1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Mujeeb, A.
Kerwin, S.M.
Kenyon, G.L.
James, T.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
US
Biochemistry
BICHAW
0033
0006-2960
32
13419
13431
10.1021/bi00212a007
8257678
Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra.
1993
10.2210/pdb140d/pdb
pdb_0000140d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3982.596
DNA (5'-D(*AP*GP*CP*TP*TP*GP*CP*CP*TP*TP*GP*AP*G)-3')
1
syn
polymer
3960.600
DNA (5'-D(*CP*TP*CP*AP*AP*GP*GP*CP*AP*AP*GP*CP*T)-3')
1
syn
polymer
no
no
(DA)(DG)(DC)(DT)(DT)(DG)(DC)(DC)(DT)(DT)(DG)(DA)(DG)
AGCTTGCCTTGAG
A
polydeoxyribonucleotide
no
no
(DC)(DT)(DC)(DA)(DA)(DG)(DG)(DC)(DA)(DA)(DG)(DC)(DT)
CTCAAGGCAAGCT
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
n
n
-6.836
1
20
A
1
B
26
-5.661
A_DA1:DT26_B
1
-13.781
0.204
-0.062
-0.100
3.453
1
19
A
2
B
25
0.029
A_DG2:DC25_B
2
-10.858
-0.321
0.451
-0.178
-10.412
1
19
A
3
B
24
-3.284
A_DC3:DG24_B
3
-14.471
0.064
0.343
-0.171
-6.435
1
20
A
4
B
23
0.084
A_DT4:DA23_B
4
-10.834
0.018
0.174
-0.166
8.000
1
20
A
5
B
22
-2.714
A_DT5:DA22_B
5
-3.940
-0.043
0.027
-0.116
9.641
1
19
A
6
B
21
-0.370
A_DG6:DC21_B
6
-13.446
-0.458
0.293
-0.228
-12.606
1
19
A
7
B
20
1.413
A_DC7:DG20_B
7
10.584
0.202
0.658
-0.158
-5.175
1
19
A
8
B
19
-0.358
A_DC8:DG19_B
8
-3.866
0.471
0.440
-0.238
-9.284
1
20
A
9
B
18
-4.437
A_DT9:DA18_B
9
-15.844
-0.227
-0.035
-0.096
1.459
1
20
A
10
B
17
1.478
A_DT10:DA17_B
10
-1.689
-0.054
-0.122
-0.138
2.391
1
19
A
11
B
16
-1.202
A_DG11:DC16_B
11
-9.655
-0.423
-0.322
-0.264
-10.687
1
20
A
12
B
15
3.462
A_DA12:DT15_B
12
-1.074
-0.018
-0.319
-0.109
0.547
1
19
A
13
B
14
-2.556
A_DG13:DC14_B
13
-3.618
-0.278
0.243
-0.203
2.897
31.203
A
A
1
2
-8.504
B
B
26
25
2.898
-4.554
0.493
-0.551
AA_DA1DG2:DC25DT26_BB
1
-2.580
4.818
30.772
-0.251
-1.355
3.341
38.412
A
A
2
3
5.583
B
B
25
24
3.448
3.666
0.092
-0.996
AA_DG2DC3:DG24DC25_BB
2
2.344
-3.570
38.174
-1.990
0.164
3.198
34.888
A
A
3
4
-1.114
B
B
24
23
3.138
-0.666
0.631
-0.504
AA_DC3DT4:DA23DG24_BB
3
4.032
-6.739
34.655
-0.742
-0.458
3.090
32.960
A
A
4
5
-3.735
B
B
23
22
3.069
-2.117
-0.081
-0.413
AA_DT4DT5:DA22DA23_BB
4
-1.184
2.089
32.873
-0.388
-0.048
2.800
29.803
A
A
5
6
11.694
B
B
22
21
3.025
5.967
0.205
-0.690
AA_DT5DG6:DC21DA22_BB
5
-2.784
5.455
29.082
-2.464
-0.922
3.236
43.058
A
A
6
7
30.954
B
B
21
20
4.058
21.751
-0.203
-0.641
AA_DG6DC7:DG20DC21_BB
6
-2.050
2.918
37.332
-3.459
0.033
2.991
34.615
A
A
7
8
16.491
B
B
20
19
3.162
9.685
0.104
-0.197
AA_DC7DC8:DG19DG20_BB
7
1.639
-2.790
33.233
-1.764
0.068
2.942
35.236
A
A
8
9
13.904
B
B
19
18
3.120
8.276
0.365
-0.435
AA_DC8DT9:DA18DG19_BB
8
7.740
-13.004
33.419
-1.891
0.492
3.045
37.453
A
A
9
10
1.446
B
B
18
17
3.006
0.928
1.290
0.190
AA_DT9DT10:DA17DA18_BB
9
1.090
-1.698
37.427
0.184
-1.877
2.541
31.199
A
A
10
11
30.607
B
B
17
16
3.080
15.733
-0.039
-0.263
AA_DT10DG11:DC16DA17_BB
10
1.487
-2.892
26.987
-3.258
0.334
2.744
33.385
A
A
11
12
17.394
B
B
16
15
3.356
9.840
-0.369
-1.705
AA_DG11DA12:DT15DC16_BB
11
-2.865
5.065
31.816
-4.529
0.187
2.953
33.982
A
A
12
13
-4.209
B
B
15
14
2.905
-2.452
-0.166
-0.790
AA_DA12DG13:DC14DT15_BB
12
-3.935
6.754
33.673
-1.000
-0.283
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1994-04-30
1
1
2008-03-03
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
1 STRUCTURE (B DNA USED AS STARTING STRUCTURE)
MINIMIZED AVERAGE STRUCTURE
Y
BNL
1993-09-24
REL
CHEMICALLY SYNTHESIZED
sample
CHEMICALLY SYNTHESIZED
sample
SUGAR PUCKER OF DEOXYRIBOSES HAS BEEN DETERMINED BY SIMULATION OF 2QF-COSY SPECTRA. A LIST OF TORSION ANGLE AND NOE DISTANCE RESTRAINTS IS AVAILABLE FROM THE PROTEIN DATA BANK AS ENTRY R140DMR.
1
ALL COORDINATES AROSE FROM ENERGY MINIMIZED AMBER4 FILES THAT WERE REFORMATTED FOR THE HELIX ANALYSIS PROGRAM CURVES. THEREFORE, ALL HYDROGEN ATOMS WERE REMOVED. THE DEPOSITORS HAVE PROVIDED THREE COORDINATE SETS FOR THIS
STRUCTURE. THE FIRST TWO COORDINATE SETS (PROTEIN DATA
BANK ENTRIES 140D AND 141D) CONTAIN THE RESULTS OF THE
NMR/RESTRAINED MOLECULAR DYNAMICS REFINEMENT WHERE A-DNA
AND B-DNA WERE USED AS STARTING MODELS, RESPECTIVELY. THE
AUTHORS DENOTED THESE STRUCTURES AS RMD-A AND RMD-B,
RESPECTIVELY. THE THIRD COORDINATE SET (PROTEIN DATA BANK
ENTRY 142D) REPRESENTS THE FINAL STRUCTURE, DENOTED
RMD-FINAL BY THE AUTHORS. ALL STRUCTURES WERE DERIVED BY
AVERAGING THE LAST 4 PS OF 30 PS RESTRAINED MD (AMBER4) AND
SUBSEQUENT RESTRAINED ENERGY MINIMIZATION. FIVE RMD RUNS
WERE AVERAGED TO EACH INTERIM STRUCTURE RMD-A AND RMD-B,
DEPENDING ON THE STARTING GEOMETRY. ALL TEN STRUCTURES
WERE AVERAGED, RESTRAINED ENERGY MINIMIZED AND A FINAL 20PS
RMD RUN WAS PERFORMED, THE LAST 4PS OF WHICH, AFTER
AVERAGING AND RESTRAINED ENERGY MINIMIZATION LEAD TO THE FINAL STRUCTURE: RMD-FINAL.
MOLECULAR DYNAMICS, ENERGY MINIMIZATION
structure solution
AMBER4
refinement
AMBER4
A
1
n
1
DA
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
T
4
n
4
DT
4
A
T
5
n
5
DT
5
A
G
6
n
6
DG
6
A
C
7
n
7
DC
7
A
C
8
n
8
DC
8
A
T
9
n
9
DT
9
A
T
10
n
10
DT
10
A
G
11
n
11
DG
11
A
A
12
n
12
DA
12
A
G
13
n
13
DG
13
A
C
14
n
1
DC
14
B
T
15
n
2
DT
15
B
C
16
n
3
DC
16
B
A
17
n
4
DA
17
B
A
18
n
5
DA
18
B
G
19
n
6
DG
19
B
G
20
n
7
DG
20
B
C
21
n
8
DC
21
B
A
22
n
9
DA
22
B
A
23
n
10
DA
23
B
G
24
n
11
DG
24
B
C
25
n
12
DC
25
B
T
26
n
13
DT
26
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
DC
3
0.086
SIDE CHAIN
1
A
DG
6
0.071
SIDE CHAIN
1
A
DC
7
0.085
SIDE CHAIN
1
A
DG
11
0.067
SIDE CHAIN
1
B
DC
16
0.081
SIDE CHAIN
1
B
DA
17
0.068
SIDE CHAIN
1
B
DA
18
0.063
SIDE CHAIN
1
B
DC
21
0.069
SIDE CHAIN
1
B
DG
24
0.092
SIDE CHAIN
1
B
DC
25
0.068
SIDE CHAIN
1
5.14
0.30
108.30
113.44
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
5.85
0.30
108.30
114.15
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
3.63
0.60
106.00
109.63
A
A
A
O4'
C4'
C3'
DT
DT
DT
4
4
4
N
1
7.34
1.10
109.80
117.14
A
A
A
C5'
C4'
O4'
DT
DT
DT
4
4
4
N
1
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
4.21
0.60
106.00
110.21
A
A
A
O4'
C4'
C3'
DT
DT
DT
5
5
5
N
1
5.98
0.30
108.30
114.28
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
3.92
0.30
108.30
112.22
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
2.29
0.30
108.30
110.59
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
5.79
0.30
108.30
114.09
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
5.14
0.60
106.00
111.14
A
A
A
O4'
C4'
C3'
DA
DA
DA
12
12
12
N
1
5.10
0.30
108.30
113.40
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
2.24
0.30
108.30
110.54
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
3.12
0.30
108.30
111.42
B
B
B
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
6.75
0.60
106.00
112.75
B
B
B
O4'
C4'
C3'
DC
DC
DC
16
16
16
N
1
8.75
1.10
109.80
118.55
B
B
B
C5'
C4'
O4'
DC
DC
DC
16
16
16
N
1
8.24
1.20
102.50
110.74
B
B
B
C3'
C2'
C1'
DC
DC
DC
16
16
16
N
1
3.63
0.30
108.30
111.93
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
5.75
0.30
108.30
114.05
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
4.69
0.30
108.30
112.99
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
4.51
0.30
108.30
112.81
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
5.25
0.60
106.00
111.25
B
B
B
O4'
C4'
C3'
DG
DG
DG
20
20
20
N
1
4.35
0.60
106.00
110.35
B
B
B
O4'
C4'
C3'
DC
DC
DC
21
21
21
N
1
6.96
1.10
109.80
116.76
B
B
B
C5'
C4'
O4'
DC
DC
DC
21
21
21
N
1
4.13
0.30
108.30
112.43
B
B
B
O4'
C1'
N9
DA
DA
DA
22
22
22
N
1
1.88
0.30
108.30
110.18
B
B
B
O4'
C1'
N9
DA
DA
DA
23
23
23
N
1
4.75
0.30
108.30
113.05
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
3.66
0.60
106.00
109.66
B
B
B
O4'
C4'
C3'
DC
DC
DC
25
25
25
N
1
1.99
0.30
108.30
110.29
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
1
3.28
0.30
108.30
111.58
B
B
B
O4'
C1'
N1
DT
DT
DT
26
26
26
N
refinement
AMBER
SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED FROM TWO-DIMENSIONAL NMR SPECTRA
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
DT
26
B
N3
DT
13
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
DT
26
B
O4
DT
13
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
25
B
N3
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
25
B
O2
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
25
B
N4
DC
12
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
24
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
24
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
24
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
23
B
N1
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
23
B
N6
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
22
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
22
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
21
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
21
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
21
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
DG
20
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
20
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
20
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
19
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
19
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
19
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
18
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
18
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
10
A
N3
DT
10
1_555
B
DA
17
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
10
A
O4
DT
10
1_555
B
DA
17
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
DC
16
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
DC
16
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
DC
16
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N1
DA
12
1_555
B
DT
15
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N6
DA
12
1_555
B
DT
15
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DG
13
A
N1
DG
13
1_555
B
DC
14
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
13
A
N2
DG
13
1_555
B
DC
14
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
13
A
O6
DG
13
1_555
B
DC
14
B
N4
DC
1
1_555
DNA
DNA, DOUBLE HELIX, CONSERVED SEQUENCE OF HIV-1 GENOME
140D
PDB
1
140D
140D
PDB
2
140D
1
13
140D
1
13
140D
A
1
1
13
14
26
140D
14
26
140D
B
2
1
13
1
P 1