0.027500
0.015877
0.000000
0.000000
0.031754
0.000000
0.000000
0.000000
0.014467
0.000000
0.000000
0.000000
Declercq, R.
Van Meervelt, L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
36.364
36.364
69.121
C11 H16 N5 O6 P
345.248
n
1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(ADENIN-9-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL
DNA linking
C10 H16 N3 O7 P
321.224
n
1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(CYTOSIN-1-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL
DNA linking
C11 H16 N5 O7 P
361.248
n
1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(GUANIN-9-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL
DNA linking
C11 H17 N2 O8 P
336.235
n
1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(THYMIN-1-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL
DNA linking
H2 O
18.015
WATER
non-polymer
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
N
C
N
12
S
C
N
13
N
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
H
N
39
N
H
N
40
N
P
N
41
N
O
N
42
N
O
N
43
N
O
N
44
N
O
N
45
N
C
N
46
R
C
N
47
N
O
N
48
S
C
N
49
N
O
N
50
N
C
N
51
S
C
N
52
N
C
N
53
N
N
N
54
N
C
N
55
N
O
N
56
N
N
N
57
N
C
N
58
N
N
N
59
N
C
N
60
N
C
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
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
P
N
78
N
O
N
79
N
O
N
80
N
O
N
81
N
O
N
82
N
C
N
83
R
C
N
84
N
O
N
85
S
C
N
86
N
O
N
87
N
C
N
88
S
C
N
89
N
C
Y
90
N
N
Y
91
N
C
Y
92
N
N
Y
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
C
N
98
N
N
N
99
N
N
Y
100
N
C
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
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
P
N
118
N
O
N
119
N
O
N
120
N
O
N
121
N
O
N
122
N
C
N
123
R
C
N
124
N
O
N
125
S
C
N
126
N
O
N
127
N
C
N
128
S
C
N
129
N
C
N
130
N
N
N
131
N
C
N
132
N
O
N
133
N
N
N
134
N
C
N
135
N
O
N
136
N
C
N
137
N
C
N
138
N
C
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
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
O
N
157
N
H
N
158
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
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
Y
27
N
sing
Y
28
N
sing
Y
29
N
doub
N
30
N
sing
Y
31
N
sing
Y
32
N
sing
Y
33
N
doub
N
34
N
sing
Y
35
N
doub
N
36
N
sing
N
37
N
sing
Y
38
N
sing
Y
39
N
doub
N
40
N
sing
Y
41
N
sing
N
42
N
doub
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
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
doub
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
doub
N
78
N
sing
N
79
N
sing
N
80
N
doub
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
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
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
Y
106
N
sing
Y
107
N
sing
Y
108
N
doub
N
109
N
sing
Y
110
N
sing
N
111
N
sing
Y
112
N
doub
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
doub
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
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
doub
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
doub
N
155
N
sing
N
156
N
sing
N
157
N
doub
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
124
928
933
10.1021/ja016570w
11829600
Crystal structure of double helical hexitol nucleic acids.
2002
GE
Angew.Chem.Int.Ed.Engl.
ACIEAY
0179
0570-0833
34
1338
1339
10.1002/anie.199513381
1',5'-Anhydrohexitol nucleic acids, a new promising antisense construct
1995
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
52
1213
1215
1',5'-anhydro-2',3'-dideoxy-2'-(guanin-9-yl)-D-arabino-hexitol
1995
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
55
279
280
Oligonucleotides with 1',5'-anhydrohexitol nucleoside building blocks: Crystallization and preliminary X-ray studies of H(GTGTACAC)
1999
10.2210/pdb1d7z/pdb
pdb_00001d7z
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
IMAGE PLATE
1999-04-11
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.9116
1.0
X11
EMBL/DESY, HAMBURG
0.9116
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
THE SUGAR MOIETIES ARE NOT DEOXYRIBOSE BUT D-ARABINO-HEXITOL
2538.831
5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'
1
syn
polymer
18.015
water
38
nat
water
no
yes
(6HG)(6HT)(6HG)(6HT)(6HA)(6HC)(6HA)(6HC)
GTGTACAC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
1
2.60
52.66
VAPOR DIFFUSION, HANGING DROP
7.0
CACODYLATE BUFFER, KCL, BACL2, SPERMINE TETRACHLORIDE AND MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K
277
CACODYLATE BUFFER
1
SPERMINE
1
KCL
1
BACL2
1
MPD
1
MPD
2
-1.986
1
A
1
A
8
13.752
A_6HG1:6HC8_A
1
6.416
0.680
-0.868
0.159
11.222
1
20
A
2
A
7
10.403
A_6HT2:6HA7_A
2
-0.257
0.425
-0.387
-0.245
-6.500
1
19
A
3
A
6
1.084
A_6HG3:6HC6_A
3
-1.143
-0.322
-0.318
-0.336
2.521
1
20
A
4
A
5
11.828
A_6HT4:6HA5_A
4
1.691
-1.002
0.022
-0.203
-2.521
1
20
A
5
A
4
11.828
A_6HA5:6HT4_A
5
1.691
1.002
0.022
-0.203
6.500
1
19
A
6
A
3
1.084
A_6HC6:6HG3_A
6
-1.143
0.322
-0.318
-0.336
-11.222
1
20
A
7
A
2
10.403
A_6HA7:6HT2_A
7
-0.257
-0.425
-0.387
-0.245
1.986
1
A
8
A
1
13.752
A_6HC8:6HG1_A
8
6.416
-0.680
-0.868
0.159
2.219
33.359
A
A
1
2
20.893
A
A
8
7
3.162
11.687
-0.732
-2.423
AA_6HG16HT2:6HA76HC8_AA
1
-5.954
10.644
30.740
-5.887
0.426
3.221
24.637
A
A
2
3
14.819
A
A
7
6
3.796
6.240
-0.728
-2.062
AA_6HT26HG3:6HC66HA7_AA
2
-3.060
7.268
23.651
-6.927
0.678
2.539
26.002
A
A
3
4
11.752
A
A
6
5
3.151
5.252
0.563
-2.701
AA_6HG36HT4:6HA56HC6_AA
3
-0.526
1.178
25.469
-7.273
-1.379
2.044
48.141
A
A
4
5
28.690
A
A
5
4
2.881
22.583
0.000
-1.194
AA_6HT46HA5:6HT46HA5_AA
4
0.000
0.000
42.797
-2.888
0.000
2.539
26.002
A
A
5
6
11.752
A
A
4
3
3.151
5.252
-0.563
-2.701
AA_6HA56HC6:6HG36HT4_AA
5
0.526
-1.178
25.469
-7.273
1.379
3.221
24.637
A
A
6
7
14.819
A
A
3
2
3.796
6.240
0.728
-2.062
AA_6HC66HA7:6HT26HG3_AA
6
3.060
-7.268
23.651
-6.927
-0.678
2.219
33.359
A
A
7
8
20.893
A
A
2
1
3.162
11.687
0.732
-2.423
AA_6HA76HC8:6HG16HT2_AA
7
5.954
-10.644
30.740
-5.887
-0.426
chem_comp_atom
chem_comp_bond
citation_author
database_2
diffrn_source
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-06-28
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_struct_conn.pdbx_leaving_atom_flag
HD0001 CONTAINS THE SAME MOLECULE CRYSTALLIZED IN P 32 1 2 AND SOLVED AT 1.6 A RESOLUTION
NDB
Y
NDB
1999-10-21
REL
REL
HOH
water
THE MOLECULE WAS CHEMICALLY SYNTESISED (SEE REFERENCE 1)
sample
HOH
10
2
HOH
HOH
10
A
HOH
12
2
HOH
HOH
12
A
HOH
13
2
HOH
HOH
13
A
HOH
16
2
HOH
HOH
16
A
HOH
18
2
HOH
HOH
18
A
HOH
19
2
HOH
HOH
19
A
HOH
20
2
HOH
HOH
20
A
HOH
21
2
HOH
HOH
21
A
HOH
24
2
HOH
HOH
24
A
HOH
25
2
HOH
HOH
25
A
HOH
26
2
HOH
HOH
26
A
HOH
28
2
HOH
HOH
28
A
HOH
30
2
HOH
HOH
30
A
HOH
32
2
HOH
HOH
32
A
HOH
33
2
HOH
HOH
33
A
HOH
34
2
HOH
HOH
34
A
HOH
37
2
HOH
HOH
37
A
HOH
38
2
HOH
HOH
38
A
HOH
39
2
HOH
HOH
39
A
HOH
40
2
HOH
HOH
40
A
HOH
42
2
HOH
HOH
42
A
HOH
45
2
HOH
HOH
45
A
HOH
48
2
HOH
HOH
48
A
HOH
49
2
HOH
HOH
49
A
HOH
50
2
HOH
HOH
50
A
HOH
53
2
HOH
HOH
53
A
HOH
55
2
HOH
HOH
55
A
HOH
56
2
HOH
HOH
56
A
HOH
58
2
HOH
HOH
58
A
HOH
60
2
HOH
HOH
60
A
HOH
62
2
HOH
HOH
62
A
HOH
64
2
HOH
HOH
64
A
HOH
65
2
HOH
HOH
65
A
HOH
66
2
HOH
HOH
66
A
HOH
68
2
HOH
HOH
68
A
HOH
69
2
HOH
HOH
69
A
HOH
70
2
HOH
HOH
70
A
HOH
71
2
HOH
HOH
71
A
6HG
1
n
1
6HG
1
A
6HT
2
n
2
6HT
2
A
6HG
3
n
3
6HG
3
A
6HT
4
n
4
6HT
4
A
6HA
5
n
5
6HA
5
A
6HC
6
n
6
6HC
6
A
6HA
7
n
7
6HA
7
A
6HC
8
n
8
6HC
8
A
author_defined_assembly
2
dimeric
A
6HG
1
A
6HG
1
DG
A
6HT
2
A
6HT
2
DT
A
6HG
3
A
6HG
3
DG
A
6HT
4
A
6HT
4
DT
A
6HA
5
A
6HA
5
DA
A
6HC
6
A
6HC
6
DC
A
6HA
7
A
6HA
7
DA
A
6HC
8
A
6HC
8
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
0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
10_665
-y+1,-x+1,-z+2/3
crystal symmetry operation
18.1820000000
31.4921477832
46.0806666667
1
A
HOH
21
B
HOH
1
A
HOH
56
B
HOH
1
34.00
1.20
119.70
153.70
A
A
A
C3'
O3'
P
6HG
6HG
6HT
1
1
2
Y
1
8.27
1.20
119.70
127.97
A
A
A
C3'
O3'
P
6HG
6HG
6HT
3
3
4
Y
1
20.50
1.20
119.70
140.20
A
A
A
C3'
O3'
P
6HA
6HA
6HC
7
7
8
Y
1
A
A
O3'
P
6HC
6HA
6
7
0.112
0.012
1.607
1.719
Y
0.2330000
0.2330000
0.2330000
2.21
20.0
1329
1329
83.8
1
NONE USED
0
0
BASES: TAYLOR AND KENNARD VALUES; THE REST: VALUES BASED ON SINGLE CRYSTAL STRUCTURE OF HNA BUILDING BLOCKS
2.21
20.0
38
207
0
169
0
0.018
0.022
50.8
2.21
20.0
1D7Z
1344
1344
0
0.0510000
1
38.8
16.8
83.8
0.1680000
2.21
2.25
74.1
phasing
GLRF
refinement
SHELXL-97
data reduction
DENZO
data scaling
SCALEPACK
CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 2.2 A RESOLUTION
1
N
N
2
N
N
covale
1.615
both
A
6HG
1
A
O3'
6HG
1
1_555
A
6HT
2
A
P
6HT
2
1_555
covale
1.647
both
A
6HT
2
A
O3'
6HT
2
1_555
A
6HG
3
A
P
6HG
3
1_555
covale
1.570
both
A
6HG
3
A
O3'
6HG
3
1_555
A
6HT
4
A
P
6HT
4
1_555
covale
1.617
both
A
6HT
4
A
O3'
6HT
4
1_555
A
6HA
5
A
P
6HA
5
1_555
covale
1.602
both
A
6HA
5
A
O3'
6HA
5
1_555
A
6HC
6
A
P
6HC
6
1_555
covale
1.719
both
A
6HC
6
A
O3'
6HC
6
1_555
A
6HA
7
A
P
6HA
7
1_555
covale
1.629
both
A
6HA
7
A
O3'
6HA
7
1_555
A
6HC
8
A
P
6HC
8
1_555
hydrog
6HG-6HC PAIR
A
6HG
1
A
N1
6HG
1
1_555
A
6HC
8
A
N3
6HC
8
10_665
hydrog
WATSON-CRICK
A
6HT
2
A
N3
6HT
2
1_555
A
6HA
7
A
N1
6HA
7
10_665
hydrog
WATSON-CRICK
A
6HT
2
A
O4
6HT
2
1_555
A
6HA
7
A
N6
6HA
7
10_665
hydrog
WATSON-CRICK
A
6HG
3
A
N1
6HG
3
1_555
A
6HC
6
A
N3
6HC
6
10_665
hydrog
WATSON-CRICK
A
6HG
3
A
N2
6HG
3
1_555
A
6HC
6
A
O2
6HC
6
10_665
hydrog
WATSON-CRICK
A
6HG
3
A
O6
6HG
3
1_555
A
6HC
6
A
N4
6HC
6
10_665
hydrog
WATSON-CRICK
A
6HT
4
A
N3
6HT
4
1_555
A
6HA
5
A
N1
6HA
5
10_665
hydrog
WATSON-CRICK
A
6HT
4
A
O4
6HT
4
1_555
A
6HA
5
A
N6
6HA
5
10_665
hydrog
WATSON-CRICK
A
6HA
5
A
N1
6HA
5
1_555
A
6HT
4
A
N3
6HT
4
10_665
hydrog
WATSON-CRICK
A
6HA
5
A
N6
6HA
5
1_555
A
6HT
4
A
O4
6HT
4
10_665
hydrog
WATSON-CRICK
A
6HC
6
A
N3
6HC
6
1_555
A
6HG
3
A
N1
6HG
3
10_665
hydrog
WATSON-CRICK
A
6HC
6
A
N4
6HC
6
1_555
A
6HG
3
A
O6
6HG
3
10_665
hydrog
WATSON-CRICK
A
6HC
6
A
O2
6HC
6
1_555
A
6HG
3
A
N2
6HG
3
10_665
hydrog
WATSON-CRICK
A
6HA
7
A
N1
6HA
7
1_555
A
6HT
2
A
N3
6HT
2
10_665
hydrog
WATSON-CRICK
A
6HA
7
A
N6
6HA
7
1_555
A
6HT
2
A
O4
6HT
2
10_665
hydrog
6HC-6HG PAIR
A
6HC
8
A
O2
6HC
8
1_555
A
6HG
1
A
N2
6HG
1
10_665
DNA
HEXITOL NUCLEIC ACID, DNA ANALOGUE, DOUBLE HELIX, DNA
1D7Z
PDB
1
1D7Z
1
8
1D7Z
1
8
1D7Z
A
1
1
8
180
hexagonal
P 62 2 2