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1
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3
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4
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4
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5
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5
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6
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6
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6
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6
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6
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6
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6
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6
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6
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6
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7
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7
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13
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13
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13
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13
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13
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13
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13
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13
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13
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1
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1
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1
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1
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1
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1
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1
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1
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1
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N
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1
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1
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O
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1
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1
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1
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1
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C
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1
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C
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2
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2
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O
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2
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2
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O
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2
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2
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C
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2
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O
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2
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C
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2
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O
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2
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C
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2
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C
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2
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N
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2
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C
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2
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O
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2
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N
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2
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C
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O
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C
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C7
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2
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C
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2
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C
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P
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P
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3
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P
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3
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O
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3
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O
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3
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O
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DC
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3
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C
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DC
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3
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C
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DC
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3
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O
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3
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C
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3
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O
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DC
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3
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C
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ATOM
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DC
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3
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C
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3
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N
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3
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C
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3
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O
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N3
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3
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N
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3
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C
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N4
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N4
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3
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N
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ATOM
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3
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C
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C6
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ATOM
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C6
DC
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3
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C
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P
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4
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P
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4
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O
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4
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O
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DA
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4
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O
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ATOM
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DA
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4
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C
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DA
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4
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C
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DA
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4
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O
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DA
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ATOM
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DA
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4
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C
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DA
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DA
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4
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O
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DA
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4
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C
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DA
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ATOM
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DA
2
4
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C
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N9
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N9
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4
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N
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ATOM
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C8
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4
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C
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N7
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ATOM
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N7
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4
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N
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ATOM
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4
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C
0.00
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ATOM
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C6
DA
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4
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C
0.00
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N6
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ATOM
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N6
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4
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N
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N1
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ATOM
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N1
DA
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4
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N
0.00
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C2
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ATOM
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C2
DA
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4
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C
0.00
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N3
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ATOM
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N3
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4
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N
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C4
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ATOM
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C4
DA
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4
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C
0.00
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B
P
DA
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ATOM
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P
DA
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5
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P
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ATOM
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DA
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5
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O
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DA
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ATOM
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DA
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5
1.00
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O
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ATOM
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O5'
DA
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5
1.00
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O
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DA
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ATOM
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C5'
DA
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5
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C
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DA
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ATOM
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C4'
DA
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5
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C
0.00
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DA
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ATOM
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O4'
DA
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5
1.00
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O
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DA
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ATOM
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C3'
DA
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5
1.00
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C
0.00
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DA
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ATOM
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O3'
DA
2
5
1.00
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O
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DA
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ATOM
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C2'
DA
2
5
1.00
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C
0.00
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B
C1'
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ATOM
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C1'
DA
2
5
1.00
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C
0.00
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B
N9
DA
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ATOM
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N9
DA
2
5
1.00
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N
0.00
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B
C8
DA
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ATOM
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C8
DA
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5
1.00
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C
0.00
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N7
DA
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ATOM
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N7
DA
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5
1.00
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N
0.00
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C5
DA
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ATOM
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C5
DA
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5
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C
0.00
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C6
DA
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ATOM
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C6
DA
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5
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C
0.00
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N6
DA
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ATOM
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N6
DA
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5
1.00
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N
0.00
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N1
DA
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ATOM
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N1
DA
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5
1.00
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N
0.00
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B
C2
DA
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ATOM
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C2
DA
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5
1.00
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C
0.00
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B
N3
DA
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ATOM
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N3
DA
2
5
1.00
1
N
0.00
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B
C4
DA
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ATOM
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C4
DA
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5
1.00
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C
0.00
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B
P
DG
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ATOM
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P
DG
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6
1.00
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P
0.00
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B
OP1
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ATOM
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OP1
DG
2
6
1.00
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O
0.00
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2
6
1.00
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O
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19
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DG
2
6
1.00
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O
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ATOM
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DG
2
6
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C
0.00
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DG
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ATOM
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C4'
DG
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6
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C
0.00
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ATOM
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O4'
DG
2
6
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O
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B
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DG
19
ATOM
B
C3'
DG
2
6
1.00
1
C
0.00
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B
O3'
DG
19
ATOM
B
O3'
DG
2
6
1.00
1
O
0.00
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-8.414
B
C2'
DG
19
ATOM
B
C2'
DG
2
6
1.00
1
C
0.00
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B
C1'
DG
19
ATOM
B
C1'
DG
2
6
1.00
1
C
0.00
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B
N9
DG
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ATOM
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N9
DG
2
6
1.00
1
N
0.00
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B
C8
DG
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ATOM
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C8
DG
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6
1.00
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C
0.00
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B
N7
DG
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ATOM
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N7
DG
2
6
1.00
1
N
0.00
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B
C5
DG
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ATOM
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C5
DG
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6
1.00
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C
0.00
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B
C6
DG
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ATOM
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C6
DG
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6
1.00
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C
0.00
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B
O6
DG
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ATOM
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O6
DG
2
6
1.00
1
O
0.00
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B
N1
DG
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ATOM
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N1
DG
2
6
1.00
1
N
0.00
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B
C2
DG
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ATOM
B
C2
DG
2
6
1.00
1
C
0.00
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B
N2
DG
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ATOM
B
N2
DG
2
6
1.00
1
N
0.00
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B
N3
DG
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ATOM
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N3
DG
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6
1.00
1
N
0.00
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B
C4
DG
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ATOM
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C4
DG
2
6
1.00
1
C
0.00
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B
P
DG
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ATOM
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P
DG
2
7
1.00
1
P
0.00
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B
OP1
DG
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ATOM
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OP1
DG
2
7
1.00
1
O
0.00
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B
OP2
DG
20
ATOM
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OP2
DG
2
7
1.00
1
O
0.00
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B
O5'
DG
20
ATOM
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O5'
DG
2
7
1.00
1
O
0.00
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B
C5'
DG
20
ATOM
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C5'
DG
2
7
1.00
1
C
0.00
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B
C4'
DG
20
ATOM
B
C4'
DG
2
7
1.00
1
C
0.00
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B
O4'
DG
20
ATOM
B
O4'
DG
2
7
1.00
1
O
0.00
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B
C3'
DG
20
ATOM
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C3'
DG
2
7
1.00
1
C
0.00
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B
O3'
DG
20
ATOM
B
O3'
DG
2
7
1.00
1
O
0.00
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B
C2'
DG
20
ATOM
B
C2'
DG
2
7
1.00
1
C
0.00
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B
C1'
DG
20
ATOM
B
C1'
DG
2
7
1.00
1
C
0.00
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B
N9
DG
20
ATOM
B
N9
DG
2
7
1.00
1
N
0.00
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B
C8
DG
20
ATOM
B
C8
DG
2
7
1.00
1
C
0.00
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B
N7
DG
20
ATOM
B
N7
DG
2
7
1.00
1
N
0.00
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B
C5
DG
20
ATOM
B
C5
DG
2
7
1.00
1
C
0.00
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B
C6
DG
20
ATOM
B
C6
DG
2
7
1.00
1
C
0.00
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B
O6
DG
20
ATOM
B
O6
DG
2
7
1.00
1
O
0.00
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B
N1
DG
20
ATOM
B
N1
DG
2
7
1.00
1
N
0.00
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B
C2
DG
20
ATOM
B
C2
DG
2
7
1.00
1
C
0.00
-7.205
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B
N2
DG
20
ATOM
B
N2
DG
2
7
1.00
1
N
0.00
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B
N3
DG
20
ATOM
B
N3
DG
2
7
1.00
1
N
0.00
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B
C4
DG
20
ATOM
B
C4
DG
2
7
1.00
1
C
0.00
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B
P
DC
21
ATOM
B
P
DC
2
8
1.00
1
P
0.00
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B
OP1
DC
21
ATOM
B
OP1
DC
2
8
1.00
1
O
0.00
-7.139
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B
OP2
DC
21
ATOM
B
OP2
DC
2
8
1.00
1
O
0.00
-8.321
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B
O5'
DC
21
ATOM
B
O5'
DC
2
8
1.00
1
O
0.00
-9.229
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B
C5'
DC
21
ATOM
B
C5'
DC
2
8
1.00
1
C
0.00
-9.081
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B
C4'
DC
21
ATOM
B
C4'
DC
2
8
1.00
1
C
0.00
-8.043
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B
O4'
DC
21
ATOM
B
O4'
DC
2
8
1.00
1
O
0.00
-9.108
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B
C3'
DC
21
ATOM
B
C3'
DC
2
8
1.00
1
C
0.00
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B
O3'
DC
21
ATOM
B
O3'
DC
2
8
1.00
1
O
0.00
-7.963
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B
C2'
DC
21
ATOM
B
C2'
DC
2
8
1.00
1
C
0.00
-7.635
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B
C1'
DC
21
ATOM
B
C1'
DC
2
8
1.00
1
C
0.00
-6.188
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B
N1
DC
21
ATOM
B
N1
DC
2
8
1.00
1
N
0.00
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B
C2
DC
21
ATOM
B
C2
DC
2
8
1.00
1
C
0.00
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B
O2
DC
21
ATOM
B
O2
DC
2
8
1.00
1
O
0.00
-4.348
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B
N3
DC
21
ATOM
B
N3
DC
2
8
1.00
1
N
0.00
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B
C4
DC
21
ATOM
B
C4
DC
2
8
1.00
1
C
0.00
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B
N4
DC
21
ATOM
B
N4
DC
2
8
1.00
1
N
0.00
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B
C5
DC
21
ATOM
B
C5
DC
2
8
1.00
1
C
0.00
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B
C6
DC
21
ATOM
B
C6
DC
2
8
1.00
1
C
0.00
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B
P
DA
22
ATOM
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P
DA
2
9
1.00
1
P
0.00
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B
OP1
DA
22
ATOM
B
OP1
DA
2
9
1.00
1
O
0.00
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B
OP2
DA
22
ATOM
B
OP2
DA
2
9
1.00
1
O
0.00
-9.947
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B
O5'
DA
22
ATOM
B
O5'
DA
2
9
1.00
1
O
0.00
-10.320
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B
C5'
DA
22
ATOM
B
C5'
DA
2
9
1.00
1
C
0.00
-9.375
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B
C4'
DA
22
ATOM
B
C4'
DA
2
9
1.00
1
C
0.00
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B
O4'
DA
22
ATOM
B
O4'
DA
2
9
1.00
1
O
0.00
-9.050
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B
C3'
DA
22
ATOM
B
C3'
DA
2
9
1.00
1
C
0.00
-9.650
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B
O3'
DA
22
ATOM
B
O3'
DA
2
9
1.00
1
O
0.00
-7.535
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B
C2'
DA
22
ATOM
B
C2'
DA
2
9
1.00
1
C
0.00
-7.118
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B
C1'
DA
22
ATOM
B
C1'
DA
2
9
1.00
1
C
0.00
-5.804
7.785
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B
N9
DA
22
ATOM
B
N9
DA
2
9
1.00
1
N
0.00
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B
C8
DA
22
ATOM
B
C8
DA
2
9
1.00
1
C
0.00
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B
N7
DA
22
ATOM
B
N7
DA
2
9
1.00
1
N
0.00
-3.765
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B
C5
DA
22
ATOM
B
C5
DA
2
9
1.00
1
C
0.00
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B
C6
DA
22
ATOM
B
C6
DA
2
9
1.00
1
C
0.00
-1.569
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B
N6
DA
22
ATOM
B
N6
DA
2
9
1.00
1
N
0.00
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B
N1
DA
22
ATOM
B
N1
DA
2
9
1.00
1
N
0.00
-3.315
7.000
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B
C2
DA
22
ATOM
B
C2
DA
2
9
1.00
1
C
0.00
-4.514
7.450
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B
N3
DA
22
ATOM
B
N3
DA
2
9
1.00
1
N
0.00
-4.683
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B
C4
DA
22
ATOM
B
C4
DA
2
9
1.00
1
C
0.00
-9.425
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B
P
DA
23
ATOM
B
P
DA
2
10
1.00
1
P
0.00
-10.536
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B
OP1
DA
23
ATOM
B
OP1
DA
2
10
1.00
1
O
0.00
-9.154
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B
OP2
DA
23
ATOM
B
OP2
DA
2
10
1.00
1
O
0.00
-8.067
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1.442
B
O5'
DA
23
ATOM
B
O5'
DA
2
10
1.00
1
O
0.00
-8.005
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2.698
B
C5'
DA
23
ATOM
B
C5'
DA
2
10
1.00
1
C
0.00
-6.625
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3.358
B
C4'
DA
23
ATOM
B
C4'
DA
2
10
1.00
1
C
0.00
-5.614
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B
O4'
DA
23
ATOM
B
O4'
DA
2
10
1.00
1
O
0.00
-6.095
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B
C3'
DA
23
ATOM
B
C3'
DA
2
10
1.00
1
C
0.00
-6.067
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4.922
B
O3'
DA
23
ATOM
B
O3'
DA
2
10
1.00
1
O
0.00
-4.740
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B
C2'
DA
23
ATOM
B
C2'
DA
2
10
1.00
1
C
0.00
-4.397
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2.787
B
C1'
DA
23
ATOM
B
C1'
DA
2
10
1.00
1
C
0.00
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B
N9
DA
23
ATOM
B
N9
DA
2
10
1.00
1
N
0.00
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B
C8
DA
23
ATOM
B
C8
DA
2
10
1.00
1
C
0.00
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-0.543
B
N7
DA
23
ATOM
B
N7
DA
2
10
1.00
1
N
0.00
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B
C5
DA
23
ATOM
B
C5
DA
2
10
1.00
1
C
0.00
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B
C6
DA
23
ATOM
B
C6
DA
2
10
1.00
1
C
0.00
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9.205
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B
N6
DA
23
ATOM
B
N6
DA
2
10
1.00
1
N
0.00
-0.104
8.947
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B
N1
DA
23
ATOM
B
N1
DA
2
10
1.00
1
N
0.00
-0.566
9.126
2.306
B
C2
DA
23
ATOM
B
C2
DA
2
10
1.00
1
C
0.00
-1.678
9.742
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B
N3
DA
23
ATOM
B
N3
DA
2
10
1.00
1
N
0.00
-2.370
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1.604
B
C4
DA
23
ATOM
B
C4
DA
2
10
1.00
1
C
0.00
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5.518
B
P
DG
24
ATOM
B
P
DG
2
11
1.00
1
P
0.00
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B
OP1
DG
24
ATOM
B
OP1
DG
2
11
1.00
1
O
0.00
-5.252
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B
OP2
DG
24
ATOM
B
OP2
DG
2
11
1.00
1
O
0.00
-3.847
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5.853
B
O5'
DG
24
ATOM
B
O5'
DG
2
11
1.00
1
O
0.00
-3.611
12.810
6.847
B
C5'
DG
24
ATOM
B
C5'
DG
2
11
1.00
1
C
0.00
-2.117
12.659
7.173
B
C4'
DG
24
ATOM
B
C4'
DG
2
11
1.00
1
C
0.00
-1.411
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6.094
B
O4'
DG
24
ATOM
B
O4'
DG
2
11
1.00
1
O
0.00
-1.464
14.010
7.492
B
C3'
DG
24
ATOM
B
C3'
DG
2
11
1.00
1
C
0.00
-0.489
13.799
8.502
B
O3'
DG
24
ATOM
B
O3'
DG
2
11
1.00
1
O
0.00
-0.795
14.324
6.158
B
C2'
DG
24
ATOM
B
C2'
DG
2
11
1.00
1
C
0.00
-0.428
12.939
5.584
B
C1'
DG
24
ATOM
B
C1'
DG
2
11
1.00
1
C
0.00
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4.112
B
N9
DG
24
ATOM
B
N9
DG
2
11
1.00
1
N
0.00
-1.073
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B
C8
DG
24
ATOM
B
C8
DG
2
11
1.00
1
C
0.00
-0.721
13.188
1.927
B
N7
DG
24
ATOM
B
N7
DG
2
11
1.00
1
N
0.00
0.423
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2.077
B
C5
DG
24
ATOM
B
C5
DG
2
11
1.00
1
C
0.00
1.312
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1.094
B
C6
DG
24
ATOM
B
C6
DG
2
11
1.00
1
C
0.00
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-0.124
B
O6
DG
24
ATOM
B
O6
DG
2
11
1.00
1
O
0.00
2.466
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B
N1
DG
24
ATOM
B
N1
DG
2
11
1.00
1
N
0.00
2.710
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2.987
B
C2
DG
24
ATOM
B
C2
DG
2
11
1.00
1
C
0.00
3.902
10.826
3.382
B
N2
DG
24
ATOM
B
N2
DG
2
11
1.00
1
N
0.00
1.861
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3.921
B
N3
DG
24
ATOM
B
N3
DG
2
11
1.00
1
N
0.00
0.735
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3.407
B
C4
DG
24
ATOM
B
C4
DG
2
11
1.00
1
C
0.00
0.511
14.967
8.996
B
P
DC
25
ATOM
B
P
DC
2
12
1.00
1
P
0.00
0.843
14.717
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B
OP1
DC
25
ATOM
B
OP1
DC
2
12
1.00
1
O
0.00
-0.063
16.272
8.597
B
OP2
DC
25
ATOM
B
OP2
DC
2
12
1.00
1
O
0.00
1.842
14.718
8.111
B
O5'
DC
25
ATOM
B
O5'
DC
2
12
1.00
1
O
0.00
2.775
13.705
8.446
B
C5'
DC
25
ATOM
B
C5'
DC
2
12
1.00
1
C
0.00
4.060
13.832
7.619
B
C4'
DC
25
ATOM
B
C4'
DC
2
12
1.00
1
C
0.00
3.910
13.420
6.275
B
O4'
DC
25
ATOM
B
O4'
DC
2
12
1.00
1
O
0.00
4.722
15.213
7.665
B
C3'
DC
25
ATOM
B
C3'
DC
2
12
1.00
1
C
0.00
5.875
15.248
8.499
B
O3'
DC
25
ATOM
B
O3'
DC
2
12
1.00
1
O
0.00
5.037
15.503
6.215
B
C2'
DC
25
ATOM
B
C2'
DC
2
12
1.00
1
C
0.00
4.701
14.246
5.446
B
C1'
DC
25
ATOM
B
C1'
DC
2
12
1.00
1
C
0.00
3.998
14.521
4.181
B
N1
DC
25
ATOM
B
N1
DC
2
12
1.00
1
N
0.00
4.613
14.280
2.962
B
C2
DC
25
ATOM
B
C2
DC
2
12
1.00
1
C
0.00
5.784
13.922
2.904
B
O2
DC
25
ATOM
B
O2
DC
2
12
1.00
1
O
0.00
3.903
14.465
1.815
B
N3
DC
25
ATOM
B
N3
DC
2
12
1.00
1
N
0.00
2.643
14.917
1.875
B
C4
DC
25
ATOM
B
C4
DC
2
12
1.00
1
C
0.00
1.954
14.970
0.741
B
N4
DC
25
ATOM
B
N4
DC
2
12
1.00
1
N
0.00
2.005
15.214
3.127
B
C5
DC
25
ATOM
B
C5
DC
2
12
1.00
1
C
0.00
2.728
14.980
4.247
B
C6
DC
25
ATOM
B
C6
DC
2
12
1.00
1
C
0.00
6.807
16.573
8.673
B
P
DT
26
ATOM
B
P
DT
2
13
1.00
1
P
0.00
7.654
16.376
9.869
B
OP1
DT
26
ATOM
B
OP1
DT
2
13
1.00
1
O
0.00
5.932
17.762
8.585
B
OP2
DT
26
ATOM
B
OP2
DT
2
13
1.00
1
O
0.00
7.785
16.580
7.375
B
O5'
DT
26
ATOM
B
O5'
DT
2
13
1.00
1
O
0.00
8.726
15.545
7.159
B
C5'
DT
26
ATOM
B
C5'
DT
2
13
1.00
1
C
0.00
9.419
15.631
5.789
B
C4'
DT
26
ATOM
B
C4'
DT
2
13
1.00
1
C
0.00
8.587
15.312
4.680
B
O4'
DT
26
ATOM
B
O4'
DT
2
13
1.00
1
O
0.00
10.156
16.940
5.488
B
C3'
DT
26
ATOM
B
C3'
DT
2
13
1.00
1
C
0.00
11.556
16.788
5.600
B
O3'
DT
26
ATOM
B
O3'
DT
2
13
1.00
1
O
0.00
9.746
17.298
4.060
B
C2'
DT
26
ATOM
B
C2'
DT
2
13
1.00
1
C
0.00
8.939
16.105
3.551
B
C1'
DT
26
ATOM
B
C1'
DT
2
13
1.00
1
C
0.00
7.734
16.514
2.774
B
N1
DT
26
ATOM
B
N1
DT
2
13
1.00
1
N
0.00
7.663
16.251
1.405
B
C2
DT
26
ATOM
B
C2
DT
2
13
1.00
1
C
0.00
8.590
15.763
0.764
B
O2
DT
26
ATOM
B
O2
DT
2
13
1.00
1
O
0.00
6.485
16.608
0.772
B
N3
DT
26
ATOM
B
N3
DT
2
13
1.00
1
N
0.00
5.398
17.214
1.365
B
C4
DT
26
ATOM
B
C4
DT
2
13
1.00
1
C
0.00
4.379
17.440
0.721
B
O4
DT
26
ATOM
B
O4
DT
2
13
1.00
1
O
0.00
5.590
17.559
2.759
B
C5
DT
26
ATOM
B
C5
DT
2
13
1.00
1
C
0.00
4.530
18.368
3.484
B
C7
DT
26
ATOM
B
C7
DT
2
13
1.00
1
C
0.00
6.727
17.196
3.400
B
C6
DT
26
ATOM
B
C6
DT
2
13
1.00
1
C
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