1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Radhakrishnan, I. 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 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 Structure STRUE6 2005 0969-2126 1 135 152 10.1016/0969-2126(93)90028-F 8069626 Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples. 1993 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 115 1615 Solution Structure of an Intramolecular Purine(Dot)Purine(Dot)Pyrimidine DNA Triplex 1993 10.2210/pdb135d/pdb pdb_0000135d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 9552.122 DNA TRIPLEX 1 syn polymer DEOXYRIBONUCLEIC ACID no no (DT)(DC)(DC)(DT)(DC)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DG)(DA)(DG)(DG)(DA)(DT) (DT)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DG)(DG)(DT) TCCTCCTTTTTTAGGAGGATTTTTTGGTGGT A 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 n n n n n -14.402 L A 5 L A 1 -10.408 A_DT5L:DT1L_A 1 -5.362 -2.477 0.755 -1.574 7.295 1 20 A 8 A 7 1.453 A_DA8:DT7_A 2 -7.242 0.032 0.112 -0.162 -1.477 1 19 A 9 A 6 0.949 A_DG9:DC6_A 3 -10.757 -0.683 -0.512 -0.339 -6.828 1 19 A 10 A 5 -2.597 A_DG10:DC5_A 4 -4.426 -0.393 0.176 -0.253 0.152 1 20 A 11 A 4 4.230 A_DA11:DT4_A 5 -13.855 0.003 0.233 -0.221 -7.273 1 19 A 12 A 3 2.937 A_DG12:DC3_A 6 -14.638 -0.755 -0.307 -0.349 -5.824 1 19 A 13 A 2 -3.751 A_DG13:DC2_A 7 -4.620 -0.291 -0.171 -0.175 -14.662 1 20 A 14 A 1 5.462 A_DA14:DT1_A 8 -17.342 -0.005 -1.180 -0.504 -38.856 2 13 L A 6 L A 10 152.402 A_DT6L:DT10L_A 9 -6.894 2.943 -0.849 3.435 3.188 40.398 L A A 5 8 -5.093 L A A 1 7 3.103 -3.506 0.380 -0.871 AA_DT5LDA8:DT7DT1L_AA 1 4.693 -6.818 39.989 -0.881 -0.040 4.175 21.832 A A 8 9 -13.308 A A 7 6 3.936 -4.994 -0.247 -1.603 AA_DA8DG9:DC6DT7_AA 2 1.291 -3.441 21.221 -1.777 1.288 3.561 31.744 A A 9 10 4.399 A A 6 5 3.667 2.401 -0.079 -1.184 AA_DG9DG10:DC5DC6_AA 3 -3.054 5.597 31.512 -2.654 -0.477 3.784 37.011 A A 10 11 -14.419 A A 5 4 3.701 -9.066 1.534 -0.783 AA_DG10DA11:DT4DC5_AA 4 0.053 -0.085 35.921 0.183 -2.408 3.243 21.635 A A 11 12 3.297 A A 4 3 3.735 1.216 -0.767 -1.039 AA_DA11DG12:DC3DT4_AA 5 6.857 -18.592 20.496 -3.298 5.035 3.209 35.858 A A 12 13 -0.085 A A 3 2 3.212 -0.052 0.144 -1.087 AA_DG12DG13:DC2DC3_AA 6 -0.791 1.285 35.850 -1.758 -0.345 3.275 36.450 A A 13 14 15.374 A A 2 1 3.634 9.509 0.665 -1.058 AA_DG13DA14:DT1DC2_AA 7 1.640 -2.651 35.191 -3.110 -0.819 3.526 -23.925 L A A 14 6 3.433 L A A 1 10 3.597 -1.420 -0.115 -1.010 AA_DA14DT6L:DT10LDT1_AA 8 2.395 5.791 -23.764 2.941 0.574 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 MINIMIZED AVERAGE STRUCTURE ENSEMBLE OF 14 STRUCTURES Y BNL 1993-08-30 REL CHEMICALLY SYNTHESIZED sample 1 RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045. RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY BRUNGER refinement X-PLOR T 1 n 1 DT 1 A C 2 n 2 DC 2 A C 3 n 3 DC 3 A T 4 n 4 DT 4 A C 5 n 5 DC 5 A C 6 n 6 DC 6 A T 7 n 7 DT 7 A T 1 n 8 L DT 1 A n 9 L 2 A n 10 L 3 A n 11 L 4 A T 5 n 12 L DT 5 A A 8 n 13 DA 8 A G 9 n 14 DG 9 A G 10 n 15 DG 10 A A 11 n 16 DA 11 A G 12 n 17 DG 12 A G 13 n 18 DG 13 A A 14 n 19 DA 14 A T 6 n 20 L DT 6 A n 21 L 7 A n 22 L 8 A n 23 L 9 A T 10 n 24 L DT 10 A T 15 n 25 DT 15 A G 16 n 26 DG 16 A G 17 n 27 DG 17 A T 18 n 28 DT 18 A G 19 n 29 DG 19 A G 20 n 30 DG 20 A T 21 n 31 DT 21 A author_defined_assembly 1 monomeric 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 L 1 A P DT 5 A P DT 12 1 Y L 1 A OP1 DT 5 A OP1 DT 12 1 Y L 1 A OP2 DT 5 A OP2 DT 12 1 Y L 1 A P DT 10 A P DT 24 1 Y L 1 A OP1 DT 10 A OP1 DT 24 1 Y L 1 A OP2 DT 10 A OP2 DT 24 1 Y L 1 A DT 2 A DT 9 1 Y L 1 A DT 3 A DT 10 1 Y L 1 A DT 4 A DT 11 1 Y L 1 A DT 7 A DT 21 1 Y L 1 A DT 8 A DT 22 1 Y L 1 A DT 9 A DT 23 1 Y 1 -5.92 0.80 105.90 99.98 A A A O4' C1' C2' DT DT DT 1 1 1 N 1 2.63 0.30 108.30 110.93 A A A O4' C1' N1 DT DT DT 1 1 1 N 1 -4.24 0.70 102.20 97.96 A A A C4' C3' C2' DC DC DC 2 2 2 N 1 -5.06 0.80 105.90 100.84 A A A O4' C1' C2' DC DC DC 2 2 2 N 1 4.25 0.60 118.90 123.15 A A A N1 C2 O2 DC DC DC 2 2 2 N 1 -4.28 0.70 121.90 117.62 A A A N3 C2 O2 DC DC DC 2 2 2 N 1 -7.14 0.70 108.00 100.86 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 -7.63 1.00 110.10 102.47 A A A C1' O4' C4' DT DT DT 4 4 4 N 1 -6.88 0.80 105.90 99.02 A A A O4' C1' C2' DT DT DT 4 4 4 N 1 8.49 0.30 108.30 116.79 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 -3.83 0.60 122.30 118.47 A A A N3 C2 O2 DT DT DT 4 4 4 N 1 3.99 0.60 118.90 122.89 A A A N1 C2 O2 DC DC DC 5 5 5 N 1 -7.06 1.00 110.10 103.04 A A A C1' O4' C4' DT DT DT 7 7 7 N 1 -6.39 0.80 105.90 99.51 A A A O4' C1' C2' DT DT DT 7 7 7 N 1 4.48 0.30 108.30 112.78 A A A O4' C1' N1 DT DT DT 7 7 7 N L L L 1 -4.82 0.60 122.90 118.08 A A A C6 C5 C7 DT DT DT 1 1 1 N L L L 1 -3.91 0.60 122.90 118.99 A A A C6 C5 C7 DT DT DT 5 5 5 N 1 1.89 0.30 108.30 110.19 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 -4.92 0.80 105.90 100.98 A A A O4' C1' C2' DG DG DG 10 10 10 N 1 3.22 0.30 108.30 111.52 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 4.64 0.30 108.30 112.94 A A A O4' C1' N9 DA DA DA 11 11 11 N 1 -8.79 0.80 105.90 97.11 A A A O4' C1' C2' DG DG DG 13 13 13 N 1 4.89 0.30 108.30 113.19 A A A O4' C1' N9 DG DG DG 13 13 13 N 1 6.91 0.30 108.30 115.21 A A A O4' C1' N9 DA DA DA 14 14 14 N L L L 1 -8.73 0.70 108.00 99.27 A A A O4' C1' N1 DT DT DT 6 6 6 N L L L 1 4.11 0.60 118.00 122.11 A A A C4 C5 C6 DT DT DT 6 6 6 N L L L 1 -3.75 0.60 122.90 119.15 A A A C6 C5 C7 DT DT DT 6 6 6 N L L L 1 -6.35 1.00 110.10 103.75 A A A C1' O4' C4' DT DT DT 10 10 10 N L L L 1 -5.69 0.80 105.90 100.21 A A A O4' C1' C2' DT DT DT 10 10 10 N L L L 1 3.18 0.30 108.30 111.48 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 -8.37 1.00 110.10 101.73 A A A C1' O4' C4' DT DT DT 15 15 15 N 1 -8.48 0.70 102.20 93.72 A A A C4' C3' C2' DT DT DT 15 15 15 N 1 5.72 0.30 108.30 114.02 A A A O4' C1' N1 DT DT DT 15 15 15 N 1 3.95 0.60 114.60 118.55 A A A N1 C2 N3 DT DT DT 15 15 15 N 1 -3.92 0.60 122.90 118.98 A A A C6 C5 C7 DT DT DT 15 15 15 N 1 -5.14 0.80 105.90 100.76 A A A O4' C1' C2' DG DG DG 16 16 16 N 1 4.35 0.70 110.30 114.65 A A A C1' O4' C4' DG DG DG 17 17 17 N 1 -4.47 0.70 102.20 97.73 A A A C4' C3' C2' DT DT DT 18 18 18 N 1 -3.64 0.60 122.30 118.66 A A A N3 C2 O2 DT DT DT 18 18 18 N 1 -5.84 0.60 122.90 117.06 A A A C6 C5 C7 DT DT DT 18 18 18 N 1 -11.60 1.90 104.00 92.40 A A A O3' P O5' DG DG DG 19 20 20 Y 1 5.62 0.70 110.30 115.92 A A A C1' O4' C4' DG DG DG 20 20 20 N 1 -3.55 0.40 104.50 100.95 A A A O4' C4' C3' DT DT DT 21 21 21 N 1 -6.34 1.00 110.10 103.76 A A A C1' O4' C4' DT DT DT 21 21 21 N 1 -5.22 0.70 102.20 96.98 A A A C4' C3' C2' DT DT DT 21 21 21 N 1 -3.62 0.60 122.90 119.28 A A A C6 C5 C7 DT DT DT 21 21 21 N 1 A A C3' C2' DT DT 1 1 0.078 0.012 1.518 1.596 N 1 A A C2' C1' DT DT 1 1 0.063 0.010 1.519 1.582 N 1 A A C5 C7 DT DT 1 1 0.038 0.006 1.496 1.534 N 1 A A N1 C6 DC DC 2 2 0.040 0.006 1.367 1.407 N 1 A A N1 C6 DC DC 3 3 0.037 0.006 1.367 1.404 N 1 A A C5 C7 DT DT 4 4 0.042 0.006 1.496 1.538 N 1 A A N1 C6 DC DC 5 5 0.047 0.006 1.367 1.414 N 1 A A C5 C7 DT DT 7 7 0.050 0.006 1.496 1.546 N L L 1 A A C5 C7 DT DT 5 5 0.042 0.006 1.496 1.538 N 1 A A C2' C1' DA DA 8 8 0.065 0.010 1.519 1.584 N 1 A A C4' C3' DG DG 9 9 0.117 0.010 1.529 1.646 N 1 A A C3' C2' DG DG 9 9 0.124 0.012 1.518 1.642 N 1 A A C2' C1' DG DG 9 9 0.063 0.010 1.519 1.582 N 1 A A C4' C3' DA DA 11 11 0.061 0.010 1.529 1.590 N 1 A A C3' C2' DA DA 11 11 0.100 0.012 1.518 1.618 N L L 1 A A C3' C2' DT DT 6 6 0.082 0.012 1.518 1.600 N L L 1 A A C2' C1' DT DT 6 6 0.102 0.010 1.519 1.621 N 1 A A C3' C2' DT DT 15 15 0.123 0.012 1.518 1.641 N 1 A A C2' C1' DT DT 15 15 0.063 0.010 1.519 1.582 N 1 A A C2' C1' DG DG 17 17 0.083 0.010 1.519 1.602 N 1 A A C3' C2' DT DT 18 18 0.128 0.012 1.518 1.646 N 1 A A C2' C1' DT DT 18 18 0.111 0.010 1.519 1.630 N 1 A A C5 C7 DT DT 18 18 0.043 0.006 1.496 1.539 N 1 A A C2' C1' DG DG 19 19 0.085 0.010 1.519 1.604 N 1 A A C3' C2' DG DG 20 20 0.077 0.012 1.518 1.595 N 1 A A C2' C1' DG DG 20 20 0.098 0.010 1.519 1.617 N 1 A A C4' C3' DT DT 21 21 0.080 0.010 1.529 1.609 N 1 A A C5 C7 DT DT 21 21 0.041 0.006 1.496 1.537 N model building X-PLOR refinement X-PLOR phasing X-PLOR SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES 1 N N hydrog WATSON-CRICK A DT 1 A N3 DT 1 1_555 A DA 14 A N1 DA 19 1_555 hydrog WATSON-CRICK A DT 1 A O4 DT 1 1_555 A DA 14 A N6 DA 19 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 13 A N1 DG 18 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 13 A O6 DG 18 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 13 A N2 DG 18 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 A DG 12 A N1 DG 17 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 A DG 12 A O6 DG 17 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 A DG 12 A N2 DG 17 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 11 A N1 DA 16 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 11 A N6 DA 16 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 10 A N1 DG 15 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 10 A O6 DG 15 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 10 A N2 DG 15 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 A DG 9 A N1 DG 14 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 A DG 9 A O6 DG 14 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 A DG 9 A N2 DG 14 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 A DA 8 A N1 DA 13 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 A DA 8 A N6 DA 13 1_555 hydrog DT-DT MISPAIR L L A DT 1 A N3 DT 8 1_555 A DT 5 A O4 DT 12 1_555 hydrog REVERSED HOOGSTEEN A DA 8 A N6 DA 13 1_555 A DT 21 A O2 DT 31 1_555 hydrog REVERSED HOOGSTEEN A DA 8 A N7 DA 13 1_555 A DT 21 A N3 DT 31 1_555 hydrog TYPE_7_PAIR A DG 9 A N7 DG 14 1_555 A DG 20 A N1 DG 30 1_555 hydrog TYPE_7_PAIR A DG 9 A O6 DG 14 1_555 A DG 20 A N2 DG 30 1_555 hydrog TYPE_7_PAIR A DG 10 A N7 DG 15 1_555 A DG 19 A N1 DG 29 1_555 hydrog TYPE_7_PAIR A DG 10 A O6 DG 15 1_555 A DG 19 A N2 DG 29 1_555 hydrog REVERSED HOOGSTEEN A DA 11 A N6 DA 16 1_555 A DT 18 A O2 DT 28 1_555 hydrog REVERSED HOOGSTEEN A DA 11 A N7 DA 16 1_555 A DT 18 A N3 DT 28 1_555 hydrog TYPE_7_PAIR A DG 12 A N7 DG 17 1_555 A DG 17 A N1 DG 27 1_555 hydrog TYPE_7_PAIR A DG 12 A O6 DG 17 1_555 A DG 17 A N2 DG 27 1_555 hydrog TYPE_7_PAIR A DG 13 A N7 DG 18 1_555 A DG 16 A N1 DG 26 1_555 hydrog TYPE_7_PAIR A DG 13 A O6 DG 18 1_555 A DG 16 A N2 DG 26 1_555 hydrog REVERSED HOOGSTEEN A DA 14 A N6 DA 19 1_555 A DT 15 A O2 DT 25 1_555 hydrog REVERSED HOOGSTEEN A DA 14 A N7 DA 19 1_555 A DT 15 A N3 DT 25 1_555 hydrog TYPE_13_PAIR L L A DT 6 A N3 DT 20 1_555 A DT 10 A O2 DT 24 1_555 hydrog TYPE_13_PAIR L L A DT 6 A O2 DT 20 1_555 A DT 10 A N3 DT 24 1_555 DNA DNA, TRIPLEX 135D PDB 1 135D 1 21 135D 1 21 135D A 1 1 31 1 P 1