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
C9 H13 N2 O8 P
308.182
y
2'-DEOXYURIDINE-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/pdb2lzv/pdb
pdb_00002lzv
3334.183
DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3')
2
syn
polymer
100.202
HEPTANE
1
syn
non-polymer
no
no
(DC)(DG)(DA)(DA)(DA)(DU)(DT)(DT)(DT)(DC)(DG)
CGAAAUTTTCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
7.521
1
19
A
1
B
11
-11.915
A_DC1:DG11_B
1
17.724
-0.480
-1.124
-0.455
-1.369
1
19
A
2
B
10
3.618
A_DG2:DC10_B
2
-5.625
-0.117
-0.595
-0.253
-1.331
1
20
A
3
B
9
7.713
A_DA3:DT9_B
3
-3.277
-0.189
-0.279
-0.264
7.129
1
20
A
4
B
8
3.253
A_DA4:DT8_B
4
-3.478
0.079
-0.186
-0.300
15.164
1
20
A
5
B
7
-6.125
A_DA5:DT7_B
5
-10.143
-0.062
0.006
-0.145
-15.103
1
20
A
7
B
5
-6.254
A_DT7:DA5_B
6
-9.968
0.066
0.013
-0.143
-7.118
1
20
A
8
B
4
3.231
A_DT8:DA4_B
7
-3.382
-0.065
-0.184
-0.300
1.303
1
20
A
9
B
3
7.490
A_DT9:DA3_B
8
-3.174
0.204
-0.276
-0.272
1.486
1
19
A
10
B
2
3.567
A_DC10:DG2_B
9
-5.664
0.127
-0.581
-0.266
-7.103
1
19
A
11
B
1
-11.829
A_DG11:DC1_B
10
17.822
0.481
-1.104
-0.470
2.524
36.238
A
A
1
2
46.211
B
B
11
10
4.121
25.930
0.956
-0.485
AA_DC1DG2:DC10DG11_BB
1
-2.056
3.664
25.452
-5.181
-1.885
2.642
35.858
A
A
2
3
20.374
B
B
10
9
3.009
12.290
0.303
-0.479
AA_DG2DA3:DT9DC10_BB
2
-3.052
5.060
33.616
-2.353
-0.884
2.675
33.795
A
A
3
4
20.833
B
B
9
8
2.975
11.865
-0.541
-0.395
AA_DA3DA4:DT8DT9_BB
3
-1.031
1.809
31.685
-2.394
0.782
3.014
37.530
A
A
4
5
9.834
B
B
8
7
2.949
6.296
-1.286
0.222
AA_DA4DA5:DT7DT8_BB
4
-2.206
3.445
36.954
-0.410
1.733
3.016
37.603
A
A
7
8
9.845
B
B
5
4
2.950
6.314
1.289
0.218
AA_DT7DT8:DA4DA5_BB
5
2.271
-3.540
37.021
-0.418
-1.729
2.676
33.795
A
A
8
9
20.826
B
B
4
3
2.977
11.861
0.536
-0.397
AA_DT8DT9:DA3DA4_BB
6
1.070
-1.879
31.685
-2.398
-0.768
2.646
35.805
A
A
9
10
20.157
B
B
3
2
3.009
12.147
-0.298
-0.484
AA_DT9DC10:DG2DA3_BB
7
3.020
-5.012
33.613
-2.349
0.874
2.517
36.276
A
A
10
11
46.135
B
B
2
1
4.111
25.922
-0.949
-0.491
AA_DC10DG11:DC1DG2_BB
8
2.105
-3.746
25.511
-5.164
1.880
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
0.5
mM
0.5
mM
0.1
7.5
ambient
298
K
0.1
7.5
ambient
273
K
simulated annealing
1
minimized average structure
0.5 mM DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3'), 100% D2O
100% D2O
0.5 mM DNA (5'-D(*CP*GP*AP*AP*AP*UP*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
DU
6
n
6
DU
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
DU
6
n
6
DU
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
C4
O4
DU
DU
6
6
0.141
0.008
1.232
1.373
N
1
B
B
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
2
A
A
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
2
B
B
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
3
A
A
C4
O4
DU
DU
6
6
0.141
0.008
1.232
1.373
N
3
B
B
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
4
A
A
C4
O4
DU
DU
6
6
0.142
0.008
1.232
1.374
N
4
B
B
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
5
A
A
C4
O4
DU
DU
6
6
0.143
0.008
1.232
1.375
N
5
B
B
C4
O4
DU
DU
6
6
0.143
0.008
1.232
1.375
N
6
A
A
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
6
B
B
C4
O4
DU
DU
6
6
0.141
0.008
1.232
1.373
N
7
A
A
C4
O4
DU
DU
6
6
0.141
0.008
1.232
1.373
N
7
B
B
C4
O4
DU
DU
6
6
0.139
0.008
1.232
1.371
N
8
A
A
C4
O4
DU
DU
6
6
0.141
0.008
1.232
1.373
N
8
B
B
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
9
A
A
C4
O4
DU
DU
6
6
0.142
0.008
1.232
1.374
N
9
B
B
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
10
A
A
C4
O4
DU
DU
6
6
0.141
0.008
1.232
1.373
N
10
B
B
C4
O4
DU
DU
6
6
0.140
0.008
1.232
1.372
N
11
A
A
C4
O4
DU
DU
6
6
0.141
0.008
1.232
1.373
N
11
B
B
C4
O4
DU
DU
6
6
0.141
0.008
1.232
1.373
N
minimized average structure, model 1
minimized average
DNA duplex containing mispair-aligned O4U-heptylene-O4U interstrand cross-link
1
N
N
1
N
N
2
N
N
covale
1.430
none
A
DU
6
A
O4
DU
6
1_555
B
HP6
101
C
C20
HP6
1_555
covale
1.429
none
B
DU
6
B
O4
DU
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
2LZV
PDB
1
2LZV
1
11
2LZV
1
11
2LZV
A
1
1
11
1
11
2LZV
1
11
2LZV
B
1
1
11
BINDING SITE FOR RESIDUE HP6 B 101
B
HP6
101
Software
2
A
DU
6
A
DU
6
2
1_555
B
DU
6
B
DU
6
2
1_555