1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kumar, S. Reed, M.W. Gamper Junior, H.B. Gorn, V.V. Lukhtanov, E.A. Foti, M. West, J. Meyer Junior, R.B. Schweitzer, B.I. 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 C50 H53 N10 O12 P 1016.989 PHOSPHONIC ACID 6-({6-[6-(6-CARBAMOYL-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONYL)-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDOCENE-2-CA RBONYL]-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONL}-AMINO)-HEXYL ESTER 5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL ESTER CDPI3 DNA linking UK Nucleic Acids Res. NARHAD 0389 0305-1048 26 831 838 10.1093/nar/26.3.831 9443977 Solution structure of a highly stable DNA duplex conjugated to a minor groove binder. 1998 10.2210/pdb1aul/pdb pdb_00001aul 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA RESIDUE WITH A HEXAMETHYLENE LINKER 3744.794 DNA (5'-D(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3') 1 syn polymer TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA RESIDUE WITH A HEXAMETHYLENE LINKER 3037.032 DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3') 1 syn polymer no yes (THX)(DG)(DA)(DT)(DT)(DA)(DT)(DC)(DT)(DG) NGATTATCTG A polydeoxyribonucleotide no no (DC)(DA)(DG)(DA)(DT)(DA)(DA)(DT)(DC)(DA) CAGATAATCA B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n 0.709 1 A 2 B 19 26.294 A_DG2:DC19_B 1 7.219 0.840 0.941 0.149 3.244 1 20 A 3 B 18 14.693 A_DA3:DT18_B 2 -20.653 -1.088 0.744 -0.539 -24.666 1 20 A 4 B 17 14.899 A_DT4:DA17_B 3 -11.516 0.144 1.258 -0.460 -9.415 1 20 A 5 B 16 4.457 A_DT5:DA16_B 4 -1.416 -0.283 0.534 -0.212 -1.083 1 20 A 6 B 15 -6.322 A_DA6:DT15_B 5 -6.569 0.467 -0.465 -0.077 16.877 1 20 A 7 B 14 1.194 A_DT7:DA14_B 6 -14.113 -0.175 -0.590 -0.122 7.590 1 19 A 8 B 13 3.882 A_DC8:DG13_B 7 -8.338 0.684 -0.424 -0.242 9.588 1 20 A 9 B 12 -5.710 A_DT9:DA12_B 8 -7.991 0.400 0.176 -0.259 6.923 1 19 A 10 B 11 -3.536 A_DG10:DC11_B 9 1.045 -0.616 0.206 -0.342 2.674 28.852 A A 2 3 14.748 B B 19 18 3.171 7.125 0.023 -0.895 AA_DG2DA3:DT18DC19_BB 1 9.932 -20.557 26.185 -3.287 2.032 4.196 42.791 A A 3 4 13.320 B B 18 17 4.347 9.642 0.458 -0.197 AA_DA3DT4:DA17DT18_BB 2 -0.655 0.905 41.736 -1.545 -0.715 2.913 29.589 A A 4 5 7.458 B B 17 16 3.031 3.791 -0.064 -0.560 AA_DT4DT5:DA16DA17_BB 3 3.245 -6.383 29.174 -1.830 0.755 2.273 35.981 A A 5 6 9.916 B B 16 15 2.762 6.010 -0.531 -1.104 AA_DT5DA6:DT15DA16_BB 4 10.725 -17.696 33.881 -2.467 2.074 2.672 34.716 A A 6 7 10.360 B B 15 14 2.782 6.151 0.506 -0.384 AA_DA6DT7:DA14DT15_BB 5 -0.186 0.313 34.183 -1.435 -0.871 3.115 38.710 A A 7 8 17.651 B B 14 13 3.388 11.535 -0.478 -0.453 AA_DT7DC8:DG13DA14_BB 6 0.019 -0.029 37.015 -2.124 0.723 3.586 37.505 A A 8 9 -9.038 B B 13 12 3.505 -5.778 -0.102 -0.869 AA_DC8DT9:DA12DG13_BB 7 -4.169 6.521 36.846 -0.524 -0.439 2.824 30.325 A A 9 10 4.864 B B 12 11 2.927 2.490 -0.705 -1.955 AA_DT9DG10:DC11DA12_BB 8 -10.600 20.704 28.346 -4.194 -0.595 chem_comp database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Structure summary 1 0 1997-12-24 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _chem_comp.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _struct_conn.pdbx_leaving_atom_flag Y BNL 1997-08-29 REL CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER sample CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER sample LEAST RESTRAINT VIOLATION 6 1 NOESY DQF-COSY HETEROTOCSY TOCSY 6.0 293.15 K CANONICAL B-TYPE STRUCTURE USED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS GENERATING SIX STRUCTURES FROM DIFFERENT RANDOM NUMBER SEEDS. THE SIX STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX REFINEMENT TO GENERATE THE SIX FINAL STRUCTURES. THESE SIX STRUCTURES WERE AVERAGED AND MINIMIZED TO GIVE THE FINAL STRUCTURE PRESENTED HERE. RESTRAINED MOLECULAR DYNAMICS/RELAXATION MATRIX REFINEMENT BRUNGER refinement X-PLOR structure solution X-PLOR 3.1 600 Varian UNITYPLUS THX 1 n 1 THX 1 A G 2 n 2 DG 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A T 5 n 5 DT 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A C 8 n 8 DC 8 A T 9 n 9 DT 9 A G 10 n 10 DG 10 A C 11 n 1 DC 11 B A 12 n 2 DA 12 B G 13 n 3 DG 13 B A 14 n 4 DA 14 B T 15 n 5 DT 15 B A 16 n 6 DA 16 B A 17 n 7 DA 17 B T 18 n 8 DT 18 B C 19 n 9 DC 19 B A 20 n 10 DA 20 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 B O4 H61 THX DA 1 20 1.39 1 A B H3 N1 THX DA 1 20 1.57 1 B DC 19 0.072 SIDE CHAIN 1 B DA 20 0.059 SIDE CHAIN 1 B B O3' P DT DC 18 19 1.75 1 -3.72 0.60 128.60 124.88 A A A C5 C6 O6 DG DG DG 10 10 10 N 1 -3.72 0.60 128.60 124.88 B B B C5 C6 O6 DG DG DG 13 13 13 N 1 A A O3' P THX DG 1 2 0.127 0.012 1.607 1.734 Y 1 A A P O5' DG DG 2 2 0.149 0.010 1.593 1.742 N 1 A A O3' P DG DA 2 3 0.123 0.012 1.607 1.730 Y 1 A A P O5' DA DA 3 3 0.133 0.010 1.593 1.726 N 1 A A N9 C4 DA DA 3 3 -0.042 0.006 1.374 1.332 N 1 A A O3' P DA DT 3 4 0.124 0.012 1.607 1.731 Y 1 A A P O5' DT DT 4 4 0.140 0.010 1.593 1.733 N 1 A A O3' P DT DT 4 5 0.118 0.012 1.607 1.725 Y 1 A A P O5' DT DT 5 5 0.123 0.010 1.593 1.716 N 1 A A O3' P DT DA 5 6 0.115 0.012 1.607 1.722 Y 1 A A P O5' DA DA 6 6 0.134 0.010 1.593 1.727 N 1 A A C3' C2' DA DA 6 6 0.134 0.012 1.518 1.652 N 1 A A O3' P DA DT 6 7 0.122 0.012 1.607 1.729 Y 1 A A P O5' DT DT 7 7 0.137 0.010 1.593 1.730 N 1 A A O3' P DT DC 7 8 0.127 0.012 1.607 1.734 Y 1 A A P O5' DC DC 8 8 0.140 0.010 1.593 1.733 N 1 A A O3' P DC DT 8 9 0.123 0.012 1.607 1.730 Y 1 A A P O5' DT DT 9 9 0.133 0.010 1.593 1.726 N 1 A A C2' C1' DT DT 9 9 0.070 0.010 1.519 1.589 N 1 A A O3' P DT DG 9 10 0.125 0.012 1.607 1.732 Y 1 A A P O5' DG DG 10 10 0.139 0.010 1.593 1.732 N 1 B B C2' C1' DC DC 11 11 0.065 0.010 1.519 1.584 N 1 B B O3' P DC DA 11 12 0.130 0.012 1.607 1.737 Y 1 B B P O5' DA DA 12 12 0.140 0.010 1.593 1.733 N 1 B B O3' P DA DG 12 13 0.119 0.012 1.607 1.726 Y 1 B B P O5' DG DG 13 13 0.134 0.010 1.593 1.727 N 1 B B O3' P DG DA 13 14 0.121 0.012 1.607 1.728 Y 1 B B P O5' DA DA 14 14 0.133 0.010 1.593 1.726 N 1 B B O3' P DA DT 14 15 0.124 0.012 1.607 1.731 Y 1 B B P O5' DT DT 15 15 0.143 0.010 1.593 1.736 N 1 B B O3' P DT DA 15 16 0.121 0.012 1.607 1.728 Y 1 B B P O5' DA DA 16 16 0.137 0.010 1.593 1.730 N 1 B B C2' C1' DA DA 16 16 0.062 0.010 1.519 1.581 N 1 B B O3' P DA DA 16 17 0.116 0.012 1.607 1.723 Y 1 B B P O5' DA DA 17 17 0.125 0.010 1.593 1.718 N 1 B B O3' P DA DT 17 18 0.117 0.012 1.607 1.724 Y 1 B B P O5' DT DT 18 18 0.151 0.010 1.593 1.744 N 1 B B O3' P DT DC 18 19 0.145 0.012 1.607 1.752 Y 1 B B P O5' DC DC 19 19 0.145 0.010 1.593 1.738 N 1 B B C2' C1' DC DC 19 19 0.082 0.010 1.519 1.601 N 1 B B O3' P DC DA 19 20 0.129 0.012 1.607 1.736 Y 1 B B P O5' DA DA 20 20 0.133 0.010 1.593 1.726 N 1 B B C3' C2' DA DA 20 20 0.075 0.012 1.518 1.593 N model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N covale 1.734 one A THX 1 A O3' THX 1 1_555 A DG 2 A P DG 2 1_555 hydrog DG-DC PAIR A DG 2 A N1 DG 2 1_555 B DC 19 B N3 DC 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 18 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 18 B O4 DT 8 1_555 hydrog DT-DA PAIR A DT 4 A O4 DT 4 1_555 B DA 16 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 17 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 17 B N6 DA 7 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 16 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 16 B N6 DA 6 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 15 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 15 B O4 DT 5 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 14 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 14 B N6 DA 4 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 13 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 13 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 13 B N2 DG 3 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 12 B N1 DA 2 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 12 B N6 DA 2 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 11 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 11 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 11 B N4 DC 1 1_555 DNA DEOXYRIBONUCLEIC ACID, CDPI3, DNA 1AUL PDB 1 1AUL 1AUL PDB 2 1AUL 1 10 1AUL 1 10 1AUL A 1 1 10 11 20 1AUL 11 20 1AUL B 2 1 10 1 P 1