1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Marzilli, L.G.
Saad, J.S.
Kuklenyik, Z.
Keating, K.A.
Xu, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
Cl2 H6 N2 Pt
300.045
Cisplatin
diammine(dichloro)platinum
non-polymer
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
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
N
1
N
PT
N
2
N
N
N
3
N
N
N
4
N
H
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
CL
N
9
N
CL
N
10
N
H
N
11
N
H
N
12
N
O
N
13
N
P
N
14
N
O
N
15
N
O
N
16
N
O
N
17
N
C
N
18
R
C
N
19
N
O
N
20
S
C
N
21
N
O
N
22
N
C
N
23
R
C
Y
24
N
N
Y
25
N
C
Y
26
N
N
Y
27
N
C
Y
28
N
C
N
29
N
N
Y
30
N
N
Y
31
N
C
Y
32
N
N
Y
33
N
C
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
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
O
N
49
N
P
N
50
N
O
N
51
N
O
N
52
N
O
N
53
N
C
N
54
R
C
N
55
N
O
N
56
S
C
N
57
N
O
N
58
N
C
N
59
R
C
N
60
N
N
N
61
N
C
N
62
N
O
N
63
N
N
N
64
N
C
N
65
N
N
N
66
N
C
N
67
N
C
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
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
O
N
83
N
P
N
84
N
O
N
85
N
O
N
86
N
O
N
87
N
C
N
88
R
C
N
89
N
O
N
90
S
C
N
91
N
O
N
92
N
C
N
93
R
C
Y
94
N
N
Y
95
N
C
Y
96
N
N
Y
97
N
C
N
98
N
C
N
99
N
O
N
100
N
N
N
101
N
C
N
102
N
N
N
103
N
N
Y
104
N
C
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
O
N
120
N
P
N
121
N
O
N
122
N
O
N
123
N
O
N
124
N
C
N
125
R
C
N
126
N
O
N
127
S
C
N
128
N
O
N
129
N
C
N
130
R
C
N
131
N
N
N
132
N
C
N
133
N
O
N
134
N
N
N
135
N
C
N
136
N
O
N
137
N
C
N
138
N
C
N
139
N
C
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
1
N
sing
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
doub
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
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
Y
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
Y
39
N
sing
Y
40
N
doub
N
41
N
sing
Y
42
N
doub
N
43
N
sing
N
44
N
sing
Y
45
N
sing
Y
46
N
doub
N
47
N
sing
Y
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
doub
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
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
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
doub
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
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
N
106
N
sing
Y
107
N
sing
Y
108
N
sing
Y
109
N
doub
N
110
N
sing
Y
111
N
sing
N
112
N
sing
Y
113
N
doub
N
114
N
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
doub
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
doub
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
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
doub
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
123
2764
2770
10.1021/ja0007915
11456962
Relationship of solution and protein-bound structures of DNA duplexes with the major intrastrand cross-link lesions formed on cisplatin binding to DNA.
2001
10.2210/pdb1ksb/pdb
pdb_00001ksb
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
x-ray
1
1.0
Cisplatin intrastrand cross-link DNA
2667.749
5'-D(*CP*TP*CP*CP*GP*GP*CP*CP*T)-3'
1
syn
polymer
2805.849
5'-D(*AP*GP*GP*CP*CP*GP*GP*AP*G)-3'
1
syn
polymer
300.045
Cisplatin
1
syn
non-polymer
no
no
(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DC)(DT)
CTCCGGCCT
A
polydeoxyribonucleotide
no
no
(DA)(DG)(DG)(DC)(DC)(DG)(DG)(DA)(DG)
AGGCCGGAG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-4.458
1
19
A
1
B
9
0.471
A_DC1:DG9_B
1
-14.431
-0.119
0.135
0.026
-2.978
1
20
A
2
B
8
-4.302
A_DT2:DA8_B
2
-11.462
-0.549
0.063
-0.075
2.381
1
19
A
3
B
7
2.838
A_DC3:DG7_B
3
-6.238
0.203
-0.195
-0.025
2.568
1
19
A
4
B
6
0.612
A_DC4:DG6_B
4
-0.051
0.451
0.393
-0.126
32.037
1
19
A
5
B
5
-1.719
A_DG5:DC5_B
5
1.835
-0.934
0.579
-0.300
-8.921
1
19
A
6
B
4
-5.597
A_DG6:DC4_B
6
10.165
-0.061
-0.558
-0.258
6.121
1
19
A
7
B
3
-7.634
A_DC7:DG3_B
7
0.358
0.742
0.214
-0.141
13.869
1
19
A
8
B
2
1.530
A_DC8:DG2_B
8
-21.544
0.133
-0.025
-0.005
-4.830
1
20
A
9
B
1
-0.896
A_DT9:DA1_B
9
-15.177
-0.236
-0.015
-0.041
3.104
32.975
A
A
1
2
10.749
B
B
9
8
3.189
6.068
-0.132
-0.185
AA_DC1DT2:DA8DG9_BB
1
-0.043
0.076
32.427
-1.327
0.226
3.150
38.079
A
A
2
3
7.078
B
B
8
7
3.128
4.603
0.550
0.089
AA_DT2DC3:DG7DA8_BB
2
3.056
-4.699
37.691
-0.428
-0.469
3.360
34.149
A
A
3
4
20.946
B
B
7
6
3.359
12.020
-0.495
0.500
AA_DC3DC4:DG6DG7_BB
3
-4.188
7.299
31.754
-1.179
0.136
2.399
28.862
A
A
4
5
-22.156
B
B
6
5
2.994
-10.656
1.497
1.840
AA_DC4DG5:DC5DG6_BB
4
7.599
-15.801
25.780
5.764
-1.526
0.915
65.829
A
A
5
6
76.687
B
B
5
4
5.591
63.763
-0.224
-0.622
AA_DG5DG6:DC4DC5_BB
5
-4.064
4.888
16.764
-5.111
-0.083
3.246
38.789
A
A
6
7
5.264
B
B
4
3
3.177
3.469
-0.761
-0.080
AA_DG6DC7:DG3DC4_BB
6
-7.853
11.916
37.863
-0.543
0.192
2.639
31.854
A
A
7
8
20.453
B
B
3
2
2.967
10.948
0.988
-0.829
AA_DC7DC8:DG2DG3_BB
7
5.568
-10.401
29.447
-3.292
-0.893
3.416
36.531
A
A
8
9
15.884
B
B
2
1
3.634
9.829
0.032
-0.311
AA_DC8DT9:DA1DG2_BB
8
3.239
-5.235
35.082
-1.991
0.441
chem_comp_atom
chem_comp_bond
database_2
pdbx_nmr_software
struct_conn
struct_site
repository
Initial release
Version format compliance
Non-polymer description
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-01-17
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-05-01
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal Structure Of HMG1 Domain A Bound To A Cisplatin-Modified DNA Duplex
NMR Solution Structure Of a DNA Dodecamer Duplex Containing a Cis-Diammineplatinum(II) d(GpG) Intrastrand Cross-Link, the Major Adduct Of the Anticancer Drug Cisplatin
RCSB
Y
RCSB
2002-01-11
REL
CPT
Cisplatin
2D 1H-31P phase-sensitive Reverse Chemical Shift Correlation (RCSC) and 1H-13C magnitude mode HMQC experiments were performed.
1
2D NOESY
DQF-COSY
7.0
1
atm
278
K
NOE-Restrained refinement
(details can be found in the paper)
AMBER
Platinated 9-mer duplex dissolved in D2O/H2O
D2O or (90% H2O, 10% D2O)
processing
Felix
97.0
Biosym/MSI
refinement
Discover
structure solution
Insight II
data analysis
Curves
Biosym/MSI
refinement
IRMA
600
GE
OMEGA
600
Varian
UNITYPLUS
PT
4
3
CPT
CPT
10
A
C
1
n
1
DC
1
A
T
2
n
2
DT
2
A
C
3
n
3
DC
3
A
C
4
n
4
DC
4
A
G
5
n
5
DG
5
A
G
6
n
6
DG
6
A
C
7
n
7
DC
7
A
C
8
n
8
DC
8
A
T3'
9
n
9
DT
9
A
A
1
n
1
DA
1
B
G
2
n
2
DG
2
B
G
3
n
3
DG
3
B
C
4
n
4
DC
4
B
C
5
n
5
DC
5
B
G
6
n
6
DG
6
B
G
7
n
7
DG
7
B
A
8
n
8
DA
8
B
G3'
9
n
9
DG
9
B
author_defined_assembly
2
dimeric
A
DG
5
A
N7
DG
5
1_555
A
CPT
10
C
PT1
CPT
1_555
A
CPT
10
C
N1
CPT
1_555
178.5
A
DG
5
A
N7
DG
5
1_555
A
CPT
10
C
PT1
CPT
1_555
A
CPT
10
C
N2
CPT
1_555
90.4
A
CPT
10
C
N1
CPT
1_555
A
CPT
10
C
PT1
CPT
1_555
A
CPT
10
C
N2
CPT
1_555
90.4
A
DG
5
A
N7
DG
5
1_555
A
CPT
10
C
PT1
CPT
1_555
A
DG
6
A
N7
DG
6
1_555
88.6
A
CPT
10
C
N1
CPT
1_555
A
CPT
10
C
PT1
CPT
1_555
A
DG
6
A
N7
DG
6
1_555
90.5
A
CPT
10
C
N2
CPT
1_555
A
CPT
10
C
PT1
CPT
1_555
A
DG
6
A
N7
DG
6
1_555
178.2
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
DC
1
0.069
SIDE CHAIN
1
B
DG
2
0.107
SIDE CHAIN
1
B
DG
3
0.109
SIDE CHAIN
1
B
DC
4
0.086
SIDE CHAIN
1
B
DG
6
0.068
SIDE CHAIN
1
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.77
0.60
106.00
109.77
A
A
A
O4'
C4'
C3'
DT
DT
DT
2
2
2
N
1
-4.56
0.70
108.00
103.44
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
1
6.52
0.50
106.80
113.32
A
A
A
O4'
C1'
C2'
DG
DG
DG
5
5
5
N
1
3.59
0.30
108.30
111.89
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
3.95
0.60
106.00
109.95
B
B
B
O4'
C4'
C3'
DG
DG
DG
2
2
2
N
1
7.42
0.30
108.30
115.72
B
B
B
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.11
0.60
106.00
110.11
B
B
B
O4'
C4'
C3'
DG
DG
DG
3
3
3
N
1
9.47
1.20
102.50
111.97
B
B
B
C3'
C2'
C1'
DG
DG
DG
3
3
3
N
1
6.89
0.30
108.30
115.19
B
B
B
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-3.22
0.50
128.60
125.38
B
B
B
N3
C4
C5
DG
DG
DG
3
3
3
N
1
3.26
0.50
106.80
110.06
B
B
B
O4'
C1'
C2'
DC
DC
DC
5
5
5
N
1
3.88
0.60
106.00
109.88
B
B
B
O4'
C4'
C3'
DA
DA
DA
8
8
8
N
1
1.84
0.30
108.30
110.14
B
B
B
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
2.32
0.30
108.30
110.62
B
B
B
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
B
B
C5'
C4'
DC
DC
4
4
0.046
0.007
1.512
1.558
N
1
B
B
O3'
C3'
DC
DC
4
4
-0.110
0.006
1.419
1.309
N
1
B
B
O3'
C3'
DC
DC
5
5
-0.050
0.006
1.419
1.369
N
Relationship of Solution and Protein-Bound Structures of DNA Duplexes with the Major Intrastrand Cross-Link Lesions Formed on Cisplatin Binding to DNA
1
N
N
2
N
N
3
N
N
metalc
2.007
A
DG
5
A
N7
DG
5
1_555
A
CPT
10
C
PT1
CPT
1_555
metalc
2.012
A
DG
6
A
N7
DG
6
1_555
A
CPT
10
C
PT1
CPT
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
9
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
9
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
9
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
8
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
8
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
7
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
7
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
7
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
6
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
6
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
6
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
5
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
5
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
5
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
4
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
4
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
4
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
DG
3
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
3
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
3
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
2
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
2
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
2
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
1
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
1
B
N6
DA
1
1_555
DNA
Deoxyribonucleic acid, Cisplatin, DNA, Duplex, 9-mer, Intrastrand cross-link, model J
1KSB
PDB
1
1KSB
1KSB
PDB
2
1KSB
1
9
1KSB
1
9
1KSB
A
1
1
9
1
9
1KSB
1
9
1KSB
B
2
1
9
BINDING SITE FOR RESIDUE CPT A 10
A
CPT
10
Software
2
A
DG
5
A
DG
5
2
1_555
A
DG
6
A
DG
6
2
1_555