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, X.-L.
Hubbard IV, R.B.
Lee, M.
Tao, Z.-F.
Sugiyama, 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
C20 H28 N11 O4 1
486.508
(2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM
TRI-IMIDAZOLE DNA MINOR GROOVE BINDER; AR-1-144
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
Nucleic Acids Res.
NARHAD
0389
0305-1048
27
4183
4190
10.1093/nar/27.21.4183
10518609
Imidazole-imidazole pair as a minor groove recognition motif for T:G mismatched base pairs
1999
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
263
646
655
10.1046/j.1432-1327.1999.00515.x
Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy
1999
10.2210/pdb1cyz/pdb
pdb_00001cyz
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3060.016
5'-D(*GP*AP*AP*CP*TP*GP*GP*TP*TP*C)-3'
2
syn
polymer
486.508
(2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM
2
syn
non-polymer
no
no
(DG)(DA)(DA)(DC)(DT)(DG)(DG)(DT)(DT)(DC)
GAACTGGTTC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
-18.277
1
19
A
1
B
25
2.396
A_DG1:DC25_B
1
-2.432
-0.477
-0.557
-0.029
-16.527
1
20
A
2
B
24
3.147
A_DA2:DT24_B
2
13.974
-0.244
0.025
-0.089
-6.924
1
20
A
3
B
23
6.155
A_DA3:DT23_B
3
-3.205
-0.338
-0.072
-0.139
-7.131
1
19
A
4
B
22
-6.604
A_DC4:DG22_B
4
-18.137
-0.112
0.330
-0.207
5.619
28
A
5
B
21
-3.995
A_DT5:DG21_B
5
-4.908
2.349
0.142
-0.450
-5.421
28
A
6
B
20
-4.016
A_DG6:DT20_B
6
-4.973
-2.334
0.143
-0.461
7.286
1
19
A
7
B
19
-6.619
A_DG7:DC19_B
7
-18.264
0.112
0.333
-0.231
6.917
1
20
A
8
B
18
6.150
A_DT8:DA18_B
8
-3.389
0.314
-0.060
-0.158
16.441
1
20
A
9
B
17
3.135
A_DT9:DA17_B
9
13.795
0.201
0.027
-0.088
18.071
1
19
A
10
B
16
2.398
A_DC10:DG16_B
10
-2.502
0.437
-0.551
0.007
3.439
36.309
A
A
1
2
-5.556
B
B
25
24
3.355
-3.454
-0.074
-1.113
AA_DG1DA2:DT24DC25_BB
1
-2.960
4.762
36.033
-1.283
-0.312
2.523
33.436
A
A
2
3
28.178
B
B
24
23
3.306
15.614
0.809
-0.927
AA_DA2DA3:DT23DT24_BB
2
0.200
-0.361
29.658
-4.058
-1.374
3.329
39.289
A
A
3
4
-19.813
B
B
23
22
3.260
-13.064
-2.033
-0.175
AA_DA3DC4:DG22DT23_BB
3
-4.056
6.152
36.919
1.360
2.521
3.002
34.456
A
A
4
5
2.094
B
B
22
21
2.981
1.240
0.491
0.513
AA_DC4DT5:DG21DG22_BB
4
0.360
-0.609
34.432
0.690
-0.777
3.009
33.787
A
A
5
6
-13.060
B
B
21
20
3.363
-7.530
0.000
1.265
AA_DT5DG6:DT20DG21_BB
5
-0.005
0.009
32.961
3.379
0.000
3.002
34.456
A
A
6
7
2.084
B
B
20
19
2.981
1.234
-0.491
0.513
AA_DG6DG7:DC19DT20_BB
6
-0.364
0.614
34.433
0.690
0.777
3.331
39.297
A
A
7
8
-19.812
B
B
19
18
3.262
-13.065
2.033
-0.175
AA_DG7DT8:DA18DC19_BB
7
4.058
-6.153
36.928
1.360
-2.520
2.523
33.434
A
A
8
9
28.157
B
B
18
17
3.305
15.602
-0.808
-0.927
AA_DT8DT9:DA17DA18_BB
8
-0.202
0.364
29.662
-4.056
1.374
3.439
36.308
A
A
9
10
-5.544
B
B
17
16
3.356
-3.446
0.074
-1.114
AA_DT9DC10:DG16DA17_BB
9
2.962
-4.764
36.032
-1.285
0.312
chem_comp
database_2
entity
pdbx_entity_nonpoly
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
Structure summary
1
0
1999-09-14
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_chem_comp.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1B0S CONTAINS THE NMR STRUCTURE OF GAACCGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX
RCSB
Y
RCSB
1999-08-31
REL
REL
AR1
(2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM
THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR TECHNIQUES WITH BACK NOE CALCULATION
REFINED AVERAGE STRUCTURE
11
1
2D NOESY
TOCSY
NO ADDITIONAL SALT
7
AMBIENT
275
K
NOE-RESTRAINED CONJUGATE GRADIENT REFINEMENT IN X-PLOR; FULL MATRIX RELAXATION
1
refined average structure
1.5 MM DNA DUPLEX; 20 MM PHOSPHATE BUFFER; 100% D2O OR 90% H2O, 10% D2O
MSI
data analysis
Felix
1.1 AND 98
BRUNGER
refinement
X-PLOR
3.851
750
Varian
INOVA
AR1
12
2
AR1
AR1
12
A
AR1
26
2
AR1
AR1
26
B
G
1
n
1
DG
1
A
A
2
n
2
DA
2
A
A
3
n
3
DA
3
A
C
4
n
4
DC
4
A
T
5
n
5
DT
5
A
G
6
n
6
DG
6
A
G
7
n
7
DG
7
A
T
8
n
8
DT
8
A
T
9
n
9
DT
9
A
C
10
n
10
DC
10
A
G
16
n
1
DG
16
B
A
17
n
2
DA
17
B
A
18
n
3
DA
18
B
C
19
n
4
DC
19
B
T
20
n
5
DT
20
B
G
21
n
6
DG
21
B
G
22
n
7
DG
22
B
T
23
n
8
DT
23
B
T
24
n
9
DT
24
B
C
25
n
10
DC
25
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
6.65
0.30
108.30
114.95
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
3.16
0.30
108.30
111.46
A
A
A
O4'
C1'
N9
DA
DA
DA
2
2
2
N
1
-4.99
0.80
105.90
100.91
A
A
A
O4'
C1'
C2'
DA
DA
DA
3
3
3
N
1
4.15
0.30
108.30
112.45
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
4.61
0.60
106.00
110.61
A
A
A
O4'
C4'
C3'
DG
DG
DG
7
7
7
N
1
-5.30
0.80
105.90
100.60
A
A
A
O4'
C1'
C2'
DG
DG
DG
7
7
7
N
1
9.17
0.30
108.30
117.47
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-4.36
0.60
122.90
118.54
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
1
6.66
0.30
108.30
114.96
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
3.18
0.30
108.30
111.48
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
-5.02
0.80
105.90
100.88
B
B
B
O4'
C1'
C2'
DA
DA
DA
18
18
18
N
1
4.13
0.30
108.30
112.43
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
4.65
0.60
106.00
110.65
B
B
B
O4'
C4'
C3'
DG
DG
DG
22
22
22
N
1
-5.34
0.80
105.90
100.56
B
B
B
O4'
C1'
C2'
DG
DG
DG
22
22
22
N
1
9.18
0.30
108.30
117.48
B
B
B
O4'
C1'
N1
DT
DT
DT
23
23
23
N
1
-4.37
0.60
122.90
118.53
B
B
B
C6
C5
C7
DT
DT
DT
24
24
24
N
1
A
A
C5'
C4'
DG
DG
1
1
0.043
0.007
1.512
1.555
N
1
A
A
C5
C7
DT
DT
5
5
0.044
0.006
1.496
1.540
N
1
B
B
C5'
C4'
DG
DG
16
16
0.044
0.007
1.512
1.556
N
1
B
B
C5
C7
DT
DT
20
20
0.044
0.006
1.496
1.540
N
NMR STRUCTURE OF THE GAACTGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX
1
N
N
1
N
N
2
N
N
2
N
N
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
25
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
25
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
25
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
DT
24
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
DT
24
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
23
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
23
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
22
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
22
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
22
B
N2
DG
7
1_555
hydrog
TYPE_28_PAIR
A
DT
5
A
N3
DT
5
1_555
B
DG
21
B
O6
DG
6
1_555
hydrog
TYPE_28_PAIR
A
DT
5
A
O2
DT
5
1_555
B
DG
21
B
N1
DG
6
1_555
hydrog
TYPE_28_PAIR
A
DG
6
A
N1
DG
6
1_555
B
DT
20
B
O2
DT
5
1_555
hydrog
TYPE_28_PAIR
A
DG
6
A
O6
DG
6
1_555
B
DT
20
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
19
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
19
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
19
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
18
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
18
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
17
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
17
B
N6
DA
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
16
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
16
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
16
B
N2
DG
1
1_555
DNA
T:G RECOGNIZED BY IM/IM PAIR IN THE DNA MINOR GROOVE, DNA
1CYZ
PDB
1
1CYZ
1
10
1CYZ
1
10
1CYZ
A
1
1
10
16
25
1CYZ
16
25
1CYZ
B
1
1
10
BINDING SITE FOR RESIDUE AR1 A 12
A
AR1
12
Software
10
BINDING SITE FOR RESIDUE AR1 B 26
B
AR1
26
Software
10
A
DC
4
A
DC
4
10
1_555
A
DT
5
A
DT
5
10
1_555
A
DG
6
A
DG
6
10
1_555
A
DG
7
A
DG
7
10
1_555
A
DT
8
A
DT
8
10
1_555
A
DT
9
A
DT
9
10
1_555
B
DC
19
B
DC
4
10
1_555
B
DG
21
B
DG
6
10
1_555
B
DG
22
B
DG
7
10
1_555
B
AR1
26
D
AR1
10
1_555
A
DC
4
A
DC
4
10
1_555
A
DG
6
A
DG
6
10
1_555
A
DG
7
A
DG
7
10
1_555
A
AR1
12
C
AR1
10
1_555
B
DC
19
B
DC
4
10
1_555
B
DT
20
B
DT
5
10
1_555
B
DG
21
B
DG
6
10
1_555
B
DG
22
B
DG
7
10
1_555
B
DT
23
B
DT
8
10
1_555
B
DT
24
B
DT
9
10
1_555
1
P 1