0.033378
0.019271
0.000000
0.000000
0.038541
0.000000
0.000000
0.000000
0.025221
0.000000
0.000000
0.000000
Lisgarten, J.N.
Coll, M.
Portugal, J.
Wright, C.W.
Aymami, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
29.960
29.960
39.650
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
C16 H12 N2
232.280
5-METHYL-5H-INDOLO[3,2-B]QUINOLINE
CRYPTOLEPINE
non-polymer
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
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
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
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
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
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
H
N
71
N
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
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
Y
108
N
C
Y
109
N
C
Y
110
N
C
Y
111
N
C
Y
112
N
C
Y
113
N
C
Y
114
N
C
Y
115
N
N
Y
116
N
C
Y
117
N
C
Y
118
N
C
Y
119
N
C
Y
120
N
C
Y
121
N
C
Y
122
N
C
Y
123
N
N
Y
124
N
C
N
125
N
C
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
O
N
139
N
P
N
140
N
O
N
141
N
O
N
142
N
O
N
143
N
C
N
144
R
C
N
145
N
O
N
146
S
C
N
147
N
O
N
148
N
C
N
149
R
C
N
150
N
N
N
151
N
C
N
152
N
O
N
153
N
N
N
154
N
C
N
155
N
O
N
156
N
C
N
157
N
C
N
158
N
C
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
H
N
172
N
H
N
173
N
H
N
174
N
O
N
175
N
H
N
176
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
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
doub
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
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
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
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
Y
113
N
doub
Y
114
N
sing
N
115
N
sing
Y
116
N
sing
N
117
N
sing
Y
118
N
doub
N
119
N
sing
Y
120
N
sing
N
121
N
sing
Y
122
N
sing
Y
123
N
doub
Y
124
N
doub
N
125
N
sing
Y
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
sing
Y
130
N
sing
Y
131
N
doub
N
132
N
sing
Y
133
N
sing
N
134
N
sing
Y
135
N
doub
N
136
N
sing
Y
137
N
sing
N
138
N
sing
Y
139
N
doub
Y
140
N
sing
Y
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
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
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
doub
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
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
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
9
57
60
10.1038/nsb729
11731803
The antimalarial and cytotoxic drug cryptolepine intercalates into DNA at cytosine-cytosine sites.
2002
10.2210/pdb1k9g/pdb
pdb_00001k9g
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
120
1
IMAGE PLATE
2000-05-26
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.1
1.0
BW7A
EMBL/DESY, HAMBURG
1.1
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE BW7A
1809.217
5'-D(*CP*CP*TP*AP*GP*G)-3'
1
syn
polymer
232.280
5-METHYL-5H-INDOLO[3,2-B]QUINOLINE
2
syn
non-polymer
18.015
water
37
nat
water
no
no
(DC)(DC)(DT)(DA)(DG)(DG)
CCTAGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
1
2.72
54.76
VAPOR DIFFUSION, HANGING DROP
6.5
Magnesium acetate, MES, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
1.602
1
19
A
1
A
6
-0.939
A_DC1:DG6_A
1
-10.972
0.186
0.119
-0.190
-9.873
1
19
A
2
A
5
-1.057
A_DC2:DG5_A
2
-1.689
0.159
0.409
-0.140
3.578
1
20
A
3
A
4
-1.593
A_DT3:DA4_A
3
-12.349
-0.050
-0.003
-0.202
-3.578
1
20
A
4
A
3
-1.593
A_DA4:DT3_A
4
-12.349
0.050
-0.003
-0.202
9.873
1
19
A
5
A
2
-1.057
A_DG5:DC2_A
5
-1.689
-0.159
0.409
-0.140
-1.602
1
19
A
6
A
1
-0.939
A_DG6:DC1_A
6
-10.972
-0.186
0.119
-0.190
6.920
24.066
A
A
1
2
1.485
A
A
6
5
6.943
0.619
0.113
0.397
AA_DC1DC2:DG5DG6_AA
1
-1.938
4.654
23.982
0.529
-1.592
2.872
27.500
A
A
2
3
8.306
A
A
5
4
2.977
3.923
-0.468
0.112
AA_DC2DT3:DA4DG5_AA
2
3.812
-8.072
26.960
-0.633
1.829
3.225
50.945
A
A
3
4
-4.267
A
A
4
3
3.357
-3.668
0.000
1.853
AA_DT3DA4:DT3DA4_AA
3
0.000
0.000
50.822
2.412
0.000
2.872
27.500
A
A
4
5
8.306
A
A
3
2
2.977
3.923
0.468
0.112
AA_DA4DG5:DC2DT3_AA
4
-3.812
8.072
26.960
-0.633
-1.829
6.920
24.066
A
A
5
6
1.485
A
A
2
1
6.943
0.619
-0.113
0.397
AA_DG5DG6:DC1DC2_AA
5
1.938
-4.654
23.982
0.529
1.592
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
software
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2001-11-30
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_software.classification
_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2001-10-29
REL
DR1
5-METHYL-5H-INDOLO[3,2-B]QUINOLINE
HOH
water
DR1
7
2
DR1
DR1
7
A
DR1
8
2
DR1
DR1
8
A
HOH
3001
3
HOH
HOH
3001
A
HOH
3002
3
HOH
HOH
3002
A
HOH
3003
3
HOH
HOH
3003
A
HOH
3004
3
HOH
HOH
3004
A
HOH
3005
3
HOH
HOH
3005
A
HOH
3006
3
HOH
HOH
3006
A
HOH
3007
3
HOH
HOH
3007
A
HOH
3008
3
HOH
HOH
3008
A
HOH
3009
3
HOH
HOH
3009
A
HOH
3010
3
HOH
HOH
3010
A
HOH
3011
3
HOH
HOH
3011
A
HOH
3012
3
HOH
HOH
3012
A
HOH
3013
3
HOH
HOH
3013
A
HOH
3014
3
HOH
HOH
3014
A
HOH
3015
3
HOH
HOH
3015
A
HOH
3016
3
HOH
HOH
3016
A
HOH
3017
3
HOH
HOH
3017
A
HOH
3018
3
HOH
HOH
3018
A
HOH
3019
3
HOH
HOH
3019
A
HOH
3020
3
HOH
HOH
3020
A
HOH
3021
3
HOH
HOH
3021
A
HOH
3022
3
HOH
HOH
3022
A
HOH
3023
3
HOH
HOH
3023
A
HOH
3026
3
HOH
HOH
3026
A
HOH
3027
3
HOH
HOH
3027
A
HOH
3028
3
HOH
HOH
3028
A
HOH
3029
3
HOH
HOH
3029
A
HOH
3030
3
HOH
HOH
3030
A
HOH
3031
3
HOH
HOH
3031
A
HOH
3032
3
HOH
HOH
3032
A
HOH
3033
3
HOH
HOH
3033
A
HOH
3034
3
HOH
HOH
3034
A
HOH
3035
3
HOH
HOH
3035
A
HOH
3036
3
HOH
HOH
3036
A
HOH
3037
3
HOH
HOH
3037
A
HOH
3038
3
HOH
HOH
3038
A
HOH
3039
3
HOH
HOH
3039
A
CYT
1
n
1
DC
1
A
CYT
2
n
2
DC
2
A
THY
3
n
3
DT
3
A
ADE
4
n
4
DA
4
A
GUA
5
n
5
DG
5
A
GUA
6
n
6
DG
6
A
0.2090000
0.2080000
0.2270000
167
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_675
-x+1,-y+2,z
crystal symmetry operation
0.0000000000
51.8922421948
0.0000000000
1
A
A
O
O
HOH
HOH
3018
3030
1.99
1
A
A
O
O
HOH
HOH
3010
3012
2.03
1
A
A
C5'
O
DT
HOH
3
3038
2.13
1
-4.64
0.70
108.00
103.36
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.66
0.50
119.90
123.56
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
1
3.12
0.50
121.00
124.12
A
A
A
C5
C6
N1
DC
DC
DC
2
2
2
N
1
-5.36
0.80
102.40
97.04
A
A
A
C3'
C2'
C1'
DT
DT
DT
3
3
3
N
1
-4.23
0.60
119.00
114.77
A
A
A
C4
C5
C7
DT
DT
DT
3
3
3
N
1
8.29
1.20
119.70
127.99
A
A
A
C3'
O3'
P
DT
DT
DA
3
3
4
Y
1
-4.96
0.70
108.00
103.04
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
-4.61
0.50
129.30
124.69
A
A
A
N1
C2
N3
DA
DA
DA
4
4
4
N
1
10.12
1.60
120.90
131.02
A
A
A
P
O5'
C5'
DG
DG
DG
6
6
6
N
1
A
A
O
O
HOH
HOH
3026
3029
2.12
1_555
3_564
0.2270000
0.2080000
0.2090000
0.2090000
1.4
10.
167
3356
3356
RANDOM
1
THROUGHOUT
0
MOLECULAR REPLACEMENT
Engh & Huber
1.4
10.
37
193
36
120
0
0.011
0.023
17.7
1.4
20
1K9G
3543
3356
2
1
0.0380000
1
29.1
87.3
0.3300000
1.4
1.45
2.4
292
73.2
phasing
AMoRE
refinement
SHELXL-97
data collection
MAR345
data scaling
SCALEPACK
Crystal Structure of the Complex of Cryptolepine-d(CCTAGG)2
1
N
N
2
N
N
2
N
N
3
N
N
The double helix is generated by the operation -x,-y+2,z.
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
6
A
N1
DG
6
4_675
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
6
A
O6
DG
6
4_675
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
6
A
N2
DG
6
4_675
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
5
A
N1
DG
5
4_675
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
5
A
O6
DG
5
4_675
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
5
A
N2
DG
5
4_675
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
A
DA
4
A
N1
DA
4
4_675
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
A
DA
4
A
N6
DA
4
4_675
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
A
DT
3
A
N3
DT
3
4_675
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
A
DT
3
A
O4
DT
3
4_675
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
A
DC
2
A
N3
DC
2
4_675
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
A
DC
2
A
O2
DC
2
4_675
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
A
DC
2
A
N4
DC
2
4_675
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
1
A
N3
DC
1
4_675
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
1
A
O2
DC
1
4_675
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
1
A
N4
DC
1
4_675
DNA
DNA intercalator complex, DNA
1K9G
PDB
1
1K9G
1
6
1K9G
1
6
1K9G
A
1
1
6
BINDING SITE FOR RESIDUE DR1 A 7
A
DR1
7
Software
4
BINDING SITE FOR RESIDUE DR1 A 8
A
DR1
8
Software
6
A
DC
1
A
DC
1
4
1_555
A
DC
2
A
DC
2
4
1_555
A
DG
5
A
DG
5
4
4_675
A
DG
6
A
DG
6
4
4_675
A
DC
1
A
DC
1
6
1_555
A
DC
1
A
DC
1
6
4_665
A
DG
6
A
DG
6
6
4_675
A
DG
6
A
DG
6
6
1_545
A
HOH
3015
D
HOH
6
4_675
A
HOH
3015
D
HOH
6
1_545
172
P 64