1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Yang, D.
Van Boom, S.S.G.E.
Reedijk, J.
Van Boom, J.H.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
Biochemistry
BICHAW
0033
0006-2960
34
12912
12920
10.1021/bi00039a054
7548048
Structure and isomerization of an intrastrand cisplatin-cross-linked octamer DNA duplex by NMR analysis.
1995
UK
Prog.Biophys.Mol.Biol.
PBIMAC
0918
0079-6107
66
81
Structural Studies of Interactions between Anticancer Platinum Drugs and DNA
1996
Urbana : University of Illinois at Urbana-Champaign (Thesis)
US
Thesis
2157
1996
10.2210/pdb1au5/pdb
pdb_00001au5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
INTRASTRAND CISPLATIN-CROSSLINKED DNA
2378.567
DNA (5'-D(*CP*CP*TP*GP*GP*TP*CP*C)-3')
1
syn
polymer
INTRASTRAND CISPLATIN-CROSSLINKED DNA
2476.643
DNA (5'-D(*GP*GP*AP*CP*CP*AP*GP*G)-3')
1
syn
polymer
300.045
Cisplatin
1
syn
non-polymer
no
no
(DC)(DC)(DT)(DG)(DG)(DT)(DC)(DC)
CCTGGTCC
A
polydeoxyribonucleotide
no
no
(DG)(DG)(DA)(DC)(DC)(DA)(DG)(DG)
GGACCAGG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
10.237
1
19
A
1
B
16
1.904
A_DC1:DG16_B
1
11.931
-0.157
-0.049
0.026
8.264
1
19
A
2
B
15
-6.400
A_DC2:DG15_B
2
-31.255
1.176
0.292
-0.650
-21.398
1
A
3
B
14
8.696
A_DT3:DA14_B
3
-25.584
0.039
1.011
-0.003
-12.524
1
19
A
4
B
13
6.001
A_DG4:DC13_B
4
-39.686
-0.479
-0.560
-0.422
-16.637
1
19
A
5
B
12
-3.720
A_DG5:DC12_B
5
1.474
-0.880
0.262
-0.356
-0.196
1
20
A
6
B
11
14.785
A_DT6:DA11_B
6
-3.572
0.293
0.333
-0.002
6.449
1
19
A
7
B
10
7.067
A_DC7:DG10_B
7
-16.777
0.651
-0.529
-0.225
-8.387
1
19
A
8
B
9
7.272
A_DC8:DG9_B
8
12.614
0.828
0.082
0.046
3.099
54.719
A
A
1
2
-42.892
B
B
16
15
4.074
-36.439
-0.292
0.039
AA_DC1DC2:DG15DG16_BB
1
2.680
-3.154
41.453
2.847
0.524
3.927
35.198
A
A
2
3
1.229
B
B
15
14
3.933
0.741
0.452
-1.475
AA_DC2DT3:DA14DG15_BB
2
4.843
-8.033
34.866
-2.572
0.123
3.024
31.341
A
A
3
4
7.536
B
B
14
13
3.269
4.005
-0.684
0.859
AA_DT3DG4:DC13DA14_BB
3
9.052
-17.034
29.774
0.845
2.951
1.148
47.658
A
A
4
5
61.927
B
B
13
12
3.721
41.033
0.993
-0.369
AA_DG4DG5:DC12DC13_BB
4
-12.224
18.448
21.442
-3.967
-2.274
2.657
30.352
A
A
5
6
4.559
B
B
12
11
2.729
2.380
0.170
-0.874
AA_DG5DT6:DA11DC12_BB
5
3.297
-6.315
30.085
-2.065
0.223
2.801
45.096
A
A
6
7
-20.262
B
B
11
10
3.040
-15.134
0.047
0.032
AA_DT6DC7:DG10DA11_BB
6
10.296
-13.785
41.392
1.313
0.804
3.904
36.543
A
A
7
8
-8.867
B
B
10
9
3.877
-5.488
0.238
-1.593
AA_DC7DC8:DG9DG10_BB
7
-8.801
14.218
35.089
-1.620
-1.856
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
struct_conn
struct_site
repository
Initial release
Version format compliance
Non-polymer description
Version format compliance
Data collection
Database references
Derived calculations
Other
1
0
1998-02-25
1
1
2008-03-24
1
2
2011-07-13
1
3
2024-04-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_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
Y
BNL
1997-09-11
REL
REL
CPT
Cisplatin
1
1
2D1HNOESY
TOCSY
150 mM NACL
7
1 ATM SOLVENT SYSTEM : H2O/D2O
275
K
NOE-RESTRAINED REFINEMENT SPEDREF
BRUNGER
refinement
X-PLOR
structure solution
X-PLOR
structure solution
QUANTA
500
Varian
VXR500
CPT
17
3
CPT
CPT
17
A
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
T
3
n
3
DT
3
A
G
4
n
4
DG
4
A
G
5
n
5
DG
5
A
T
6
n
6
DT
6
A
C
7
n
7
DC
7
A
C
8
n
8
DC
8
A
G
9
n
1
DG
9
B
G
10
n
2
DG
10
B
A
11
n
3
DA
11
B
C
12
n
4
DC
12
B
C
13
n
5
DC
13
B
A
14
n
6
DA
14
B
G
15
n
7
DG
15
B
G
16
n
8
DG
16
B
author_defined_assembly
2
dimeric
A
DG
4
A
N7
DG
4
1_555
A
CPT
17
C
PT1
CPT
1_555
A
CPT
17
C
N1
CPT
1_555
91.2
A
DG
4
A
N7
DG
4
1_555
A
CPT
17
C
PT1
CPT
1_555
A
CPT
17
C
N2
CPT
1_555
177.6
A
CPT
17
C
N1
CPT
1_555
A
CPT
17
C
PT1
CPT
1_555
A
CPT
17
C
N2
CPT
1_555
91.2
A
DG
4
A
N7
DG
4
1_555
A
CPT
17
C
PT1
CPT
1_555
A
DG
5
A
N7
DG
5
1_555
87.4
A
CPT
17
C
N1
CPT
1_555
A
CPT
17
C
PT1
CPT
1_555
A
DG
5
A
N7
DG
5
1_555
178.5
A
CPT
17
C
N2
CPT
1_555
A
CPT
17
C
PT1
CPT
1_555
A
DG
5
A
N7
DG
5
1_555
90.2
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
B
DA
11
0.082
SIDE CHAIN
1
-4.51
0.70
102.20
97.69
A
A
A
C4'
C3'
C2'
DC
DC
DC
1
1
1
N
1
5.02
0.30
108.30
113.32
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
6.50
0.30
108.30
114.80
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
3.46
0.30
108.30
111.76
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
8.29
1.20
119.70
127.99
A
A
A
C3'
O3'
P
DT
DT
DG
3
3
4
Y
1
-4.22
0.70
102.20
97.98
A
A
A
C4'
C3'
C2'
DG
DG
DG
4
4
4
N
1
8.52
0.30
108.30
116.82
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-5.04
0.80
105.90
100.86
A
A
A
O4'
C1'
C2'
DG
DG
DG
5
5
5
N
1
7.54
0.30
108.30
115.84
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
5.30
0.30
108.30
113.60
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
6.71
0.30
108.30
115.01
B
B
B
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
2.39
0.30
108.30
110.69
B
B
B
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
12.57
0.30
108.30
120.87
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
4.31
0.60
118.90
123.21
B
B
B
N1
C2
O2
DC
DC
DC
12
12
12
N
1
7.52
1.10
109.80
117.32
B
B
B
C5'
C4'
O4'
DC
DC
DC
13
13
13
N
1
-6.09
0.80
105.90
99.81
B
B
B
O4'
C1'
C2'
DA
DA
DA
14
14
14
N
1
3.25
0.30
108.30
111.56
B
B
B
O4'
C1'
N9
DA
DA
DA
14
14
14
N
1
2.85
0.30
108.30
111.15
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
-5.25
0.80
105.90
100.65
B
B
B
O4'
C1'
C2'
DG
DG
DG
16
16
16
N
1
10.59
0.30
108.30
118.89
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
A
A
C5'
C4'
DT
DT
3
3
0.058
0.007
1.512
1.570
N
1
A
A
C5
C7
DT
DT
3
3
0.066
0.006
1.496
1.562
N
1
A
A
C5
C7
DT
DT
6
6
0.061
0.006
1.496
1.557
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
SOLUTION STRUCTURE OF INTRASTRAND CISPLATIN-CROSSLINKED DNA OCTAMER D(CCTG*G*TCC):D(GGACCAGG), NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
3
N
N
metalc
1.984
A
DG
4
A
N7
DG
4
1_555
A
CPT
17
C
PT1
CPT
1_555
metalc
1.963
A
DG
5
A
N7
DG
5
1_555
A
CPT
17
C
PT1
CPT
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
16
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
16
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
16
B
N2
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
15
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
15
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
15
B
N2
DG
7
1_555
hydrog
DT-DA PAIR
A
DT
3
A
N3
DT
3
1_555
B
DA
14
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
13
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
13
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
13
B
N4
DC
5
1_555
hydrog
DG-DA MISPAIR
A
DG
5
A
O6
DG
5
1_555
B
DA
11
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
12
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
12
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
12
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
11
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
11
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
DG
10
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
10
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
10
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
9
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
9
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
9
B
N2
DG
1
1_555
DNA
INTRASTRAND, CISPLATIN, DNA, DEOXYRIBONUCLEIC ACID
1AU5
PDB
1
1AU5
1AU5
PDB
2
1AU5
1
8
1AU5
1
8
1AU5
A
1
1
8
9
16
1AU5
9
16
1AU5
B
2
1
8
BINDING SITE FOR RESIDUE CPT A 17
A
CPT
17
Software
3
A
DG
4
A
DG
4
3
1_555
A
DG
5
A
DG
5
3
1_555
A
DT
6
A
DT
6
3
1_555
1
P 1