0.032960
0.000000
0.000000
0.000000
0.022222
0.000000
0.000000
0.000000
0.020292
0.00000
0.00000
0.00000
Eldrup, A.B.
Nielsen, B.B.
Haaima, G.
Rasmussen, H.
Kastrup, J.S.
Christensen, C.
Nielsen, P.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
30.340
45.000
49.280
C11 H16 N7 O3 1
294.290
2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
peptide-like
C10 H16 N5 O4 1
270.265
2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
peptide-like
C11 H16 N7 O4 1
310.289
2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE
peptide-like
H2 O
18.015
WATER
non-polymer
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
H2 N
16.023
AMINO GROUP
non-polymer
C14 H17 N4 O4 1
305.309
{(2-AMINO-ETHYL)-[2-(2-OXO-1,2-DIHYDRO-[1,8]NAPHTHYRIDIN-3-YL)-ACETYL]-AMINO}-ACETIC ACID
non-polymer
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
N
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
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
C
N
39
N
C
N
40
N
O
N
41
N
C
N
42
N
C
N
43
N
O
N
44
N
O
N
45
N
N
N
46
N
C
N
47
N
C
N
48
N
N
N
49
N
N
N
50
N
C
N
51
N
N
N
52
N
C
N
53
N
C
N
54
N
C
N
55
N
O
N
56
N
N
N
57
N
H
N
58
N
H
N
59
N
H
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
C
N
74
N
C
N
75
N
O
N
76
N
C
N
77
N
C
N
78
N
O
N
79
N
O
N
80
N
N
N
81
N
C
N
82
N
C
N
83
N
N
Y
84
N
N
Y
85
N
C
Y
86
N
N
Y
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
N
Y
94
N
C
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
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
H
N
113
N
H
N
114
N
N
N
115
S
C
N
116
N
C
N
117
N
O
N
118
N
C
N
119
N
C
N
120
N
C
N
121
N
C
N
122
N
N
N
123
N
O
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
H
N
137
N
H
N
138
N
H
N
139
N
N
N
140
N
H
N
141
N
H
N
142
N
N
N
143
N
C
N
144
N
C
N
145
N
N
N
146
N
C
N
147
N
C
N
148
N
O
N
149
N
C
N
150
N
O
N
151
N
C
Y
152
N
C
Y
153
N
C
Y
154
N
C
N
155
N
O
Y
156
N
N
Y
157
N
C
Y
158
N
C
Y
159
N
C
Y
160
N
C
Y
161
N
C
Y
162
N
N
N
163
N
O
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
N
H
N
179
N
H
N
180
N
H
N
181
N
C
N
182
N
C
N
183
N
O
N
184
N
C
N
185
N
C
N
186
N
O
N
187
N
O
N
188
N
N
N
189
N
C
N
190
N
C
N
191
N
N
N
192
N
N
N
193
N
C
N
194
N
C
N
195
N
O
N
196
N
N
N
197
N
C
N
198
N
O
N
199
N
C
N
200
N
C
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
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
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
N
23
N
sing
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
doub
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
doub
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
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
doub
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
doub
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
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
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
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
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
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
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
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
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
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
Y
163
N
doub
Y
164
N
sing
Y
165
N
sing
N
166
N
sing
N
167
N
doub
Y
168
N
sing
Y
169
N
sing
N
170
N
sing
Y
171
N
doub
Y
172
N
sing
Y
173
N
sing
Y
174
N
doub
N
175
N
sing
Y
176
N
sing
N
177
N
sing
Y
178
N
doub
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
doub
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
doub
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
doub
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
doub
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
GE
Eur.J.Org.Chem.
1434-193X
9
1781
1790
-1
1,8-Naphthyridin-2(1H)-ones. Novel Bicyclic and Tricyclic Analogues of Thymine in Peptide Nucleic Acids (PNAs)
2001
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
4
98
101
Crystal Structure of a Peptide Nucleic Acid (PNA) Duplex at 1.7 A Resolution
1997
FR
New J.Chem.
1144-0546
23
833
840
10.1039/a902091h
Peptide Nucleic Acids (PNA) Derived from N-(N-methylaminoethyl)glycine. Synthesis, Hybridization and Structural Properties
1999
10.2210/pdb1hzs/pdb
pdb_00001hzs
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293.0
1
segmental toroidal mirror
IMAGE PLATE
1999-08-18
MARRESEARCH
silicon
SINGLE WAVELENGTH
M
x-ray
1
1.0500
1.0
X31
EMBL/DESY, HAMBURG
1.0500
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X31
1733.858
PEPTIDE NUCLEIC ACID
4
syn
polymer
18.015
water
110
nat
water
no
yes
(GPN)(OPN)(APN)(TPN)(APN)(CPN)K(NH2)
XXXXXXKX
A,B,C,D
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
1
2.43
49.28
VAPOR DIFFUSION, HANGING DROP
4
2-propanol, ammonium sulphate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
293.0
2-propanol
1
ammonium sulphate
1
-1.985
1
19
A
1
B
14
2.092
A_GPN1:CPN14_B
1
-2.068
0.160
-0.109
-0.118
5.222
1
20
A
3
B
12
-2.164
A_APN3:TPN12_B
2
-12.214
0.101
0.249
-0.136
-7.999
1
20
A
4
B
11
-2.245
A_TPN4:APN11_B
3
-12.504
-0.237
0.320
-0.120
-5.590
1
19
A
6
B
9
-2.408
A_CPN6:GPN9_B
4
-1.561
0.157
0.166
-0.126
0.076
1
19
C
22
D
25
-4.407
C_CPN22:GPN25_D
5
1.091
0.123
-0.115
-0.199
-3.755
1
19
C
17
D
30
-2.453
C_GPN17:CPN30_D
6
0.114
-0.176
-0.048
-0.121
3.799
1
20
C
19
D
28
-0.599
C_APN19:TPN28_D
7
8.516
-0.064
0.133
-0.173
-6.622
1
20
C
20
D
27
-1.541
C_TPN20:APN27_D
8
11.676
0.137
0.364
-0.160
3.806
23.404
A
A
3
4
-5.041
B
B
12
11
3.571
-2.041
-0.172
-2.842
AA_APN3TPN4:APN11TPN12_BB
1
-1.340
3.310
23.278
-6.223
-0.091
3.056
177.558
A
C
6
22
-0.326
B
D
9
25
3.056
-0.652
-3.562
3.118
AC_CPN6CPN22:GPN25GPN9_DB
2
-0.396
0.198
177.558
1.560
1.782
3.804
-24.228
C
C
19
20
-6.530
D
D
28
27
3.534
2.735
-0.239
-2.705
CC_APN19TPN20:APN27TPN28_DD
3
-0.768
-1.835
-24.064
5.469
-0.844
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
pdbx_initial_refinement_model
struct_conn
struct_site
atom_site
chem_comp_atom
chem_comp_bond
struct_conn
repository
Initial release
Version format compliance
Non-polymer description
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
Atomic model
Data collection
Derived calculations
1
0
2001-07-26
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-08-09
2
0
2023-11-15
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_atom_site.auth_atom_id
_atom_site.label_atom_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr2_label_atom_id
Peptide Nucleic Acid duplex
Peptide Nucleic Acid complexed with DNA
Peptide Nucleic Acid/DNA triplex
Peptide Nucleic Acid complexed with RNA
BIOMOLECULE: 1,2
THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR
INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
CHAINS A AND B BUILD A RIGHT-HANDED PNA DOUBLE HELIX
AND CHAINS C AND D BUILD A LEFT-HANDED DOUBLE HELIX.
RCSB
Y
RCSB
2001-01-26
REL
REL
HOH
water
Synthesized as described in the primary reference
sample
1PUP
PDB entry 1PUP
PDB
experimental model
HOH
35
2
HOH
HOH
35
A
HOH
46
2
HOH
HOH
46
A
HOH
48
2
HOH
HOH
48
A
HOH
49
2
HOH
HOH
49
A
HOH
55
2
HOH
HOH
55
A
HOH
60
2
HOH
HOH
60
A
HOH
62
2
HOH
HOH
62
A
HOH
70
2
HOH
HOH
70
A
HOH
72
2
HOH
HOH
72
A
HOH
74
2
HOH
HOH
74
A
HOH
76
2
HOH
HOH
76
A
HOH
77
2
HOH
HOH
77
A
HOH
81
2
HOH
HOH
81
A
HOH
87
2
HOH
HOH
87
A
HOH
100
2
HOH
HOH
100
A
HOH
101
2
HOH
HOH
101
A
HOH
105
2
HOH
HOH
105
A
HOH
119
2
HOH
HOH
119
A
HOH
127
2
HOH
HOH
127
A
HOH
129
2
HOH
HOH
129
A
HOH
139
2
HOH
HOH
139
A
HOH
34
2
HOH
HOH
34
B
HOH
37
2
HOH
HOH
37
B
HOH
38
2
HOH
HOH
38
B
HOH
47
2
HOH
HOH
47
B
HOH
50
2
HOH
HOH
50
B
HOH
51
2
HOH
HOH
51
B
HOH
57
2
HOH
HOH
57
B
HOH
58
2
HOH
HOH
58
B
HOH
65
2
HOH
HOH
65
B
HOH
68
2
HOH
HOH
68
B
HOH
71
2
HOH
HOH
71
B
HOH
79
2
HOH
HOH
79
B
HOH
85
2
HOH
HOH
85
B
HOH
86
2
HOH
HOH
86
B
HOH
89
2
HOH
HOH
89
B
HOH
94
2
HOH
HOH
94
B
HOH
95
2
HOH
HOH
95
B
HOH
98
2
HOH
HOH
98
B
HOH
99
2
HOH
HOH
99
B
HOH
103
2
HOH
HOH
103
B
HOH
109
2
HOH
HOH
109
B
HOH
111
2
HOH
HOH
111
B
HOH
112
2
HOH
HOH
112
B
HOH
114
2
HOH
HOH
114
B
HOH
120
2
HOH
HOH
120
B
HOH
121
2
HOH
HOH
121
B
HOH
124
2
HOH
HOH
124
B
HOH
125
2
HOH
HOH
125
B
HOH
133
2
HOH
HOH
133
B
HOH
137
2
HOH
HOH
137
B
HOH
33
2
HOH
HOH
33
C
HOH
39
2
HOH
HOH
39
C
HOH
40
2
HOH
HOH
40
C
HOH
41
2
HOH
HOH
41
C
HOH
43
2
HOH
HOH
43
C
HOH
44
2
HOH
HOH
44
C
HOH
53
2
HOH
HOH
53
C
HOH
64
2
HOH
HOH
64
C
HOH
66
2
HOH
HOH
66
C
HOH
67
2
HOH
HOH
67
C
HOH
69
2
HOH
HOH
69
C
HOH
73
2
HOH
HOH
73
C
HOH
80
2
HOH
HOH
80
C
HOH
84
2
HOH
HOH
84
C
HOH
91
2
HOH
HOH
91
C
HOH
96
2
HOH
HOH
96
C
HOH
107
2
HOH
HOH
107
C
HOH
108
2
HOH
HOH
108
C
HOH
110
2
HOH
HOH
110
C
HOH
115
2
HOH
HOH
115
C
HOH
117
2
HOH
HOH
117
C
HOH
122
2
HOH
HOH
122
C
HOH
126
2
HOH
HOH
126
C
HOH
130
2
HOH
HOH
130
C
HOH
131
2
HOH
HOH
131
C
HOH
132
2
HOH
HOH
132
C
HOH
134
2
HOH
HOH
134
C
HOH
135
2
HOH
HOH
135
C
HOH
138
2
HOH
HOH
138
C
HOH
140
2
HOH
HOH
140
C
HOH
141
2
HOH
HOH
141
C
HOH
36
2
HOH
HOH
36
D
HOH
42
2
HOH
HOH
42
D
HOH
45
2
HOH
HOH
45
D
HOH
52
2
HOH
HOH
52
D
HOH
54
2
HOH
HOH
54
D
HOH
56
2
HOH
HOH
56
D
HOH
59
2
HOH
HOH
59
D
HOH
61
2
HOH
HOH
61
D
HOH
63
2
HOH
HOH
63
D
HOH
75
2
HOH
HOH
75
D
HOH
78
2
HOH
HOH
78
D
HOH
82
2
HOH
HOH
82
D
HOH
83
2
HOH
HOH
83
D
HOH
88
2
HOH
HOH
88
D
HOH
90
2
HOH
HOH
90
D
HOH
92
2
HOH
HOH
92
D
HOH
93
2
HOH
HOH
93
D
HOH
97
2
HOH
HOH
97
D
HOH
102
2
HOH
HOH
102
D
HOH
104
2
HOH
HOH
104
D
HOH
106
2
HOH
HOH
106
D
HOH
113
2
HOH
HOH
113
D
HOH
116
2
HOH
HOH
116
D
HOH
118
2
HOH
HOH
118
D
HOH
123
2
HOH
HOH
123
D
HOH
128
2
HOH
HOH
128
D
HOH
136
2
HOH
HOH
136
D
HOH
142
2
HOH
HOH
142
D
GPN
1
n
1
GPN
1
A
BPN
2
n
2
OPN
2
A
APN
3
n
3
APN
3
A
TPN
4
n
4
TPN
4
A
APN
5
n
5
APN
5
A
CPN
6
n
6
CPN
6
A
LYS
7
n
7
LYS
7
A
NH2
8
n
8
NH2
8
A
GPN
9
n
1
GPN
9
B
BPN
10
n
2
OPN
10
B
APN
11
n
3
APN
11
B
TPN
12
n
4
TPN
12
B
APN
13
n
5
APN
13
B
CPN
14
n
6
CPN
14
B
LYS
15
n
7
LYS
15
B
NH2
16
n
8
NH2
16
B
GPN
17
n
1
GPN
17
C
BPN
18
n
2
OPN
18
C
APN
19
n
3
APN
19
C
TPN
20
n
4
TPN
20
C
APN
21
n
5
APN
21
C
CPN
22
n
6
CPN
22
C
LYS
23
n
7
LYS
23
C
NH2
24
n
8
NH2
24
C
GPN
25
n
1
GPN
25
D
BPN
26
n
2
OPN
26
D
APN
27
n
3
APN
27
D
TPN
28
n
4
TPN
28
D
APN
29
n
5
APN
29
D
CPN
30
n
6
CPN
30
D
LYS
31
n
7
LYS
31
D
NH2
32
n
8
NH2
32
D
author_defined_assembly
2
dimeric
author_defined_assembly
2
dimeric
A
GPN
1
A
GPN
1
DG
A
APN
3
A
APN
3
DA
A
TPN
4
A
TPN
4
DT
A
APN
5
A
APN
5
DA
A
CPN
6
A
CPN
6
DC
B
GPN
9
B
GPN
1
DG
B
APN
11
B
APN
3
DA
B
TPN
12
B
TPN
4
DT
B
APN
13
B
APN
5
DA
B
CPN
14
B
CPN
6
DC
C
GPN
17
C
GPN
1
DG
C
APN
19
C
APN
3
DA
C
TPN
20
C
TPN
4
DT
C
APN
21
C
APN
5
DA
C
CPN
22
C
CPN
6
DC
D
GPN
25
D
GPN
1
DG
D
APN
27
D
APN
3
DA
D
TPN
28
D
TPN
4
DT
D
APN
29
D
APN
5
DA
D
CPN
30
D
CPN
6
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
D
A
O
O
LYS
HOH
31
129
2.18
1_555
1_556
16.2
OWN PARAMETER AND TOPOLOGY FILE CREATED
0.264
0.208
1.82
6.0
455
6024
4196
10
random
1
THROUGHOUT
3.0
0
MOLECULAR REPLACEMENT
PDB entry 1PUP
own target values
1.82
6.0
110
626
0
0
516
0.013
3.0
0.266
0.241
1.90
41
281
8
10
19.1
1.82
30.0
1HZS
6245
6233
0.0
0.0
0.055
1
20.1
3.8
97.2
0.281
1.82
1.84
2.6
169
1
2.9
81.6
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
X-PLOR
3.851
Crystal structure of a peptide nucleic acid duplex (BT-PNA) containing a bicyclic analogue of thymine
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
PNA double helix
covale
1.339
one
A
GPN
1
A
C
GPN
1
1_555
A
OPN
2
A
N1'
OPN
2
1_555
covale
1.343
both
A
OPN
2
A
C'
OPN
2
1_555
A
APN
3
A
N
APN
3
1_555
covale
1.336
both
A
APN
3
A
C
APN
3
1_555
A
TPN
4
A
N
TPN
4
1_555
covale
1.327
both
A
TPN
4
A
C
TPN
4
1_555
A
APN
5
A
N
APN
5
1_555
covale
1.334
both
A
APN
5
A
C
APN
5
1_555
A
CPN
6
A
N
CPN
6
1_555
covale
1.340
both
A
CPN
6
A
C
CPN
6
1_555
A
LYS
7
A
N
LYS
7
1_555
covale
1.335
both
A
LYS
7
A
C
LYS
7
1_555
A
NH2
8
A
N
NH2
8
1_555
covale
1.340
one
B
GPN
9
B
C
GPN
1
1_555
B
OPN
10
B
N1'
OPN
2
1_555
covale
1.340
both
B
OPN
10
B
C'
OPN
2
1_555
B
APN
11
B
N
APN
3
1_555
covale
1.344
both
B
APN
11
B
C
APN
3
1_555
B
TPN
12
B
N
TPN
4
1_555
covale
1.338
both
B
TPN
12
B
C
TPN
4
1_555
B
APN
13
B
N
APN
5
1_555
covale
1.334
both
B
APN
13
B
C
APN
5
1_555
B
CPN
14
B
N
CPN
6
1_555
covale
1.324
both
B
CPN
14
B
C
CPN
6
1_555
B
LYS
15
B
N
LYS
7
1_555
covale
1.337
both
B
LYS
15
B
C
LYS
7
1_555
B
NH2
16
B
N
NH2
8
1_555
covale
1.348
one
C
GPN
17
C
C
GPN
1
1_555
C
OPN
18
C
N1'
OPN
2
1_555
covale
1.333
both
C
OPN
18
C
C'
OPN
2
1_555
C
APN
19
C
N
APN
3
1_555
covale
1.334
both
C
APN
19
C
C
APN
3
1_555
C
TPN
20
C
N
TPN
4
1_555
covale
1.338
both
C
TPN
20
C
C
TPN
4
1_555
C
APN
21
C
N
APN
5
1_555
covale
1.325
both
C
APN
21
C
C
APN
5
1_555
C
CPN
22
C
N
CPN
6
1_555
covale
1.324
both
C
CPN
22
C
C
CPN
6
1_555
C
LYS
23
C
N
LYS
7
1_555
covale
1.323
both
C
LYS
23
C
C
LYS
7
1_555
C
NH2
24
C
N
NH2
8
1_555
covale
1.336
one
D
GPN
25
D
C
GPN
1
1_555
D
OPN
26
D
N1'
OPN
2
1_555
covale
1.336
both
D
OPN
26
D
C'
OPN
2
1_555
D
APN
27
D
N
APN
3
1_555
covale
1.336
both
D
APN
27
D
C
APN
3
1_555
D
TPN
28
D
N
TPN
4
1_555
covale
1.323
both
D
TPN
28
D
C
TPN
4
1_555
D
APN
29
D
N
APN
5
1_555
covale
1.358
both
D
APN
29
D
C
APN
5
1_555
D
CPN
30
D
N
CPN
6
1_555
covale
1.350
both
D
CPN
30
D
C
CPN
6
1_555
D
LYS
31
D
N
LYS
7
1_555
covale
1.328
both
D
LYS
31
D
C
LYS
7
1_555
D
NH2
32
D
N
NH2
8
1_555
hydrog
WATSON-CRICK
A
GPN
1
A
N1
GPN
1
1_555
B
CPN
14
B
N3
CPN
6
1_555
hydrog
WATSON-CRICK
A
GPN
1
A
N2
GPN
1
1_555
B
CPN
14
B
O2
CPN
6
1_555
hydrog
WATSON-CRICK
A
GPN
1
A
O6
GPN
1
1_555
B
CPN
14
B
N4
CPN
6
1_555
hydrog
WATSON-CRICK
A
APN
3
A
N1
APN
3
1_555
B
TPN
12
B
N3
TPN
4
1_555
hydrog
WATSON-CRICK
A
APN
3
A
N6
APN
3
1_555
B
TPN
12
B
O4
TPN
4
1_555
hydrog
WATSON-CRICK
A
TPN
4
A
N3
TPN
4
1_555
B
APN
11
B
N1
APN
3
1_555
hydrog
WATSON-CRICK
A
TPN
4
A
O4
TPN
4
1_555
B
APN
11
B
N6
APN
3
1_555
hydrog
WATSON-CRICK
A
CPN
6
A
N3
CPN
6
1_555
B
GPN
9
B
N1
GPN
1
1_555
hydrog
WATSON-CRICK
A
CPN
6
A
N4
CPN
6
1_555
B
GPN
9
B
O6
GPN
1
1_555
hydrog
WATSON-CRICK
A
CPN
6
A
O2
CPN
6
1_555
B
GPN
9
B
N2
GPN
1
1_555
hydrog
WATSON-CRICK
C
GPN
17
C
N1
GPN
1
1_555
D
CPN
30
D
N3
CPN
6
1_555
hydrog
WATSON-CRICK
C
GPN
17
C
N2
GPN
1
1_555
D
CPN
30
D
O2
CPN
6
1_555
hydrog
WATSON-CRICK
C
GPN
17
C
O6
GPN
1
1_555
D
CPN
30
D
N4
CPN
6
1_555
hydrog
WATSON-CRICK
C
APN
19
C
N1
APN
3
1_555
D
TPN
28
D
N3
TPN
4
1_555
hydrog
WATSON-CRICK
C
APN
19
C
N6
APN
3
1_555
D
TPN
28
D
O4
TPN
4
1_555
hydrog
WATSON-CRICK
C
TPN
20
C
N3
TPN
4
1_555
D
APN
27
D
N1
APN
3
1_555
hydrog
WATSON-CRICK
C
TPN
20
C
O4
TPN
4
1_555
D
APN
27
D
N6
APN
3
1_555
hydrog
WATSON-CRICK
C
CPN
22
C
N3
CPN
6
1_555
D
GPN
25
D
N1
GPN
1
1_555
hydrog
WATSON-CRICK
C
CPN
22
C
N4
CPN
6
1_555
D
GPN
25
D
O6
GPN
1
1_555
hydrog
WATSON-CRICK
C
CPN
22
C
O2
CPN
6
1_555
D
GPN
25
D
N2
GPN
1
1_555
PEPTIDE NUCLEIC ACID
peptide nucleic acid, double helix, nucleobase analogue, P-form helix, left-handed, right-handed
1HZS
PDB
1
1HZS
1
8
1HZS
1
8
1HZS
A
1
1
8
9
16
1HZS
9
16
1HZS
B
1
1
8
17
24
1HZS
17
24
1HZS
C
1
1
8
25
32
1HZS
25
32
1HZS
D
1
1
8
BINDING SITE FOR RESIDUE NH2 A 8
A
NH2
8
Software
1
BINDING SITE FOR RESIDUE NH2 B 16
B
NH2
16
Software
1
BINDING SITE FOR RESIDUE NH2 C 24
C
NH2
24
Software
1
BINDING SITE FOR RESIDUE NH2 D 32
D
NH2
32
Software
2
A
LYS
7
A
LYS
7
1
1_555
B
LYS
15
B
LYS
7
1
1_555
C
LYS
23
C
LYS
7
1
1_555
D
CPN
30
D
CPN
6
2
1_555
D
LYS
31
D
LYS
7
2
1_555
18
P 21 21 2