1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Han, X.
Leroy, J.L.
Gueron, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N3 O4
241.244
n
5-METHYL-2'-DEOXYCYTIDINE
DNA linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
278
949
965
10.1006/jmbi.1998.1740
9600855
An intramolecular i-motif: the solution structure and base-pair opening kinetics of d(5mCCT3CCT3ACCT3CC).
1998
10.2210/pdb1a83/pdb
pdb_00001a83
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
THE INTRAMOLECULAR FOLDING OF THIS I-MOTIF MAY RELATED TO
THE CYTOSINE-RICH STRANDS OF TELOMERES AND HUMAN
CENTROMERE.
THE FIRST CYTOSINE IS C5-METHYLATED AND IS NAMED MCY IN
THIS ENTRY.
5253.485
DNA (5'-(MCY)CTTTCCTTTACCTTTCC-3')
1
syn
polymer
no
yes
(MCY)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DT)(DT)(DA)(DC)(DC)(DT)(DT)(DT)(DC)(DC)
CCTTTCCTTTACCTTTCC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
43.080
2
12
A
5
A
16
-165.512
A_DT5:DT16_A
1
10.456
-2.049
0.463
2.191
-34.212
2
14
A
2
A
13
-176.443
A_DC2:DC13_A
2
-18.246
-2.088
-0.194
-0.547
-15.103
2
14
A
6
A
17
175.431
A_DC6:DC17_A
3
-3.729
2.060
-0.210
0.789
1.927
2
14
A
1
A
12
178.377
A_MCY1:DC12_A
4
-6.724
2.020
-0.130
0.382
-7.791
2
14
A
7
A
18
173.817
A_DC7:DC18_A
5
6.867
2.071
-0.379
0.868
-0.604
169.812
A
A
5
2
72.414
A
A
16
13
-0.874
138.785
-2.634
1.414
AA_DT5DC2:DC13DT16_AA
1
96.918
-50.569
36.333
1.150
1.015
-0.495
177.800
A
A
2
6
-66.424
A
A
13
17
-0.555
-132.622
-2.096
-1.921
AA_DC2DC6:DC17DC13_AA
2
108.956
-54.571
149.468
-1.015
1.004
0.261
179.673
A
A
6
1
66.008
A
A
17
12
0.006
131.993
-1.020
2.780
AA_DC6MCY1:DC12DC17_AA
3
119.778
-59.899
158.637
1.381
0.519
-0.715
-176.529
A
A
1
7
49.101
A
A
12
18
-0.167
-97.434
-2.319
1.905
AA_MCY1DC7:DC18DC12_AA
4
-145.301
-73.224
-93.236
-1.051
-1.014
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
1
0
1998-06-17
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
Y
BNL
1998-04-01
REL
LEAST ENERGY OF NOE VIOLATION
60
6
NOESY
TOCSY
HETERO-TOCSY
4.8
270
K
7.0
270
K
molecular dynamics
BRUNGER
refinement
X-PLOR
3.0
structure solution
Felix
600
Bruker
AMX600
MCY
1
n
1
MCY
1
A
C
2
n
2
DC
2
A
T
3
n
3
DT
3
A
T
4
n
4
DT
4
A
T
5
n
5
DT
5
A
C
6
n
6
DC
6
A
C
7
n
7
DC
7
A
T
8
n
8
DT
8
A
T
9
n
9
DT
9
A
T
10
n
10
DT
10
A
A
11
n
11
DA
11
A
C
12
n
12
DC
12
A
C
13
n
13
DC
13
A
T
14
n
14
DT
14
A
T
15
n
15
DT
15
A
T
16
n
16
DT
16
A
C
17
n
17
DC
17
A
C
18
n
18
DC
18
A
author_defined_assembly
1
monomeric
A
MCY
1
5-METHYL-2'-DEOXYCYTIDINE
A
MCY
1
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
2
A
A
H41
O2
DC
DC
2
13
1.57
2
A
A
N4
O2
DC
DC
2
13
2.14
3
A
A
H41
O2
DC
DC
2
13
1.54
3
A
A
N4
O2
DC
DC
2
13
2.14
2
A
DC
2
0.082
SIDE CHAIN
3
A
DC
2
0.073
SIDE CHAIN
5
A
DC
2
0.062
SIDE CHAIN
1
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
3.46
0.30
108.30
111.76
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
1
3.92
0.50
113.80
117.72
A
A
A
N7
C8
N9
DA
DA
DA
11
11
11
N
1
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
3.21
0.50
119.90
123.11
A
A
A
C2
N3
C4
DC
DC
DC
12
12
12
N
1
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
3.32
0.50
119.90
123.22
A
A
A
C2
N3
C4
DC
DC
DC
13
13
13
N
1
3.78
0.60
118.90
122.68
A
A
A
N1
C2
O2
DC
DC
DC
13
13
13
N
1
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DC
DC
DC
17
17
17
N
1
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N1
DC
DC
DC
18
18
18
N
2
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
2
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
2
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
2
3.36
0.30
108.30
111.66
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
2
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
2
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
2
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
2
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
2
2.29
0.30
108.30
110.59
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
2
4.10
0.50
113.80
117.90
A
A
A
N7
C8
N9
DA
DA
DA
11
11
11
N
2
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
2
3.12
0.50
119.90
123.02
A
A
A
C2
N3
C4
DC
DC
DC
12
12
12
N
2
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
2
4.24
0.50
119.90
124.14
A
A
A
C2
N3
C4
DC
DC
DC
13
13
13
N
2
3.82
0.60
118.90
122.72
A
A
A
N1
C2
O2
DC
DC
DC
13
13
13
N
2
3.99
0.30
108.30
112.29
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
2
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
2
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DT
DT
DT
16
16
16
N
2
2.78
0.30
108.30
111.08
A
A
A
O4'
C1'
N1
DC
DC
DC
17
17
17
N
2
2.29
0.30
108.30
110.59
A
A
A
O4'
C1'
N1
DC
DC
DC
18
18
18
N
3
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
3
3.23
0.30
108.30
111.53
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
3
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
3
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
3
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
3
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
3
3.46
0.30
108.30
111.76
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
3
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
3
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
3
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
3
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
3
4.06
0.50
113.80
117.86
A
A
A
N7
C8
N9
DA
DA
DA
11
11
11
N
3
2.85
0.30
108.30
111.15
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
3
3.90
0.50
119.90
123.80
A
A
A
C2
N3
C4
DC
DC
DC
12
12
12
N
3
4.11
0.60
118.90
123.01
A
A
A
N1
C2
O2
DC
DC
DC
12
12
12
N
3
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
3
-4.28
0.70
119.20
114.92
A
A
A
N1
C2
N3
DC
DC
DC
13
13
13
N
3
4.26
0.50
119.90
124.16
A
A
A
C2
N3
C4
DC
DC
DC
13
13
13
N
3
3.99
0.60
118.90
122.89
A
A
A
N1
C2
O2
DC
DC
DC
13
13
13
N
3
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
3
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
3
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DT
DT
DT
16
16
16
N
3
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DC
DC
DC
17
17
17
N
3
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DC
DC
DC
18
18
18
N
4
1.93
0.30
108.30
110.23
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
4
3.31
0.30
108.30
111.61
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
4
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
4
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
4
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
4
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
4
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
4
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
4
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
4
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
4
3.92
0.50
113.80
117.72
A
A
A
N7
C8
N9
DA
DA
DA
11
11
11
N
4
2.86
0.30
108.30
111.16
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
4
3.78
0.50
119.90
123.68
A
A
A
C2
N3
C4
DC
DC
DC
12
12
12
N
4
3.99
0.60
118.90
122.89
A
A
A
N1
C2
O2
DC
DC
DC
12
12
12
N
4
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
4
3.30
0.50
119.90
123.20
A
A
A
C2
N3
C4
DC
DC
DC
13
13
13
N
4
3.70
0.60
118.90
122.60
A
A
A
N1
C2
O2
DC
DC
DC
13
13
13
N
4
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
4
3.97
0.30
108.30
112.27
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
4
2.92
0.30
108.30
111.22
A
A
A
O4'
C1'
N1
DT
DT
DT
16
16
16
N
4
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DC
DC
DC
17
17
17
N
4
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DC
DC
DC
18
18
18
N
5
1.96
0.30
108.30
110.26
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
5
4.11
0.30
108.30
112.41
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
5
2.86
0.30
108.30
111.16
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
5
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
5
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
5
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
5
3.09
0.30
108.30
111.39
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
5
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
5
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
5
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
5
3.92
0.50
113.80
117.72
A
A
A
N7
C8
N9
DA
DA
DA
11
11
11
N
5
2.88
0.30
108.30
111.18
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
5
3.78
0.50
119.90
123.68
A
A
A
C2
N3
C4
DC
DC
DC
12
12
12
N
5
4.23
0.60
118.90
123.13
A
A
A
N1
C2
O2
DC
DC
DC
12
12
12
N
5
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
5
3.34
0.50
119.90
123.24
A
A
A
C2
N3
C4
DC
DC
DC
13
13
13
N
5
3.88
0.60
118.90
122.78
A
A
A
N1
C2
O2
DC
DC
DC
13
13
13
N
5
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
5
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
5
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N1
DT
DT
DT
16
16
16
N
5
2.86
0.30
108.30
111.16
A
A
A
O4'
C1'
N1
DC
DC
DC
17
17
17
N
5
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N1
DC
DC
DC
18
18
18
N
6
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
6
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
6
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
6
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
6
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
6
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
6
3.25
0.30
108.30
111.55
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
6
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
6
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
6
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
6
3.99
0.50
113.80
117.79
A
A
A
N7
C8
N9
DA
DA
DA
11
11
11
N
6
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
6
3.81
0.50
119.90
123.71
A
A
A
C2
N3
C4
DC
DC
DC
12
12
12
N
6
3.97
0.60
118.90
122.87
A
A
A
N1
C2
O2
DC
DC
DC
12
12
12
N
6
2.04
0.30
108.30
110.34
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
6
4.12
0.50
119.90
124.02
A
A
A
C2
N3
C4
DC
DC
DC
13
13
13
N
6
4.45
0.60
118.90
123.35
A
A
A
N1
C2
O2
DC
DC
DC
13
13
13
N
6
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
6
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
6
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DT
DT
DT
16
16
16
N
6
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N1
DC
DC
DC
17
17
17
N
6
3.05
0.50
119.90
122.95
A
A
A
C2
N3
C4
DC
DC
DC
17
17
17
N
6
2.12
0.30
108.30
110.42
A
A
A
O4'
C1'
N1
DC
DC
DC
18
18
18
N
2
A
A
C5
C7
DT
DT
10
10
0.036
0.006
1.496
1.532
N
model building
X-PLOR
3.0
refinement
X-PLOR
3.0
phasing
X-PLOR
3.0
INTRAMOLECULAR I-MOTIF, NMR, 6 STRUCTURES
1
N
N
covale
1.613
both
A
MCY
1
A
O3'
MCY
1
1_555
A
DC
2
A
P
DC
2
1_555
hydrog
TYPE_14_PAIR
A
MCY
1
A
N3
MCY
1
1_555
A
DC
12
A
N4
DC
12
1_555
hydrog
TYPE_14_PAIR
A
MCY
1
A
N4
MCY
1
1_555
A
DC
12
A
N3
DC
12
1_555
hydrog
MCY-DC MISPAIR
A
MCY
1
A
N4
MCY
1
1_555
A
DC
17
A
O2
DC
17
1_555
hydrog
TYPE_14_PAIR
A
DC
2
A
N3
DC
2
1_555
A
DC
13
A
N4
DC
13
1_555
hydrog
TYPE_14_PAIR
A
DC
2
A
N4
DC
2
1_555
A
DC
13
A
N3
DC
13
1_555
hydrog
DT-DC MISPAIR
A
DT
5
A
O4
DT
5
1_555
A
DC
13
A
N4
DC
13
1_555
hydrog
TYPE_12_PAIR
A
DT
5
A
N3
DT
5
1_555
A
DT
16
A
O4
DT
16
1_555
hydrog
TYPE_12_PAIR
A
DT
5
A
O4
DT
5
1_555
A
DT
16
A
N3
DT
16
1_555
hydrog
TYPE_14_PAIR
A
DC
6
A
N3
DC
6
1_555
A
DC
17
A
N4
DC
17
1_555
hydrog
TYPE_14_PAIR
A
DC
6
A
N4
DC
6
1_555
A
DC
17
A
N3
DC
17
1_555
hydrog
TYPE_14_PAIR
A
DC
7
A
N3
DC
7
1_555
A
DC
18
A
N4
DC
18
1_555
hydrog
TYPE_14_PAIR
A
DC
7
A
N4
DC
7
1_555
A
DC
18
A
N3
DC
18
1_555
DNA
DEOXYRIBONUCLEIC ACID, DNA, I-MOTIF, SOLUTION STRUCTURE, TELOMERE, CENTROMERE
1A83
PDB
1
1A83
1
18
1A83
1
18
1A83
A
1
1
18
1
P 1