0.016026
0.000000
0.005861
0.000000
0.040866
0.000000
0.000000
0.000000
0.029325
0.00000
0.00000
0.00000
Shi, K.
Mitra, S.N.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
110.09
90.00
62.400
24.470
36.310
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H13 N4 O7 P
332.207
y
2'-DEOXYINOSINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
C18 H26 N10 O3
430.464
NETROPSIN
non-polymer
N
1
N
O
N
2
N
P
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
R
C
N
13
N
N
N
14
N
C
N
15
N
O
N
16
N
N
N
17
N
C
N
18
N
N
N
19
N
C
N
20
N
C
N
21
N
H
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
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
N
C
N
46
R
C
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
Y
56
N
C
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
O
N
71
N
H
N
72
N
H
N
73
N
C
N
74
N
N
N
75
N
N
N
76
N
N
N
77
N
C
N
78
N
C
N
79
N
O
N
80
N
N
Y
81
N
C
Y
82
N
C
Y
83
N
C
Y
84
N
N
N
85
N
C
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
Y
90
N
C
Y
91
N
C
Y
92
N
C
Y
93
N
N
N
94
N
C
Y
95
N
C
N
96
N
C
N
97
N
O
N
98
N
N
N
99
N
C
N
100
N
C
N
101
N
C
N
102
N
N
N
103
N
N
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
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
1
N
sing
N
2
N
sing
N
3
N
doub
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
doub
N
27
N
sing
N
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
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
sing
N
57
N
sing
N
58
N
sing
Y
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
sing
N
64
N
sing
Y
65
N
doub
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
doub
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
doub
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
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
doub
N
87
N
sing
N
88
N
sing
N
89
N
sing
Y
90
N
sing
Y
91
N
doub
Y
92
N
doub
N
93
N
sing
Y
94
N
sing
N
95
N
sing
N
96
N
sing
Y
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
Y
106
N
sing
Y
107
N
doub
Y
108
N
doub
N
109
N
sing
Y
110
N
sing
N
111
N
sing
N
112
N
sing
Y
113
N
sing
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
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
58
601
606
10.1107/S0907444902001889
11914483
Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin.
2002
10.2210/pdb1dvl/pdb
pdb_00001dvl
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
1
IMAGE PLATE
RIGAKU RAXIS IIC
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
2971.911
5'-D(*CP*CP*IP*IP*CP*IP*CP*CP*IP*I)-3'
2
syn
polymer
430.464
NETROPSIN
1
syn
non-polymer
18.015
water
31
nat
water
no
no
(DC)(DC)(DI)(DI)(DC)(DI)(DC)(DC)(DI)(DI)
CCIICICCII
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.08
40.81
VAPOR DIFFUSION, HANGING DROP
6.5
4 MM DNA (SINGLE STRAND), 0.008M MGCL2, 0.04 M NA CACODYLATE (PH 6.5), 2MM NETROPSIN, VAPOR DIFFUSION, HANGING DROP at 293K
293
SODIUM CACODYLATE
1
MGCL2
1
MGCL2
2
software
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
1
0
2002-03-29
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2000-01-21
REL
REL
NT
NETROPSIN
HOH
water
NT
25
2
NT
NT
25
A
HOH
103
3
HOH
HOH
103
A
HOH
106
3
HOH
HOH
106
A
HOH
107
3
HOH
HOH
107
A
HOH
113
3
HOH
HOH
113
A
HOH
115
3
HOH
HOH
115
A
HOH
121
3
HOH
HOH
121
A
HOH
125
3
HOH
HOH
125
A
HOH
128
3
HOH
HOH
128
A
HOH
129
3
HOH
HOH
129
A
HOH
130
3
HOH
HOH
130
A
HOH
101
3
HOH
HOH
101
B
HOH
102
3
HOH
HOH
102
B
HOH
105
3
HOH
HOH
105
B
HOH
108
3
HOH
HOH
108
B
HOH
109
3
HOH
HOH
109
B
HOH
110
3
HOH
HOH
110
B
HOH
111
3
HOH
HOH
111
B
HOH
112
3
HOH
HOH
112
B
HOH
114
3
HOH
HOH
114
B
HOH
116
3
HOH
HOH
116
B
HOH
117
3
HOH
HOH
117
B
HOH
118
3
HOH
HOH
118
B
HOH
119
3
HOH
HOH
119
B
HOH
120
3
HOH
HOH
120
B
HOH
122
3
HOH
HOH
122
B
HOH
123
3
HOH
HOH
123
B
HOH
124
3
HOH
HOH
124
B
HOH
126
3
HOH
HOH
126
B
HOH
127
3
HOH
HOH
127
B
HOH
131
3
HOH
HOH
131
B
HOH
132
3
HOH
HOH
132
B
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
I
3
n
3
DI
3
A
I
4
n
4
DI
4
A
C
5
n
5
DC
5
A
I
6
n
6
DI
6
A
C
7
n
7
DC
7
A
C
8
n
8
DC
8
A
I
9
n
9
DI
9
A
I
10
n
10
DI
10
A
C
11
n
1
DC
11
B
C
12
n
2
DC
12
B
I
13
n
3
DI
13
B
I
14
n
4
DI
14
B
C
15
n
5
DC
15
B
I
16
n
6
DI
16
B
C
17
n
7
DC
17
B
C
18
n
8
DC
18
B
I
19
n
9
DI
19
B
I
20
n
10
DI
20
B
author_defined_assembly
2
dimeric
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
A
B
N1
N3
DI
DC
4
17
2.12
0.2450000
0.1960000
0.1960000
0.1960000
2.4
8.0
1795
10
85.8
RANDOM
1
THROUGHOUT
2.0
MOLECULAR REPLACEMENT
2.4
8.0
31
456
31
394
0
0.013
2.1
18.6
1.7
2.40
1DVL
1795
1.0
0.0370000
1
2.40
2.50
model building
X-PLOR
refinement
X-PLOR
3.1
phasing
X-PLOR
CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
DNA
DRUG BINDING, DNA
1DVL
PDB
1
1DVL
1
10
1DVL
1
10
1DVL
A
1
1
10
11
20
1DVL
11
20
1DVL
B
1
1
10
BINDING SITE FOR RESIDUE NT A 25
A
NT
25
Software
10
A
DC
2
A
DC
2
10
1_555
A
DI
3
A
DI
3
10
1_555
A
DI
4
A
DI
4
10
1_555
A
DC
5
A
DC
5
10
1_555
A
DI
6
A
DI
6
10
1_555
B
DI
16
B
DI
6
10
1_555
B
DC
17
B
DC
7
10
1_555
B
DC
18
B
DC
8
10
1_555
B
DI
19
B
DI
9
10
1_555
B
DI
20
B
DI
10
10
1_555
5
monoclinic
C 1 2 1