N
O
N
222
N
N
N
223
N
C
N
224
N
N
N
225
N
C
N
226
N
C
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
O
N
242
N
P
N
243
N
O
N
244
N
O
N
245
N
O
N
246
N
C
N
247
R
C
N
248
N
O
N
249
S
C
N
250
N
O
N
251
N
C
N
252
R
C
Y
253
N
N
Y
254
N
C
Y
255
N
N
Y
256
N
C
N
257
N
C
N
258
N
O
N
259
N
N
N
260
N
C
N
261
N
N
N
262
N
N
Y
263
N
C
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
275
N
H
N
276
N
H
N
277
N
H
N
278
N
O
N
279
N
P
N
280
N
O
N
281
N
O
N
282
N
O
N
283
N
C
N
284
R
C
N
285
N
O
N
286
S
C
N
287
N
O
N
288
N
C
N
289
R
C
N
290
N
N
N
291
N
C
N
292
N
O
N
293
N
N
N
294
N
C
N
295
N
O
N
296
N
C
N
297
N
C
N
298
N
C
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
C
N
315
N
C
N
316
N
O
N
317
N
C
N
318
N
C
N
319
N
O
N
320
N
O
N
321
N
N
N
322
N
C
N
323
N
C
N
324
N
N
Y
325
N
N
Y
326
N
C
Y
327
N
N
Y
328
N
C
N
329
N
C
N
330
N
O
N
331
N
N
N
332
N
C
N
333
N
N
N
334
N
N
Y
335
N
C
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
O
N
353
N
H
N
354
N
H
N
355
N
MG
N
356
N
N
N
357
N
H
N
358
N
H
N
359
N
C
N
360
N
C
N
361
N
O
N
362
R
C
N
363
N
C
N
364
N
O
N
365
N
O
N
366
N
N
N
367
N
C
N
368
N
C
N
369
N
N
N
370
N
N
N
371
N
C
N
372
N
C
N
373
N
O
N
374
N
N
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
C
N
380
N
C
N
381
N
C
N
382
N
C
N
383
N
N
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
C
N
410
N
C
N
411
N
O
N
412
N
C
N
413
N
C
N
414
N
O
N
415
N
O
N
416
N
N
N
417
N
C
N
418
N
C
N
419
N
N
N
420
N
N
N
421
N
C
N
422
N
C
N
423
N
O
N
424
N
N
N
425
N
C
N
426
N
O
N
427
N
C
N
428
N
C
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
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
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
doub
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
Y
23
N
sing
Y
24
N
sing
Y
25
N
doub
N
26
N
sing
Y
27
N
sing
Y
28
N
sing
Y
29
N
doub
N
30
N
sing
Y
31
N
doub
N
32
N
sing
N
33
N
sing
Y
34
N
sing
Y
35
N
doub
N
36
N
sing
Y
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
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
doub
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
doub
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
Y
75
N
sing
Y
76
N
sing
Y
77
N
doub
N
78
N
sing
Y
79
N
sing
Y
80
N
sing
Y
81
N
doub
N
82
N
sing
Y
83
N
doub
N
84
N
sing
N
85
N
sing
Y
86
N
sing
Y
87
N
doub
N
88
N
sing
Y
89
N
sing
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
doub
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
N
115
N
doub
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
doub
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
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
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
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
doub
N
165
N
doub
N
166
N
sing
N
167
N
sing
N
168
N
doub
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
doub
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
sing
Y
196
N
sing
Y
197
N
sing
Y
198
N
doub
N
199
N
sing
Y
200
N
sing
Y
201
N
sing
Y
202
N
doub
N
203
N
sing
Y
204
N
doub
N
205
N
sing
N
206
N
sing
Y
207
N
sing
Y
208
N
doub
N
209
N
sing
Y
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
doub
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
doub
N
237
N
sing
N
238
N
doub
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
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
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
sing
Y
269
N
sing
Y
270
N
sing
Y
271
N
doub
N
272
N
sing
Y
273
N
sing
N
274
N
sing
Y
275
N
doub
N
276
N
doub
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
doub
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
doub
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
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
doub
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
doub
N
315
N
sing
N
316
N
sing
N
317
N
doub
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
doub
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
doub
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
sing
Y
346
N
sing
Y
347
N
doub
N
348
N
sing
Y
349
N
sing
N
350
N
sing
Y
351
N
doub
N
352
N
doub
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
doub
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
doub
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
doub
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
doub
N
390
N
sing
N
391
N
doub
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
doub
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
doub
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
doub
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
doub
N
441
N
sing
N
442
N
doub
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
doub
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
100
12021
12026
10.1073/pnas.2034746100
14512516
Insights into peptide nucleic acid (PNA) structural features: The
crystal structure of a D-lysine-based chiral PNA-DNA duplex
2003
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
58
553
555
10.1107/S0907444902001427
Crystallization and preliminary X-ray diffraction studies of a D-Lysine-based
chiral PNA-DNA duplex
2002
10.2210/pdb1nr8/pdb
pdb_00001nr8
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
100
2
CCD
2002-02-11
MARRESEARCH
CCD
MARRESEARCH
SAD
M
x-ray
1
1.200
1.0
0.918
1.0
ID14-1
ESRF
1.200
SYNCHROTRON
ESRF BEAMLINE ID14-1
5.2R
ELETTRA
0.918
SYNCHROTRON
ELETTRA BEAMLINE 5.2R
DNA
3044.017
5'-D(P*AP*GP*TP*GP*AP*TP*CP*TP*AP*C)-3'
1
syn
polymer
peptide nucleic acid
2883.044
H-((GPN)*(TPN)*(APN)*(GPN)*(A66)*(T66)*(C66)*(APN)*(CPN)*(TPN))-NH2
1
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
80
nat
water
no
no
(DA)(DG)(DT)(DG)(DA)(DT)(DC)(DT)(DA)(DC)
AGTGATCTAC
A
polydeoxyribonucleotide
no
yes
(GPN)(TPN)(APN)(GPN)(A66)(T66)(C66)(APN)(CPN)(TPN)(NH2)
XXXXXXXXXXX
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
1.81
31.5
VAPOR DIFFUSION, HANGING DROP
6.3
PEG 8000, AMMONIUM ACETATE, SODIUM CACODYLATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
VAPOR DIFFUSION, HANGING DROP
6.0
ISOPROPANOL, MAGNESIUM CHLORIDE, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
AMMONIUM ACETATE
1
PEG 8000
1
Na CACODYLATE
1
AMMONIUM ACETATE
2
PEG 8000
2
MgCl2
1
MES
1
ISOPROPANOL
1
MgCl2
2
ISOPROPANOL
2
7.882
1
20
A
1
B
10
0.415
A_DA1:TPN10_B
1
-12.647
-0.103
0.023
-0.161
-0.439
1
19
A
2
B
9
2.390
A_DG2:CPN9_B
2
-8.591
-0.476
0.028
-0.140
-1.331
1
20
A
3
B
8
3.602
A_DT3:APN8_B
3
-8.927
0.025
-0.118
-0.163
13.205
1
19
A
7
B
4
0.570
A_DC7:GPN4_B
4
0.152
0.159
-0.439
-0.130
3.338
1
20
A
8
B
3
2.710
A_DT8:APN3_B
5
-4.141
-0.091
-0.214
-0.133
16.341
1
20
A
9
B
2
2.835
A_DA9:TPN2_B
6
-3.207
0.186
0.069
-0.186
16.486
1
19
A
10
B
1
5.945
A_DC10:GPN1_B
7
-17.118
0.221
-0.136
-0.063
3.303
25.459
A
A
1
2
7.455
B
B
10
9
3.512
3.267
-0.909
-2.134
AA_DA1DG2:CPN9TPN10_BB
1
-3.382
7.718
25.028
-5.827
1.043
3.383
27.249
A
A
2
3
-1.039
B
B
9
8
3.372
-0.489
-1.213
-1.710
AA_DG2DT3:APN8CPN9_BB
2
0.432
-0.918
27.241
-3.504
2.686
4.001
24.412
A
A
7
8
-4.361
B
B
4
3
3.748
-1.832
-0.878
-2.237
AA_DC7DT8:APN3GPN4_BB
3
-4.582
10.909
23.916
-4.605
0.365
1.931
24.313
A
A
8
9
32.608
B
B
3
2
3.037
12.964
-0.674
-1.347
AA_DT8DA9:TPN2APN3_BB
4
-4.052
10.192
20.213
-6.593
0.539
3.817
17.291
A
A
9
10
-12.636
B
B
2
1
3.522
-3.765
0.547
-2.003
AA_DA9DC10:GPN1TPN2_BB
5
-1.368
4.593
16.824
-3.988
-2.791
atom_site
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Non-polymer description
Version format compliance
Atomic model
Data collection
Database references
Derived calculations
1
0
2003-10-28
1
1
2008-04-29
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
_struct_conn.pdbx_leaving_atom_flag
_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_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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
AN ACHIRAL PNA-DNA NMR STRUCTURE
AN ACHIRAL PNA-PNA CRYSTAL STRUCTURE
RCSB
Y
RCSB
2003-01-24
REL
REL
MG
MAGNESIUM ION
HOH
water
MG
9001
3
MG
MG
9001
B
HOH
5
4
HOH
HOH
11
A
HOH
9
4
HOH
HOH
12
A
HOH
11
4
HOH
HOH
13
A
HOH
12
4
HOH
HOH
14
A
HOH
13
4
HOH
HOH
15
A
HOH
14
4
HOH
HOH
16
A
HOH
17
4
HOH
HOH
17
A
HOH
22
4
HOH
HOH
18
A
HOH
24
4
HOH
HOH
19
A
HOH
25
4
HOH
HOH
20
A
HOH
26
4
HOH
HOH
21
A
HOH
28
4
HOH
HOH
22
A
HOH
29
4
HOH
HOH
23
A
HOH
30
4
HOH
HOH
24
A
HOH
33
4
HOH
HOH
25
A
HOH
34
4
HOH
HOH
26
A
HOH
35
4
HOH
HOH
27
A
HOH
36
4
HOH
HOH
28
A
HOH
37
4
HOH
HOH
29
A
HOH
38
4
HOH
HOH
30
A
HOH
39
4
HOH
HOH
31
A
HOH
40
4
HOH
HOH
32
A
HOH
41
4
HOH
HOH
33
A
HOH
42
4
HOH
HOH
34
A
HOH
47
4
HOH
HOH
35
A
HOH
51
4
HOH
HOH
36
A
HOH
52
4
HOH
HOH
37
A
HOH
54
4
HOH
HOH
38
A
HOH
55
4
HOH
HOH
39
A
HOH
56
4
HOH
HOH
40
A
HOH
57
4
HOH
HOH
41
A
HOH
61
4
HOH
HOH
42
A
HOH
62
4
HOH
HOH
43
A
HOH
63
4
HOH
HOH
44
A
HOH
66
4
HOH
HOH
45
A
HOH
67
4
HOH
HOH
46
A
HOH
68
4
HOH
HOH
47
A
HOH
69
4
HOH
HOH
48
A
HOH
70
4
HOH
HOH
49
A
HOH
72
4
HOH
HOH
50
A
HOH
75
4
HOH
HOH
51
A
HOH
79
4
HOH
HOH
52
A
HOH
1
4
HOH
HOH
9002
B
HOH
2
4
HOH
HOH
9003
B
HOH
3
4
HOH
HOH
9004
B
HOH
4
4
HOH
HOH
9005
B
HOH
6
4
HOH
HOH
9006
B
HOH
7
4
HOH
HOH
9007
B
HOH
8
4
HOH
HOH
9008
B
HOH
10
4
HOH
HOH
9009
B
HOH
15
4
HOH
HOH
9010
B
HOH
16
4
HOH
HOH
9011
B
HOH
18
4
HOH
HOH
9012
B
HOH
19
4
HOH
HOH
9013
B
HOH
20
4
HOH
HOH
9014
B
HOH
21
4
HOH
HOH
9015
B
HOH
23
4
HOH
HOH
9016
B
HOH
27
4
HOH
HOH
9017
B
HOH
31
4
HOH
HOH
9018
B
HOH
32
4
HOH
HOH
9019
B
HOH
43
4
HOH
HOH
9020
B
HOH
44
4
HOH
HOH
9021
B
HOH
45
4
HOH
HOH
9022
B
HOH
46
4
HOH
HOH
9023
B
HOH
48
4
HOH
HOH
9024
B
HOH
49
4
HOH
HOH
9025
B
HOH
50
4
HOH
HOH
9026
B
HOH
53
4
HOH
HOH
9027
B
HOH
58
4
HOH
HOH
9028
B
HOH
59
4
HOH
HOH
9029
B
HOH
60
4
HOH
HOH
9030
B
HOH
64
4
HOH
HOH
9031
B
HOH
65
4
HOH
HOH
9032
B
HOH
71
4
HOH
HOH
9033
B
HOH
73
4
HOH
HOH
9034
B
HOH
74
4
HOH
HOH
9035
B
HOH
76
4
HOH
HOH
9036
B
HOH
77
4
HOH
HOH
9037
B
HOH
78
4
HOH
HOH
9038
B
HOH
80
4
HOH
HOH
9039
B
A
1
n
1
DA
1
A
G
2
n
2
DG
2
A
T
3
n
3
DT
3
A
G
4
n
4
DG
4
A
A
5
n
5
DA
5
A
T
6
n
6
DT
6
A
C
7
n
7
DC
7
A
T
8
n
8
DT
8
A
A
9
n
9
DA
9
A
C
10
n
10
DC
10
A
GPN
1
n
1
GPN
1
B
TPN
2
n
2
TPN
2
B
APN
3
n
3
APN
3
B
GPN
4
n
4
GPN
4
B
A66
5
n
5
A66
5
B
T66
6
n
6
T66
6
B
C66
7
n
7
C66
7
B
APN
8
n
8
APN
8
B
CPN
9
n
9
CPN
9
B
TPN
10
n
10
TPN
10
B
NH2
11
n
11
NH2
11
B
author_defined_assembly
2
dimeric
B
GPN
4
B
N3
GPN
4
1_555
B
MG
9001
C
MG
MG
1_555
B
A66
5
B
N1'
A66
5
1_555
120.1
B
GPN
4
B
N3
GPN
4
1_555
B
MG
9001
C
MG
MG
1_555
B
HOH
9017
E
O
HOH
1_555
90.8
B
A66
5
B
N1'
A66
5
1_555
B
MG
9001
C
MG
MG
1_555
B
HOH
9017
E
O
HOH
1_555
117.8
B
GPN
1
B
GPN
1
DG
B
TPN
2
B
TPN
2
DT
B
APN
3
B
APN
3
DA
B
GPN
4
B
GPN
4
DG
B
APN
8
B
APN
8
DA
B
CPN
9
B
CPN
9
DC
B
TPN
10
B
TPN
10
DT
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
NH2
11
B
NH2
11
0
Y
1
A
DA
9
0.066
SIDE CHAIN
0.228
0.197
0.214
0.214
1.66
20.0
579
5429
5429
10.7
RANDOM
2
THROUGHOUT
0
SAD
Engh & Huber
1.66
20.0
80
494
1
202
211
0.011
1.11
1.66
20.0
1NR8
5429
5429
0
0
0.06
2
15.4
97.8
1.66
1.72
5.1
525
0.185
2
95.1
data reduction
DENZO
data scaling
SCALEPACK
phasing
SOLVE
refinement
CNS
1.1
The crystal structure of a D-Lysine-based chiral PNA-DNA duplex
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
covale
1.331
both
B
GPN
1
B
C
GPN
1
1_555
B
TPN
2
B
N
TPN
2
1_555
covale
1.330
both
B
TPN
2
B
C
TPN
2
1_555
B
APN
3
B
N
APN
3
1_555
covale
1.336
both
B
APN
3
B
C
APN
3
1_555
B
GPN
4
B
N
GPN
4
1_555
covale
1.333
one
B
GPN
4
B
C
GPN
4
1_555
B
A66
5
B
N1'
A66
5
1_555
covale
1.336
one
B
A66
5
B
C'
A66
5
1_555
B
T66
6
B
N1'
T66
6
1_555
covale
1.320
one
B
T66
6
B
C'
T66
6
1_555
B
C66
7
B
N1'
C66
7
1_555
covale
1.336
both
B
C66
7
B
C'
C66
7
1_555
B
APN
8
B
N
APN
8
1_555
covale
1.328
both
B
APN
8
B
C
APN
8
1_555
B
CPN
9
B
N
CPN
9
1_555
covale
1.333
both
B
CPN
9
B
C
CPN
9
1_555
B
TPN
10
B
N
TPN
10
1_555
covale
1.324
both
B
TPN
10
B
C
TPN
10
1_555
B
NH2
11
B
N
NH2
11
1_555
metalc
2.851
B
GPN
4
B
N3
GPN
4
1_555
B
MG
9001
C
MG
MG
1_555
metalc
3.095
B
A66
5
B
N1'
A66
5
1_555
B
MG
9001
C
MG
MG
1_555
metalc
2.810
B
MG
9001
C
MG
MG
1_555
B
HOH
9017
E
O
HOH
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
TPN
10
B
N3
TPN
10
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
TPN
10
B
O4
TPN
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
CPN
9
B
N3
CPN
9
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
CPN
9
B
O2
CPN
9
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
CPN
9
B
N4
CPN
9
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
APN
8
B
N1
APN
8
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
APN
8
B
N6
APN
8
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
GPN
4
B
N1
GPN
4
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
GPN
4
B
O6
GPN
4
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
GPN
4
B
N2
GPN
4
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
APN
3
B
N1
APN
3
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
APN
3
B
N6
APN
3
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N1
DA
9
1_555
B
TPN
2
B
N3
TPN
2
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N6
DA
9
1_555
B
TPN
2
B
O4
TPN
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
GPN
1
B
N1
GPN
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
GPN
1
B
O6
GPN
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
GPN
1
B
N2
GPN
1
1_555
DNA/PEPTIDE NUCLEIC ACID
CHIRAL PEPTIDE NUCLEIC ACID, DOUBLE STRANDED HELIX, P-FORM, DNA-PEPTIDE NUCLEIC ACID COMPLEX
1NR8
PDB
1
1NR8
1NR8
PDB
2
1NR8
1
10
1NR8
1
10
1NR8
A
1
1
10
1
11
1NR8
1
11
1NR8
B
2
1
11
BINDING SITE FOR RESIDUE MG B 9001
B
MG
9001
Software
3
B
GPN
4
B
GPN
4
3
1_555
B
A66
5
B
A66
5
3
1_555
B
HOH
9017
E
HOH
3
1_555
144
trigonal
P 31