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.
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/pdb141d/pdb
pdb_0000141d
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
-11.086
1
20
A
1
B
26
-4.437
A_DA1:DT26_B
1
-10.093
0.232
-0.284
-0.112
2.778
1
19
A
2
B
25
0.800
A_DG2:DC25_B
2
-7.737
-0.344
0.298
-0.169
-10.888
1
19
A
3
B
24
-2.715
A_DC3:DG24_B
3
-11.083
0.166
0.189
-0.175
-5.813
1
20
A
4
B
23
0.641
A_DT4:DA23_B
4
-9.621
0.028
0.005
-0.166
7.477
1
20
A
5
B
22
-2.283
A_DT5:DA22_B
5
-0.911
-0.083
0.008
-0.113
10.454
1
19
A
6
B
21
-0.184
A_DG6:DC21_B
6
-12.403
-0.452
0.211
-0.218
-9.837
1
19
A
7
B
20
0.697
A_DC7:DG20_B
7
4.591
0.260
0.451
-0.148
-0.723
1
19
A
8
B
19
-0.754
A_DC8:DG19_B
8
-7.507
0.470
0.204
-0.235
-5.239
1
20
A
9
B
18
-2.923
A_DT9:DA18_B
9
-16.456
-0.039
-0.182
-0.166
4.680
1
20
A
10
B
17
0.407
A_DT10:DA17_B
10
-7.193
0.055
-0.091
-0.141
-1.252
1
19
A
11
B
16
-1.461
A_DG11:DC16_B
11
-14.171
-0.424
-0.357
-0.279
-11.729
1
20
A
12
B
15
2.843
A_DA12:DT15_B
12
-1.819
-0.049
-0.220
-0.121
-0.006
1
19
A
13
B
14
-3.067
A_DG13:DC14_B
13
-5.538
-0.278
0.308
-0.216
2.832
28.994
A
A
1
2
-6.881
B
B
26
25
2.815
-3.431
0.464
-0.859
AA_DA1DG2:DC25DT26_BB
1
-3.079
6.175
28.633
-1.058
-1.517
3.253
38.358
A
A
2
3
8.437
B
B
25
24
3.450
5.523
0.109
-1.184
AA_DG2DC3:DG24DC25_BB
2
2.291
-3.501
37.907
-2.513
0.129
3.081
32.626
A
A
3
4
3.900
B
B
24
23
3.080
2.184
0.683
-0.806
AA_DC3DT4:DA23DG24_BB
3
4.077
-7.280
32.305
-1.794
-0.545
3.032
30.274
A
A
4
5
2.906
B
B
23
22
3.064
1.516
-0.174
-0.688
AA_DT4DT5:DA22DA23_BB
4
-1.689
3.237
30.191
-1.603
0.015
2.727
28.947
A
A
5
6
12.497
B
B
22
21
2.982
6.193
0.191
-0.779
AA_DT5DG6:DC21DA22_BB
5
-2.424
4.891
28.188
-2.771
-0.857
3.075
42.886
A
A
6
7
29.182
B
B
21
20
3.892
20.530
-0.282
-0.837
AA_DG6DC7:DG20DC21_BB
6
-1.643
2.335
37.822
-3.474
0.199
2.910
32.865
A
A
7
8
8.527
B
B
20
19
3.024
4.807
-0.048
-0.560
AA_DC7DC8:DG19DG20_BB
7
1.219
-2.162
32.499
-1.741
0.275
2.976
35.851
A
A
8
9
12.287
B
B
19
18
3.129
7.464
0.349
-0.479
AA_DC8DT9:DA18DG19_BB
8
7.059
-11.621
34.394
-1.800
0.399
2.940
34.407
A
A
9
10
5.125
B
B
18
17
3.023
3.027
0.715
-0.394
AA_DT9DT10:DA17DA18_BB
9
-1.720
2.912
34.236
-1.096
-1.453
2.665
33.839
A
A
10
11
30.627
B
B
17
16
3.206
17.034
0.128
-0.253
AA_DT10DG11:DC16DA17_BB
10
2.639
-4.745
29.230
-3.095
0.193
2.863
33.660
A
A
11
12
13.969
B
B
16
15
3.282
8.001
-0.360
-1.509
AA_DG11DA12:DT15DC16_BB
11
-3.619
6.319
32.527
-3.853
0.058
2.919
34.283
A
A
12
13
-3.577
B
B
15
14
2.883
-2.103
-0.121
-0.753
AA_DA12DG13:DC14DT15_BB
12
-3.864
6.571
34.008
-0.983
-0.334
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
2008-03-24
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 (A 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
0.074
SIDE CHAIN
1
A
DG
6
0.074
SIDE CHAIN
1
A
DC
7
0.071
SIDE CHAIN
1
A
DG
11
0.068
SIDE CHAIN
1
B
DC
16
0.096
SIDE CHAIN
1
B
DG
24
0.081
SIDE CHAIN
1
5.78
0.30
108.30
114.08
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
6.09
0.30
108.30
114.39
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
7.67
1.10
109.80
117.47
A
A
A
C5'
C4'
O4'
DT
DT
DT
4
4
4
N
1
2.93
0.30
108.30
111.23
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
4.04
0.60
106.00
110.04
A
A
A
O4'
C4'
C3'
DT
DT
DT
5
5
5
N
1
5.99
0.30
108.30
114.29
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
3.61
0.30
108.30
111.91
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
5.76
0.30
108.30
114.06
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
5.20
0.60
106.00
111.20
A
A
A
O4'
C4'
C3'
DA
DA
DA
12
12
12
N
1
5.16
0.30
108.30
113.46
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
2.42
0.30
108.30
110.72
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
2.61
0.30
108.30
110.91
B
B
B
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
6.78
0.60
106.00
112.78
B
B
B
O4'
C4'
C3'
DC
DC
DC
16
16
16
N
1
8.57
1.10
109.80
118.37
B
B
B
C5'
C4'
O4'
DC
DC
DC
16
16
16
N
1
9.07
1.20
102.50
111.57
B
B
B
C3'
C2'
C1'
DC
DC
DC
16
16
16
N
1
3.77
0.30
108.30
112.07
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
4.71
0.30
108.30
113.01
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
3.79
0.60
106.00
109.79
B
B
B
O4'
C4'
C3'
DA
DA
DA
18
18
18
N
1
5.44
0.30
108.30
113.74
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
3.67
0.60
106.00
109.67
B
B
B
O4'
C4'
C3'
DG
DG
DG
19
19
19
N
1
5.19
0.30
108.30
113.49
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
5.35
0.60
106.00
111.35
B
B
B
O4'
C4'
C3'
DG
DG
DG
20
20
20
N
1
6.87
1.10
109.80
116.67
B
B
B
C5'
C4'
O4'
DG
DG
DG
20
20
20
N
1
4.08
0.60
106.00
110.08
B
B
B
O4'
C4'
C3'
DC
DC
DC
21
21
21
N
1
7.08
1.10
109.80
116.88
B
B
B
C5'
C4'
O4'
DC
DC
DC
21
21
21
N
1
4.55
0.30
108.30
112.85
B
B
B
O4'
C1'
N9
DA
DA
DA
22
22
22
N
1
2.87
0.30
108.30
111.17
B
B
B
O4'
C1'
N9
DA
DA
DA
23
23
23
N
1
5.14
0.30
108.30
113.44
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
3.70
0.60
106.00
109.70
B
B
B
O4'
C4'
C3'
DC
DC
DC
25
25
25
N
1
1.94
0.30
108.30
110.24
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
1
3.18
0.30
108.30
111.48
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
141D
PDB
1
141D
141D
PDB
2
141D
1
13
141D
1
13
141D
A
1
1
13
14
26
141D
14
26
141D
B
2
1
13
1
P 1