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/pdb1pg9/pdb
pdb_00001pg9
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
0.145
1
19
A
1
B
24
1.662
A_DC1:DG24_B
1
-0.010
0.506
-0.026
-0.330
-3.048
1
19
A
2
B
23
2.725
A_DC2:DG23_B
2
1.579
0.281
-0.064
-0.240
-4.488
1
20
A
3
B
22
-2.255
A_DT3:DA22_B
3
-6.001
0.048
0.090
-0.307
-6.419
1
19
A
4
B
21
-1.396
A_DC4:DG21_B
4
-5.475
-0.140
0.044
-0.177
2.218
1
20
A
5
B
20
-1.235
A_DA5:DT20_B
5
-4.377
-0.122
-0.031
-0.279
10.590
1
19
A
6
B
19
2.498
A_DG6:DC19_B
6
-9.921
-0.513
0.122
-0.361
-5.649
1
19
A
7
B
18
6.423
A_DG7:DC18_B
7
-0.508
-0.667
-0.007
-0.254
-1.703
1
19
A
8
B
17
-2.309
A_DC8:DG17_B
8
-4.115
0.302
-0.033
-0.238
-5.072
1
19
A
9
B
16
-5.200
A_DC9:DG16_B
9
-2.410
0.272
-0.020
-0.165
2.492
1
20
A
10
B
15
-2.235
A_DT10:DA15_B
10
0.288
0.112
-0.013
-0.299
1.697
1
19
A
11
B
14
3.440
A_DC11:DG14_B
11
-1.252
-0.080
0.005
-0.124
0.988
1
19
A
12
B
13
2.258
A_DC12:DG13_B
12
-0.581
0.079
0.098
-0.255
4.165
29.877
A
A
1
2
18.603
B
B
24
23
4.222
9.427
0.012
0.517
AA_DC1DC2:DG23DG24_BB
1
-2.047
4.040
28.311
-1.577
-0.584
2.973
28.288
A
A
2
3
22.284
B
B
23
22
3.556
10.624
-1.011
-1.067
AA_DC2DT3:DA22DG23_BB
2
-2.022
4.241
26.178
-4.742
1.581
2.985
35.880
A
A
3
4
11.357
B
B
22
21
3.115
6.953
0.054
-0.394
AA_DT3DC4:DG21DA22_BB
3
1.547
-2.527
35.189
-1.577
0.121
3.158
31.470
A
A
4
5
16.655
B
B
21
20
3.406
8.910
0.651
-0.251
AA_DC4DA5:DT20DG21_BB
4
-1.963
3.670
30.150
-2.170
-1.576
3.119
22.906
A
A
5
6
10.192
B
B
20
19
3.378
4.015
0.198
-0.873
AA_DA5DG6:DC19DT20_BB
5
-3.096
7.861
22.345
-3.631
-1.604
1.434
38.274
A
A
6
7
49.177
B
B
19
18
3.606
28.702
0.986
-1.260
AA_DG6DG7:DC18DC19_BB
6
-2.448
4.195
25.472
-5.311
-1.792
3.654
36.423
A
A
7
8
2.381
B
B
18
17
3.638
1.488
-1.375
0.991
AA_DG7DC8:DG17DC18_BB
7
0.544
-0.870
36.390
1.356
2.283
3.230
36.277
A
A
8
9
0.736
B
B
17
16
3.244
0.458
0.184
-1.100
AA_DC8DC9:DG16DG17_BB
8
-0.159
0.256
36.274
-1.831
-0.318
3.425
28.343
A
A
9
10
-16.277
B
B
16
15
3.254
-7.868
0.614
-1.018
AA_DC9DT10:DA15DG16_BB
9
0.885
-1.831
27.236
-0.185
-1.041
3.093
39.480
A
A
10
11
12.057
B
B
15
14
3.155
8.070
1.103
-0.572
AA_DT10DC11:DG14DA15_BB
10
5.134
-7.671
38.348
-1.769
-1.047
3.408
36.409
A
A
11
12
36.169
B
B
14
13
3.591
21.242
-0.832
0.750
AA_DC11DC12:DG13DG14_BB
11
-1.559
2.655
29.702
-2.309
1.073
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)
closest to the average
20
1
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
1
closest to the average
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
molecualr 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
91.9
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
177.6
A
1PT
77
C
N1
1PT
1_555
A
1PT
77
C
PT
1PT
1_555
A
1PT
77
C
N2
1PT
1_555
85.7
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
90.6
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
91.9
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
1.45
1
A
B
O2
H21
DC
DG
12
13
1.52
1
A
B
O2
H21
DC
DG
2
23
1.54
1
A
B
O2
H21
DC
DG
1
24
1.56
1
A
B
H21
O2
DG
DC
6
19
1.60
1
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
2.013
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
1PG9
PDB
1
1PG9
1PG9
PDB
2
1PG9
1
12
1PG9
1
12
1PG9
A
1
1
12
13
24
1PG9
13
24
1PG9
B
2
1
12
BINDING SITE FOR RESIDUE 1PT A 77
A
1PT
77
Software
2
A
DG
6
A
DG
6
2
1_555
A
DG
7
A
DG
7
2
1_555