1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Denisov, A.Y.
McManus, F.P.
Noronha, A.M.
Wilds, C.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
C7 H16
100.202
HEPTANE
non-polymer
UK
Org.Biomol.Chem.
1477-0539
15
8361
8370
10.1039/c7ob02093g
28937154
Structural basis of interstrand cross-link repair by O 6 -alkylguanine DNA alkyltransferase.
2017
10.2210/pdb2lzw/pdb
pdb_00002lzw
3373.222
DNA (5'-D(*CP*GP*AP*AP*AP*GP*TP*TP*TP*CP*G)-3')
2
syn
polymer
100.202
HEPTANE
1
syn
non-polymer
no
no
(DC)(DG)(DA)(DA)(DA)(DG)(DT)(DT)(DT)(DC)(DG)
CGAAAGTTTCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
18.773
1
19
A
1
B
11
1.920
A_DC1:DG11_B
1
-4.259
0.245
-0.992
-0.271
-8.010
1
19
A
2
B
10
8.691
A_DG2:DC10_B
2
-14.898
-0.635
-0.728
-0.276
10.390
1
20
A
3
B
9
1.066
A_DA3:DT9_B
3
-12.119
-0.083
-0.239
-0.360
8.177
1
20
A
4
B
8
7.887
A_DA4:DT8_B
4
-12.783
-0.058
-0.313
-0.331
18.549
1
20
A
5
B
7
-1.271
A_DA5:DT7_B
5
-3.904
-0.082
0.528
-0.285
-17.669
1
20
A
7
B
5
-1.047
A_DT7:DA5_B
6
-4.146
0.082
0.484
-0.286
-7.983
1
20
A
8
B
4
7.737
A_DT8:DA4_B
7
-12.659
0.074
-0.315
-0.333
-10.176
1
20
A
9
B
3
1.057
A_DT9:DA3_B
8
-11.975
0.099
-0.236
-0.365
8.203
1
19
A
10
B
2
8.547
A_DC10:DG2_B
9
-14.860
0.643
-0.723
-0.285
-18.486
1
19
A
11
B
1
1.892
A_DG11:DC1_B
10
-4.212
-0.236
-0.969
-0.284
3.544
33.509
A
A
1
2
37.090
B
B
11
10
4.788
20.023
0.307
-0.573
AA_DC1DG2:DC10DG11_BB
1
0.171
-0.316
27.007
-5.675
-0.492
2.837
34.086
A
A
2
3
14.716
B
B
10
9
2.708
8.506
-0.560
0.646
AA_DG2DA3:DT9DC10_BB
2
-5.277
9.130
32.625
-0.071
0.227
2.840
34.597
A
A
3
4
24.194
B
B
9
8
3.330
13.999
0.142
-0.552
AA_DA3DA4:DT8DT9_BB
3
-0.585
1.011
31.713
-3.059
-0.328
2.902
35.679
A
A
4
5
13.856
B
B
8
7
3.009
8.388
-0.604
-0.356
AA_DA4DA5:DT7DT8_BB
4
-5.028
8.306
34.355
-1.701
0.314
2.926
35.774
A
A
7
8
13.943
B
B
5
4
3.034
8.464
0.599
-0.342
AA_DT7DT8:DA4DA5_BB
5
4.782
-7.878
34.469
-1.689
-0.335
2.842
34.550
A
A
8
9
24.133
B
B
4
3
3.331
13.946
-0.139
-0.553
AA_DT8DT9:DA3DA4_BB
6
0.606
-1.049
31.683
-3.060
0.326
2.837
34.004
A
A
9
10
14.794
B
B
3
2
2.710
8.529
0.559
0.642
AA_DT9DC10:DG2DA3_BB
7
5.339
-9.260
32.523
-0.085
-0.216
3.546
33.618
A
A
10
11
36.963
B
B
2
1
4.783
20.027
-0.305
-0.577
AA_DC10DG11:DC1DG2_BB
8
-0.280
0.517
27.140
-5.644
0.462
citation
pdbx_entity_src_syn
citation
database_2
pdbx_nmr_software
struct_conn
struct_site
pdbx_database_status
repository
Initial release
Database references
Source and taxonomy
Data collection
Database references
Derived calculations
Other
1
0
2013-10-16
1
1
2017-10-04
1
2
2022-08-24
1
3
2023-06-14
_citation.country
_citation.journal_abbrev
_citation.journal_id_CSD
_citation.journal_id_ISSN
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_citation.year
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.title
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_pdbx_database_status.status_code_nmr_data
BMRB
Y
RCSB
2012-10-11
REL
REL
REL
REL
HP6
HEPTANE
32630
synthetic construct
sample
structures with the least restraint violations and the lowest energy
20
11
2D NOESY
2D TOCSY
2D DQF-COSY
2D 1H-31P HSQC
2D NOESY
1
mM
1
mM
0.1
7.5
ambient
298
K
0.1
7.5
ambient
273
K
simulated annealing
1
minimized average structure
1 mM DNA (5'-D(*CP*GP*AP*AP*AP*GP*TP*TP*TP*CP*G)-3'), 100% D2O
100% D2O
1 mM DNA (5'-D(*CP*GP*AP*AP*AP*GP*TP*TP*TP*CP*G)-3'), 90% H2O/10% D2O
90% H2O/10% D2O
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
1.2
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Johnson, One Moon Scientific
data analysis
NMRView
Varian
collection
VnmrJ
500
Varian
Unity Inova
Varian Unity Inova
800
Varian
Unity Inova
Varian Unity Inova
500
Varian
VNMRS
Varian VNMRS
HP6
12
2
HP6
HP6
101
B
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
DA
3
n
3
DA
3
A
DA
4
n
4
DA
4
A
DA
5
n
5
DA
5
A
DG
6
n
6
DG
6
A
DT
7
n
7
DT
7
A
DT
8
n
8
DT
8
A
DT
9
n
9
DT
9
A
DC
10
n
10
DC
10
A
DG
11
n
11
DG
11
A
DC
1
n
1
DC
1
B
DG
2
n
2
DG
2
B
DA
3
n
3
DA
3
B
DA
4
n
4
DA
4
B
DA
5
n
5
DA
5
B
DG
6
n
6
DG
6
B
DT
7
n
7
DT
7
B
DT
8
n
8
DT
8
B
DT
9
n
9
DT
9
B
DC
10
n
10
DC
10
B
DG
11
n
11
DG
11
B
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
A
A
C6
O6
DG
DG
6
6
0.134
0.009
1.237
1.371
N
1
B
B
C6
O6
DG
DG
6
6
0.134
0.009
1.237
1.371
N
2
A
A
C6
O6
DG
DG
6
6
0.137
0.009
1.237
1.374
N
2
B
B
C6
O6
DG
DG
6
6
0.136
0.009
1.237
1.373
N
3
A
A
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
3
B
B
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
4
A
A
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
4
B
B
C6
O6
DG
DG
6
6
0.134
0.009
1.237
1.371
N
5
A
A
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
5
B
B
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
6
A
A
C6
O6
DG
DG
6
6
0.134
0.009
1.237
1.371
N
6
B
B
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
7
A
A
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
7
B
B
C6
O6
DG
DG
6
6
0.136
0.009
1.237
1.373
N
8
A
A
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
8
B
B
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
9
A
A
C6
O6
DG
DG
6
6
0.133
0.009
1.237
1.370
N
9
B
B
C6
O6
DG
DG
6
6
0.134
0.009
1.237
1.371
N
10
A
A
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
10
B
B
C6
O6
DG
DG
6
6
0.134
0.009
1.237
1.371
N
11
A
A
C6
O6
DG
DG
6
6
0.135
0.009
1.237
1.372
N
11
B
B
C6
O6
DG
DG
6
6
0.134
0.009
1.237
1.371
N
minimized average structure, model 1
minimized average
DNA duplex containing mispair-aligned O6G-heptylene-O6G interstrand cross-link
1
N
N
1
N
N
2
N
N
covale
1.428
none
A
DG
6
A
O6
DG
6
1_555
B
HP6
101
C
C20
HP6
1_555
covale
1.427
none
B
DG
6
B
O6
DG
6
1_555
B
HP6
101
C
C26
HP6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
11
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
11
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
11
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
10
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
10
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
10
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
9
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
9
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
8
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
8
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
7
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
7
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
5
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
5
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
4
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
4
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
3
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
3
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
2
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
2
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
2
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
DC
1
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
DC
1
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
DC
1
B
N4
DC
1
1_555
DNA
INTERSTRAND CROSS-LINK, DNA
2LZW
PDB
1
2LZW
1
11
2LZW
1
11
2LZW
A
1
1
11
1
11
2LZW
1
11
2LZW
B
1
1
11
BINDING SITE FOR RESIDUE HP6 B 101
B
HP6
101
Software
2
A
DG
6
A
DG
6
2
1_555
B
DG
6
B
DG
6
2
1_555