1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Wu, Y.
Pradhan, P.
Havener, J.
Chaney, S.G.
Campbel, S.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C6 H14 N2 Pt 2
309.267
CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II)
OXALIPLATIN
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
341
1251
1269
10.1016/j.jmb.2004.06.066
15321720
NMR solution structure of an oxaliplatin 1,2-d(GG) intrastrand cross-link in a DNA dodecamer duplex
2004
10.2210/pdb1pgc/pdb
pdb_00001pgc
G6 and G7 are Cross-Linked by a cis-Pt compound, residue 1PT
3559.319
5'-D(*CP*CP*TP*CP*AP*GP*GP*CP*CP*TP*CP*C)-3'
1
syn
polymer
3768.453
5'-D(*GP*GP*AP*GP*GP*CP*CP*TP*GP*AP*GP*G)-3'
1
syn
polymer
309.267
CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II)
1
syn
non-polymer
no
no
(DC)(DC)(DT)(DC)(DA)(DG)(DG)(DC)(DC)(DT)(DC)(DC)
CCTCAGGCCTCC
A
polydeoxyribonucleotide
no
no
(DG)(DG)(DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG)(DG)
GGAGGCCTGAGG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-0.439
1
19
A
1
B
24
2.540
A_DC1:DG24_B
1
0.346
0.270
0.014
-0.242
-3.208
1
19
A
2
B
23
3.727
A_DC2:DG23_B
2
2.806
-0.003
0.004
-0.135
-3.418
1
20
A
3
B
22
-2.180
A_DT3:DA22_B
3
-4.560
-0.145
0.198
-0.274
-6.331
1
19
A
4
B
21
-6.588
A_DC4:DG21_B
4
-6.254
-0.198
0.018
-0.147
2.239
1
20
A
5
B
20
-0.961
A_DA5:DT20_B
5
-5.830
-0.064
0.010
-0.278
10.120
1
19
A
6
B
19
2.449
A_DG6:DC19_B
6
-8.227
-0.373
0.101
-0.337
-2.964
1
19
A
7
B
18
4.774
A_DG7:DC18_B
7
3.173
-0.597
0.028
-0.314
-1.012
1
19
A
8
B
17
-2.947
A_DC8:DG17_B
8
-3.804
0.276
-0.072
-0.208
-4.045
1
19
A
9
B
16
-5.254
A_DC9:DG16_B
9
-1.321
0.249
-0.080
-0.162
3.079
1
20
A
10
B
15
-1.954
A_DT10:DA15_B
10
1.817
0.109
-0.048
-0.302
1.945
1
19
A
11
B
14
3.320
A_DC11:DG14_B
11
-0.429
-0.084
-0.004
-0.128
1.037
1
19
A
12
B
13
2.431
A_DC12:DG13_B
12
-0.644
0.114
0.099
-0.253
3.457
33.445
A
A
1
2
36.994
B
B
24
23
3.944
19.926
-0.148
0.441
AA_DC1DC2:DG23DG24_BB
1
-2.131
3.956
26.915
-3.391
-0.187
2.905
27.047
A
A
2
3
29.852
B
B
23
22
3.557
13.363
-1.277
-0.522
AA_DC2DT3:DA22DG23_BB
2
-1.228
2.744
23.537
-4.712
2.399
3.029
37.895
A
A
3
4
7.331
B
B
22
21
3.093
4.744
0.052
-0.292
AA_DT3DC4:DG21DA22_BB
3
3.166
-4.893
37.479
-1.021
0.302
2.898
35.496
A
A
4
5
6.657
B
B
21
20
3.057
4.046
0.383
-0.888
AA_DC4DA5:DT20DG21_BB
4
-3.040
5.002
35.145
-1.998
-1.036
3.067
24.358
A
A
5
6
10.135
B
B
20
19
3.340
4.241
0.118
-1.016
AA_DA5DG6:DC19DT20_BB
5
-3.433
8.203
23.748
-3.727
-1.347
1.228
38.550
A
A
6
7
55.670
B
B
19
18
3.639
31.604
0.897
-1.033
AA_DG6DG7:DC18DC19_BB
6
-2.574
4.534
22.210
-5.334
-1.665
3.808
33.842
A
A
7
8
-2.400
B
B
18
17
3.922
-1.396
-1.112
1.062
AA_DG7DC8:DG17DC18_BB
7
1.940
-3.336
33.760
2.091
2.280
3.464
36.995
A
A
8
9
-4.546
B
B
17
16
3.393
-2.882
0.265
-1.091
AA_DC8DC9:DG16DG17_BB
8
-0.194
0.306
36.886
-1.313
-0.446
3.507
28.320
A
A
9
10
-18.011
B
B
16
15
3.345
-8.675
0.666
-1.018
AA_DC9DT10:DA15DG16_BB
9
0.477
-0.990
26.980
0.074
-1.244
3.052
39.463
A
A
10
11
15.388
B
B
15
14
3.207
10.255
1.021
-0.601
AA_DT10DC11:DG14DA15_BB
10
4.842
-7.266
37.860
-2.073
-0.954
3.457
36.183
A
A
11
12
35.455
B
B
14
13
3.638
20.749
-0.772
0.746
AA_DC11DC12:DG13DG14_BB
11
-1.400
2.392
29.774
-2.302
1.007
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2004-07-06
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2003-05-28
REL
REL
1PT
CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II)
structures with the lowest energy
20
15
2D NOESY
2D TOCSY
DQF-COSY
2D NOESY
100mM NaCl, 5mM NaPi
7.0
1
atm
275
K
100mM NaCl, 5mM NaPi
7.0
1
atm
298
K
simulated annealing
15
lowest energy
100mM NaCl, 5mM NaPi buffer, 95% H2O, 5% D2O
95% H2O/5% D2O
100mM NaCl, 5mM NaPi buffer, 100% D2O
100% D2O
Brunger
structure solution
CNS
1.0
Molecular Simulations Inc.
data analysis
Felix
2000
Delaglio
processing
NMRPipe
2.1
Brunger
refinement
CNS
1.0
600
Varian
UNITYPLUS
800
Varian
UNITYPLUS
1PT
77
3
1PT
1PT
77
A
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
T
3
n
3
DT
3
A
C
4
n
4
DC
4
A
A
5
n
5
DA
5
A
G
6
n
6
DG
6
A
G
7
n
7
DG
7
A
C
8
n
8
DC
8
A
C
9
n
9
DC
9
A
T
10
n
10
DT
10
A
C
11
n
11
DC
11
A
C
12
n
12
DC
12
A
G
13
n
1
DG
13
B
G
14
n
2
DG
14
B
A
15
n
3
DA
15
B
G
16
n
4
DG
16
B
G
17
n
5
DG
17
B
C
18
n
6
DC
18
B
C
19
n
7
DC
19
B
T
20
n
8
DT
20
B
G
21
n
9
DG
21
B
A
22
n
10
DA
22
B
G
23
n
11
DG
23
B
G
24
n
12
DG
24
B
author_defined_assembly
2
dimeric
A
DG
6
A
N7
DG
6
1_555
A
1PT
77
C
PT
1PT
1_555
A
1PT
77
C
N1
1PT
1_555
92.5
A
DG
6
A
N7
DG
6
1_555
A
1PT
77
C
PT
1PT
1_555
A
1PT
77
C
N2
1PT
1_555
178.1
A
1PT
77
C
N1
1PT
1_555
A
1PT
77
C
PT
1PT
1_555
A
1PT
77
C
N2
1PT
1_555
85.6
A
DG
6
A
N7
DG
6
1_555
A
1PT
77
C
PT
1PT
1_555
A
DG
7
A
N7
DG
7
1_555
89.8
A
1PT
77
C
N1
1PT
1_555
A
1PT
77
C
PT
1PT
1_555
A
DG
7
A
N7
DG
7
1_555
177.6
A
1PT
77
C
N2
1PT
1_555
A
1PT
77
C
PT
1PT
1_555
A
DG
7
A
N7
DG
7
1_555
92.0
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
H21
O2
DG
DC
7
18
1.47
1
A
B
O2
H21
DC
DG
12
13
1.52
1
A
B
O2
H21
DC
DG
1
24
1.54
1
A
B
H21
O2
DG
DC
6
19
1.56
1
A
B
O2
H21
DC
DG
2
23
1.58
2
A
B
H21
O2
DG
DC
7
18
1.48
2
A
B
O2
H21
DC
DG
12
13
1.53
2
A
B
O2
H21
DC
DG
1
24
1.54
2
A
B
O2
H21
DC
DG
2
23
1.55
2
A
B
O2
H21
DC
DG
11
14
1.59
3
A
B
H21
O2
DG
DC
7
18
1.48
3
A
B
O2
H21
DC
DG
12
13
1.54
3
A
B
O2
H21
DC
DG
1
24
1.56
3
A
B
O2
H21
DC
DG
11
14
1.57
3
A
B
O2
H21
DC
DG
2
23
1.60
4
A
B
H21
O2
DG
DC
7
18
1.46
4
A
B
O2
H21
DC
DG
12
13
1.52
4
A
B
O2
H21
DC
DG
1
24
1.54
4
A
B
O2
H21
DC
DG
11
14
1.60
4
A
B
O2
H21
DC
DG
2
23
1.60
5
A
B
H21
O2
DG
DC
7
18
1.46
5
A
B
O2
H21
DC
DG
12
13
1.52
5
A
B
O2
H21
DC
DG
1
24
1.55
5
A
B
O2
H21
DC
DG
11
14
1.60
5
A
B
O2
H21
DC
DG
2
23
1.60
6
A
B
H21
O2
DG
DC
7
18
1.48
6
A
B
O2
H21
DC
DG
12
13
1.53
6
A
B
O2
H21
DC
DG
2
23
1.55
6
A
B
O2
H21
DC
DG
1
24
1.55
6
A
B
H21
O2
DG
DC
6
19
1.55
6
A
B
O2
H21
DC
DG
11
14
1.60
7
A
B
H21
O2
DG
DC
7
18
1.45
7
A
B
O2
H21
DC
DG
12
13
1.52
7
A
B
O2
H21
DC
DG
2
23
1.54
7
A
B
O2
H21
DC
DG
1
24
1.57
7
A
B
H21
O2
DG
DC
6
19
1.58
7
A
B
O2
H21
DC
DG
11
14
1.59
8
A
B
H21
O2
DG
DC
7
18
1.47
8
A
B
O2
H21
DC
DG
12
13
1.53
8
A
B
O2
H21
DC
DG
1
24
1.55
8
A
B
O2
H21
DC
DG
2
23
1.55
9
A
B
H21
O2
DG
DC
7
18
1.45
9
A
B
O2
H21
DC
DG
12
13
1.53
9
A
B
O2
H21
DC
DG
1
24
1.54
9
A
B
H21
O2
DG
DC
6
19
1.56
9
A
B
O2
H21
DC
DG
2
23
1.59
9
A
B
O2
H21
DC
DG
11
14
1.60
10
A
B
H21
O2
DG
DC
7
18
1.49
10
A
B
O2
H21
DC
DG
12
13
1.53
10
A
B
O2
H21
DC
DG
2
23
1.55
10
A
B
O2
H21
DC
DG
1
24
1.56
10
A
B
O2
H21
DC
DG
11
14
1.60
11
A
B
H21
O2
DG
DC
7
18
1.49
11
A
B
O2
H21
DC
DG
12
13
1.53
11
A
B
O2
H21
DC
DG
2
23
1.55
11
A
B
O2
H21
DC
DG
1
24
1.55
11
A
B
O2
H21
DC
DG
11
14
1.60
12
A
B
H21
O2
DG
DC
7
18
1.46
12
A
B
O2
H21
DC
DG
12
13
1.52
12
A
B
O2
H21
DC
DG
1
24
1.56
12
A
B
H21
O2
DG
DC
6
19
1.59
12
A
B
O2
H21
DC
DG
11
14
1.59
12
A
B
O2
H21
DC
DG
2
23
1.60
13
A
B
H21
O2
DG
DC
7
18
1.48
13
A
B
O2
H21
DC
DG
12
13
1.52
13
A
B
O2
H21
DC
DG
1
24
1.55
13
A
B
O2
H21
DC
DG
2
23
1.56
13
A
B
H21
O2
DG
DC
6
19
1.56
14
A
B
H21
O2
DG
DC
7
18
1.49
14
A
B
O2
H21
DC
DG
12
13
1.52
14
A
B
O2
H21
DC
DG
1
24
1.55
14
A
B
O2
H21
DC
DG
2
23
1.57
14
A
B
O2
H21
DC
DG
11
14
1.60
15
A
B
H21
O2
DG
DC
7
18
1.48
15
A
B
O2
H21
DC
DG
12
13
1.52
15
A
B
O2
H21
DC
DG
1
24
1.55
15
A
B
O2
H21
DC
DG
2
23
1.56
15
A
B
O2
H21
DC
DG
11
14
1.60
NMR Solution Structure of an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link in a DNA Dodecamer Duplex
1
N
N
2
N
N
3
N
N
metalc
2.008
A
DG
6
A
N7
DG
6
1_555
A
1PT
77
C
PT
1PT
1_555
metalc
2.012
A
DG
7
A
N7
DG
7
1_555
A
1PT
77
C
PT
1PT
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
24
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
24
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
24
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
23
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
23
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
23
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
22
B
N1
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
22
B
N6
DA
10
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
21
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
21
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
21
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
20
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
20
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
19
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
19
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
19
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
18
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
18
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
18
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
17
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
17
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
17
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
16
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DT
10
A
N3
DT
10
1_555
B
DA
15
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
10
A
O4
DT
10
1_555
B
DA
15
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N3
DC
12
1_555
B
DG
13
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N4
DC
12
1_555
B
DG
13
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
12
A
O2
DC
12
1_555
B
DG
13
B
N2
DG
1
1_555
DNA
DEOXYRIBONUCLEIC ACID; OXALIPLATIN; DNA; DUPLEX; DODECAMER; NMR, DNA
1PGC
PDB
1
1PGC
1PGC
PDB
2
1PGC
1
12
1PGC
1
12
1PGC
A
1
1
12
13
24
1PGC
13
24
1PGC
B
2
1
12
BINDING SITE FOR RESIDUE 1PT A 77
A
1PT
77
Software
3
A
DA
5
A
DA
5
3
1_555
A
DG
6
A
DG
6
3
1_555
A
DG
7
A
DG
7
3
1_555