1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
ALA D 2 - CYS D 3 MODEL 1 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
ALA C 2 - CYS C 3 MODEL 2 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
ALA D 2 - CYS D 3 MODEL 3 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
ALA D 2 - CYS D 3 MODEL 4 OMEGA = 359.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
SER C 1 IS A D-SERINE.
SER D 1 IS A D-SERINE.
Chen, H.
Patel, D.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H11 N O2
129.157
2-METHYL-1-METHYLAMINO-CYCLOPROPANE CARBOXYLIC ACID
L-peptide linking
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
C3 H7 N O3
105.093
D-SERINE
D-peptide linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H7 N O3
189.167
3-HYDROXYQUINALDIC ACID
non-polymer
C4 H9 N O2 S
135.185
N-METHYLCYSTEINE
L-peptide linking
C8 H17 N O2 S
191.291
n
N-METHYL-S-[(1R)-1-METHYLPROPYL]-L-CYSTEINE
L-peptide linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
246
164
10.1006/JMBI.1994.0074
7853395
Solution Structure of a Quinomycin Bisintercalator-DNA Complex.
1995
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2426.617
DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*T)-3')
2
syn
polymer
847.056
QUINOMYCIN
1
syn
polymer
189.167
3-HYDROXYQUINALDIC ACID
2
syn
non-polymer
QUINOMYCIN A, UK-63052
no
no
(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DT)
ACACGTGT
A,B
polydeoxyribonucleotide
no
yes
(DSN)A(NYB)(CPC)(DSN)A(NCY)(CPC)
SAXXSAXX
C
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-20.633
1
20
A
1
B
8
-1.999
A_DA1:DT8_B
1
-17.637
-0.006
-0.134
-0.210
-17.459
1
19
A
2
B
7
-1.260
A_DC2:DG7_B
2
-0.855
0.561
0.357
-0.284
9.576
1
20
A
3
B
6
-2.211
A_DA3:DT6_B
3
-1.872
0.436
0.197
-0.145
-21.667
1
19
A
4
B
5
0.200
A_DC4:DG5_B
4
5.574
0.957
0.495
-0.358
20.252
1
19
A
5
B
4
-4.361
A_DG5:DC4_B
5
1.744
-0.632
0.355
-0.317
-6.019
1
20
A
6
B
3
0.338
A_DT6:DA3_B
6
-0.421
-0.348
0.256
-0.221
16.481
1
19
A
7
B
2
-1.791
A_DG7:DC2_B
7
1.863
-0.474
0.181
-0.281
26.186
1
20
A
8
B
1
-1.220
A_DT8:DA1_B
8
-14.958
-0.025
-0.331
-0.167
3.182
30.174
A
A
1
2
6.511
B
B
8
7
3.271
3.381
-0.570
-0.857
AA_DA1DC2:DG7DT8_BB
1
-1.514
2.915
29.951
-2.327
0.791
1.661
24.502
A
A
2
3
25.384
B
B
7
6
2.364
10.435
-0.102
-1.133
AA_DC2DA3:DT6DG7_BB
2
1.121
-2.727
22.172
-4.761
0.466
7.256
22.863
A
A
3
4
11.035
B
B
6
5
7.172
4.317
0.664
1.223
AA_DA3DC4:DG5DT6_BB
3
4.711
-12.041
21.964
-0.377
2.102
-1.245
3.286
A
A
4
5
-60.162
B
B
5
4
2.438
-2.839
-0.191
2.795
AA_DC4DG5:DC4DG5_BB
4
0.392
-8.303
1.607
60.805
4.988
6.800
23.146
A
A
5
6
5.826
B
B
4
3
6.967
2.267
-0.847
1.216
AA_DG5DT6:DA3DC4_BB
5
-9.428
24.227
21.042
1.291
-5.124
1.957
23.147
A
A
6
7
18.180
B
B
3
2
2.456
7.177
-0.161
-1.231
AA_DT6DG7:DC2DA3_BB
6
0.441
-1.116
22.017
-4.794
0.508
3.022
29.114
A
A
7
8
1.424
B
B
2
1
3.014
0.716
0.756
-0.929
AA_DG7DT8:DA1DC2_BB
7
1.385
-2.757
29.073
-1.993
-1.224
atom_site
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
pdbx_validate_polymer_linkage
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Other
Advisory
Atomic model
Derived calculations
Other
1
0
1995-02-27
1
1
2011-06-14
1
2
2011-07-13
1
3
2011-07-27
1
4
2012-12-12
2
0
2017-11-01
_atom_site.auth_atom_id
_atom_site.label_atom_id
_pdbx_database_status.process_site
_pdbx_struct_assembly.details
_pdbx_struct_assembly.method_details
_pdbx_struct_oper_list.symmetry_operation
SOLUTION STRUCTURE OF D(GACGTC) COMPLEXED WITH TRIOSTIN A
CRYSTAL STRUCTURE OF D(GCGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P6322
CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A
CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632
CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632
CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP C21
CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P42212
SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN A AT POSITIONS 4 AND 8
CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P41212
Y
BNL
1994-09-30
REL
HQU
3-HYDROXYQUINALDIC ACID
CHEMICALLY SYNTHESIZED
sample
CHEMICALLY SYNTHESIZED
STREPTOMYCES
sample
QUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE,
A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS.
HERE, QUINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE
SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) HQU
Antibiotic
QUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE.
BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND
THE C- TERMINI, AND A THIOACETAL BOND BETWEEN
RESIDUES 3 AND 7.
THE TWO HYDROXYQUINOXALINE CHROMOPHORES ARE LINKED
TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
uk63052
Cyclic depsipeptide
all calculated structures submitted
4
4
TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE- RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. TWO INITIAL VELOCITY SEEDS WERE USED FOR EACH STARTING STRUCTURE WHICH YIELDS FOUR DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 0.5 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 120 AND 180 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 R(1/6) FACTOR 0.023 0.024 0.024 0.026 BOND (ANG) 0.011 0.011 0.011 0.011 ANGLES (DEG) 3.616 3.657 3.700 3.725 IMPROPERS (DEG) 0.274 0.285 0.241 0.298
MOLECULAR DYNAMICS, MATRIX RELAXATION
D2O
BRUNGER
refinement
X-PLOR
HQU
0
3
HQU
HQU
0
C
HQU
9
3
HQU
HQU
9
C
DA
1
n
1
DA
1
A
DC
2
n
2
DC
2
A
DA
3
n
3
DA
3
A
DC
4
n
4
DC
4
A
DG
5
n
5
DG
5
A
DT
6
n
6
DT
6
A
DG
7
n
7
DG
7
A
DT
8
n
8
DT
8
A
DA
1
n
1
DA
1
B
DC
2
n
2
DC
2
B
DA
3
n
3
DA
3
B
DC
4
n
4
DC
4
B
DG
5
n
5
DG
5
B
DT
6
n
6
DT
6
B
DG
7
n
7
DG
7
B
DT
8
n
8
DT
8
B
DSN
1
n
1
DSN
1
C
ALA
2
n
2
ALA
2
C
NYB
3
n
3
NYB
3
C
CPC
4
n
4
CPC
4
C
DSN
5
n
5
DSN
5
C
ALA
6
n
6
ALA
6
C
NCY
7
n
7
NCY
7
C
CPC
8
n
8
CPC
8
C
author_defined_assembly
3
trimeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
1
4.29
0.50
113.80
118.09
A
A
A
N7
C8
N9
DA
DA
DA
1
1
1
N
1
-4.24
0.70
108.00
103.76
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
-5.43
0.80
105.90
100.47
A
A
A
O4'
C1'
C2'
DG
DG
DG
5
5
5
N
1
3.17
0.50
113.10
116.27
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
1
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
1
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
-4.44
0.60
122.90
118.46
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
1
2.72
0.30
108.30
111.03
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
3.09
0.50
113.10
116.19
A
A
A
N7
C8
N9
DG
DG
DG
7
7
7
N
1
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
4.16
0.50
113.80
117.96
B
B
B
N7
C8
N9
DA
DA
DA
1
1
1
N
1
3.63
0.60
118.90
122.53
B
B
B
N1
C2
O2
DC
DC
DC
2
2
2
N
1
7.58
1.20
119.70
127.28
B
B
B
C3'
O3'
P
DC
DC
DA
2
2
3
Y
1
2.48
0.30
108.30
110.78
B
B
B
O4'
C1'
N1
DC
DC
DC
4
4
4
N
1
4.14
0.60
118.90
123.04
B
B
B
N1
C2
O2
DC
DC
DC
4
4
4
N
1
-6.55
1.00
110.10
103.55
B
B
B
C1'
O4'
C4'
DT
DT
DT
6
6
6
N
1
4.97
0.30
108.30
113.27
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.72
0.30
108.30
111.02
B
B
B
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
3.02
0.50
113.10
116.12
B
B
B
N7
C8
N9
DG
DG
DG
7
7
7
N
1
2.41
0.30
108.30
110.71
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
2
4.21
0.50
113.80
118.01
A
A
A
N7
C8
N9
DA
DA
DA
1
1
1
N
2
-4.21
0.70
108.00
103.79
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
2
8.56
1.20
119.70
128.26
A
A
A
C3'
O3'
P
DC
DC
DA
2
2
3
Y
2
3.49
0.30
108.30
111.79
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
2
4.06
0.60
118.90
122.96
A
A
A
N1
C2
O2
DC
DC
DC
4
4
4
N
2
3.51
0.50
113.10
116.61
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
2
-2.73
0.40
106.40
103.67
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
2
1.93
0.30
108.30
110.23
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
2
3.28
0.50
113.10
116.38
A
A
A
N7
C8
N9
DG
DG
DG
7
7
7
N
2
-2.43
0.40
106.40
103.97
A
A
A
C8
N9
C4
DG
DG
DG
7
7
7
N
2
3.16
0.30
108.30
111.46
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
2
-3.05
0.50
103.90
100.85
B
B
B
C5
N7
C8
DA
DA
DA
1
1
1
N
2
4.39
0.50
113.80
118.19
B
B
B
N7
C8
N9
DA
DA
DA
1
1
1
N
2
7.24
1.20
115.70
122.94
B
B
B
C5'
C4'
C3'
DC
DC
DC
2
2
2
N
2
-4.29
0.70
108.00
103.71
B
B
B
O4'
C1'
N1
DC
DC
DC
2
2
2
N
2
9.76
1.20
119.70
129.46
B
B
B
C3'
O3'
P
DC
DC
DA
2
2
3
Y
2
4.65
0.30
108.30
112.95
B
B
B
O4'
C1'
N9
DA
DA
DA
3
3
3
N
2
5.39
0.30
108.30
113.69
B
B
B
O4'
C1'
N1
DC
DC
DC
4
4
4
N
2
3.93
0.60
118.90
122.83
B
B
B
N1
C2
O2
DC
DC
DC
4
4
4
N
2
3.63
0.30
108.30
111.93
B
B
B
O4'
C1'
N9
DG
DG
DG
5
5
5
N
2
2.62
0.30
108.30
110.92
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
1.97
0.30
108.30
110.27
B
B
B
O4'
C1'
N9
DG
DG
DG
7
7
7
N
2
3.24
0.50
113.10
116.34
B
B
B
N7
C8
N9
DG
DG
DG
7
7
7
N
2
-2.41
0.40
106.40
103.99
B
B
B
C8
N9
C4
DG
DG
DG
7
7
7
N
2
3.35
0.30
108.30
111.65
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
3
4.17
0.30
108.30
112.47
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
3
-3.08
0.50
103.90
100.82
A
A
A
C5
N7
C8
DA
DA
DA
1
1
1
N
3
4.60
0.50
113.80
118.40
A
A
A
N7
C8
N9
DA
DA
DA
1
1
1
N
3
-4.66
0.70
108.00
103.34
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
3
4.20
0.60
118.90
123.10
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
3
-5.03
0.80
105.90
100.87
A
A
A
O4'
C1'
C2'
DA
DA
DA
3
3
3
N
3
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
3
3.86
0.60
118.90
122.76
A
A
A
N1
C2
O2
DC
DC
DC
4
4
4
N
3
10.01
1.20
119.70
129.71
A
A
A
C3'
O3'
P
DC
DC
DG
4
4
5
Y
3
3.36
0.50
113.10
116.46
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
3
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
3
-3.84
0.60
122.90
119.06
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
3
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
3
3.49
0.50
113.10
116.59
A
A
A
N7
C8
N9
DG
DG
DG
7
7
7
N
3
-2.41
0.40
106.40
103.99
A
A
A
C8
N9
C4
DG
DG
DG
7
7
7
N
3
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
3
4.27
0.30
108.30
112.57
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
3
-3.06
0.50
103.90
100.84
B
B
B
C5
N7
C8
DA
DA
DA
1
1
1
N
3
4.63
0.50
113.80
118.43
B
B
B
N7
C8
N9
DA
DA
DA
1
1
1
N
3
-4.77
0.70
108.00
103.23
B
B
B
O4'
C1'
N1
DC
DC
DC
2
2
2
N
3
4.18
0.60
118.90
123.08
B
B
B
N1
C2
O2
DC
DC
DC
2
2
2
N
3
4.03
0.60
118.90
122.93
B
B
B
N1
C2
O2
DC
DC
DC
4
4
4
N
3
3.16
0.50
113.10
116.26
B
B
B
N7
C8
N9
DG
DG
DG
5
5
5
N
3
-2.73
0.40
106.40
103.67
B
B
B
C8
N9
C4
DG
DG
DG
5
5
5
N
3
3.98
0.30
108.30
112.28
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
-3.98
0.60
122.90
118.92
B
B
B
C6
C5
C7
DT
DT
DT
6
6
6
N
3
2.75
0.30
108.30
111.05
B
B
B
O4'
C1'
N9
DG
DG
DG
7
7
7
N
3
3.54
0.50
113.10
116.64
B
B
B
N7
C8
N9
DG
DG
DG
7
7
7
N
3
-2.45
0.40
106.40
103.95
B
B
B
C8
N9
C4
DG
DG
DG
7
7
7
N
3
2.22
0.30
108.30
110.52
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
4
2.31
0.30
108.30
110.61
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
4
-3.10
0.50
103.90
100.80
A
A
A
C5
N7
C8
DA
DA
DA
1
1
1
N
4
4.44
0.50
113.80
118.24
A
A
A
N7
C8
N9
DA
DA
DA
1
1
1
N
4
7.25
1.20
115.70
122.95
A
A
A
C5'
C4'
C3'
DC
DC
DC
2
2
2
N
4
-7.37
0.70
108.00
100.63
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
4
8.55
1.20
119.70
128.25
A
A
A
C3'
O3'
P
DC
DC
DA
2
2
3
Y
4
4.06
0.30
108.30
112.36
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
4
3.81
0.60
118.90
122.71
A
A
A
N1
C2
O2
DC
DC
DC
4
4
4
N
4
3.38
0.50
113.10
116.48
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
4
-2.77
0.40
106.40
103.63
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
4
-5.35
0.80
105.90
100.55
A
A
A
O4'
C1'
C2'
DT
DT
DT
6
6
6
N
4
7.28
0.30
108.30
115.58
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
4
9.89
1.10
109.80
119.69
A
A
A
C5'
C4'
O4'
DT
DT
DT
8
8
8
N
4
2.48
0.30
108.30
110.78
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
4
4.27
0.50
113.80
118.07
B
B
B
N7
C8
N9
DA
DA
DA
1
1
1
N
4
3.79
0.60
106.00
109.79
B
B
B
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
4
-7.52
0.70
108.00
100.48
B
B
B
O4'
C1'
N1
DC
DC
DC
2
2
2
N
4
7.02
0.30
108.30
115.32
B
B
B
O4'
C1'
N9
DA
DA
DA
3
3
3
N
4
4.55
0.30
108.30
112.85
B
B
B
O4'
C1'
N1
DC
DC
DC
4
4
4
N
4
1.90
0.30
108.30
110.20
B
B
B
O4'
C1'
N9
DG
DG
DG
5
5
5
N
4
3.30
0.50
113.10
116.40
B
B
B
N7
C8
N9
DG
DG
DG
5
5
5
N
4
-2.47
0.40
106.40
103.93
B
B
B
C8
N9
C4
DG
DG
DG
5
5
5
N
4
3.23
0.30
108.30
111.53
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
4
-4.38
0.60
122.90
118.52
B
B
B
C6
C5
C7
DT
DT
DT
6
6
6
N
4
7.14
0.30
108.30
115.44
B
B
B
O4'
C1'
N9
DG
DG
DG
7
7
7
N
4
9.47
1.10
109.80
119.27
B
B
B
C5'
C4'
O4'
DT
DT
DT
8
8
8
N
1
A
A
C8
N9
DA
DA
1
1
-0.048
0.008
1.373
1.325
N
1
A
A
C5
C7
DT
DT
8
8
0.040
0.006
1.496
1.536
N
1
B
B
C5
C7
DT
DT
6
6
0.041
0.006
1.496
1.537
N
1
B
B
C5
C7
DT
DT
8
8
0.039
0.006
1.496
1.535
N
2
A
A
C8
N9
DA
DA
1
1
-0.049
0.008
1.373
1.324
N
2
B
B
C8
N9
DA
DA
1
1
-0.048
0.008
1.373
1.325
N
2
B
B
C5
C7
DT
DT
6
6
0.037
0.006
1.496
1.533
N
2
B
B
C5
C7
DT
DT
8
8
0.038
0.006
1.496
1.534
N
3
A
A
C8
N9
DA
DA
1
1
-0.050
0.008
1.373
1.323
N
3
A
A
C5
C7
DT
DT
8
8
0.040
0.006
1.496
1.536
N
3
B
B
C8
N9
DA
DA
1
1
-0.049
0.008
1.373
1.324
N
3
B
B
C5
C7
DT
DT
8
8
0.041
0.006
1.496
1.537
N
4
A
A
C8
N9
DA
DA
1
1
-0.053
0.008
1.373
1.320
N
4
B
B
C8
N9
DA
DA
1
1
-0.051
0.008
1.373
1.322
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
QUINOMYCIN/DNA Complex, 3-HYDROXYQUINALDIC ACID
SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
covale
1.312
C
HQU
0
D
C
HQU
1_555
C
DSN
1
C
N
DSN
1
1_555
covale
1.314
C
DSN
1
C
C
DSN
1
1_555
C
ALA
2
C
N
ALA
2
1_555
covale
1.386
C
DSN
1
C
OG
DSN
1
1_555
C
CPC
8
C
C
CPC
8
1_555
covale
1.333
C
ALA
2
C
C
ALA
2
1_555
C
NYB
3
C
N
NYB
3
1_555
covale
1.808
C
NYB
3
C
CB
NYB
3
1_555
C
NCY
7
C
SG
NCY
7
1_555
covale
1.332
C
NYB
3
C
C
NYB
3
1_555
C
CPC
4
C
N
CPC
4
1_555
covale
1.394
C
CPC
4
C
C
CPC
4
1_555
C
DSN
5
C
OG
DSN
5
1_555
covale
1.312
C
DSN
5
C
C
DSN
5
1_555
C
ALA
6
C
N
ALA
6
1_555
covale
1.313
C
DSN
5
C
N
DSN
5
1_555
C
HQU
9
E
C
HQU
1_555
covale
1.332
C
ALA
6
C
C
ALA
6
1_555
C
NCY
7
C
N
NCY
7
1_555
covale
1.326
C
NCY
7
C
C
NCY
7
1_555
C
CPC
8
C
N
CPC
8
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
DT
8
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
DT
8
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
7
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
7
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
7
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
6
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
6
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
5
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
5
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
5
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
4
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
4
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
4
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
3
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
3
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
2
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
2
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
2
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
1
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
1
B
N6
DA
1
1_555
DNA/ANTIBIOTIC
BISINTERCALATOR, DEPSIPEPTIDE, QUINOXALINE, THIOACETAL, ANTIBIOTIC, ANTITUMOR, DNA-ANTIBIOTIC COMPLEX
193D
PDB
1
193D
193D
PDB
2
193D
1
8
193D
1
8
193D
A
1
1
8
1
8
193D
1
8
193D
B
1
1
8
1
8
193D
1
8
193D
C
2
1
8
BINDING SITE FOR CHAIN C OF QUINOMYCIN
Software
8
A
DA
3
A
DA
3
8
1_555
A
DC
4
A
DC
4
8
1_555
A
DG
5
A
DG
5
8
1_555
A
DT
6
A
DT
6
8
1_555
B
DA
3
B
DA
3
8
1_555
B
DC
4
B
DC
4
8
1_555
B
DG
5
B
DG
5
8
1_555
B
DT
6
B
DT
6
8
1_555
1
P 1