0.016026 0.000000 0.005861 0.000000 0.040866 0.000000 0.000000 0.000000 0.029325 0.00000 0.00000 0.00000 Shi, K. Mitra, S.N. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 110.09 90.00 62.400 24.470 36.310 C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H13 N4 O7 P 332.207 y 2'-DEOXYINOSINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer C18 H26 N10 O3 430.464 NETROPSIN non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C N 13 N N N 14 N C N 15 N O N 16 N N N 17 N C N 18 N N N 19 N C N 20 N C N 21 N H N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 N C N 46 R C Y 47 N N Y 48 N C Y 49 N N Y 50 N C N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N Y 56 N C N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N O N 71 N H N 72 N H N 73 N C N 74 N N N 75 N N N 76 N N N 77 N C N 78 N C N 79 N O N 80 N N Y 81 N C Y 82 N C Y 83 N C Y 84 N N N 85 N C Y 86 N C N 87 N C N 88 N O N 89 N N Y 90 N C Y 91 N C Y 92 N C Y 93 N N N 94 N C Y 95 N C N 96 N C N 97 N O N 98 N N N 99 N C N 100 N C N 101 N C N 102 N N N 103 N N N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N doub N 27 N sing N 28 N doub N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing Y 59 N sing Y 60 N sing Y 61 N doub N 62 N sing Y 63 N sing N 64 N sing Y 65 N doub N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N doub N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N doub N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N doub N 87 N sing N 88 N sing N 89 N sing Y 90 N sing Y 91 N doub Y 92 N doub N 93 N sing Y 94 N sing N 95 N sing N 96 N sing Y 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing Y 106 N sing Y 107 N doub Y 108 N doub N 109 N sing Y 110 N sing N 111 N sing N 112 N sing Y 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N doub N 129 N sing N 130 N sing N 131 N sing N 132 N sing DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 58 601 606 10.1107/S0907444902001889 11914483 Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin. 2002 10.2210/pdb1dvl/pdb pdb_00001dvl 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 293 1 IMAGE PLATE RIGAKU RAXIS IIC GRAPHITE SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 2971.911 5'-D(*CP*CP*IP*IP*CP*IP*CP*CP*IP*I)-3' 2 syn polymer 430.464 NETROPSIN 1 syn non-polymer 18.015 water 31 nat water no no (DC)(DC)(DI)(DI)(DC)(DI)(DC)(DC)(DI)(DI) CCIICICCII A,B polydeoxyribonucleotide n n n n n n n n n n 1 2.08 40.81 VAPOR DIFFUSION, HANGING DROP 6.5 4 MM DNA (SINGLE STRAND), 0.008M MGCL2, 0.04 M NA CACODYLATE (PH 6.5), 2MM NETROPSIN, VAPOR DIFFUSION, HANGING DROP at 293K 293 SODIUM CACODYLATE 1 MGCL2 1 MGCL2 2 software chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Refinement description Data collection Database references Derived calculations 1 0 2002-03-29 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 1 4 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2000-01-21 REL REL NT NETROPSIN HOH water NT 25 2 NT NT 25 A HOH 103 3 HOH HOH 103 A HOH 106 3 HOH HOH 106 A HOH 107 3 HOH HOH 107 A HOH 113 3 HOH HOH 113 A HOH 115 3 HOH HOH 115 A HOH 121 3 HOH HOH 121 A HOH 125 3 HOH HOH 125 A HOH 128 3 HOH HOH 128 A HOH 129 3 HOH HOH 129 A HOH 130 3 HOH HOH 130 A HOH 101 3 HOH HOH 101 B HOH 102 3 HOH HOH 102 B HOH 105 3 HOH HOH 105 B HOH 108 3 HOH HOH 108 B HOH 109 3 HOH HOH 109 B HOH 110 3 HOH HOH 110 B HOH 111 3 HOH HOH 111 B HOH 112 3 HOH HOH 112 B HOH 114 3 HOH HOH 114 B HOH 116 3 HOH HOH 116 B HOH 117 3 HOH HOH 117 B HOH 118 3 HOH HOH 118 B HOH 119 3 HOH HOH 119 B HOH 120 3 HOH HOH 120 B HOH 122 3 HOH HOH 122 B HOH 123 3 HOH HOH 123 B HOH 124 3 HOH HOH 124 B HOH 126 3 HOH HOH 126 B HOH 127 3 HOH HOH 127 B HOH 131 3 HOH HOH 131 B HOH 132 3 HOH HOH 132 B C 1 n 1 DC 1 A C 2 n 2 DC 2 A I 3 n 3 DI 3 A I 4 n 4 DI 4 A C 5 n 5 DC 5 A I 6 n 6 DI 6 A C 7 n 7 DC 7 A C 8 n 8 DC 8 A I 9 n 9 DI 9 A I 10 n 10 DI 10 A C 11 n 1 DC 11 B C 12 n 2 DC 12 B I 13 n 3 DI 13 B I 14 n 4 DI 14 B C 15 n 5 DC 15 B I 16 n 6 DI 16 B C 17 n 7 DC 17 B C 18 n 8 DC 18 B I 19 n 9 DI 19 B I 20 n 10 DI 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 N1 N3 DI DC 4 17 2.12 0.2450000 0.1960000 0.1960000 0.1960000 2.4 8.0 1795 10 85.8 RANDOM 1 THROUGHOUT 2.0 MOLECULAR REPLACEMENT 2.4 8.0 31 456 31 394 0 0.013 2.1 18.6 1.7 2.40 1DVL 1795 1.0 0.0370000 1 2.40 2.50 model building X-PLOR refinement X-PLOR 3.1 phasing X-PLOR CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END 1 N N 1 N N 2 N N 3 N N 3 N N DNA DRUG BINDING, DNA 1DVL PDB 1 1DVL 1 10 1DVL 1 10 1DVL A 1 1 10 11 20 1DVL 11 20 1DVL B 1 1 10 BINDING SITE FOR RESIDUE NT A 25 A NT 25 Software 10 A DC 2 A DC 2 10 1_555 A DI 3 A DI 3 10 1_555 A DI 4 A DI 4 10 1_555 A DC 5 A DC 5 10 1_555 A DI 6 A DI 6 10 1_555 B DI 16 B DI 6 10 1_555 B DC 17 B DC 7 10 1_555 B DC 18 B DC 8 10 1_555 B DI 19 B DI 9 10 1_555 B DI 20 B DI 10 10 1_555 5 monoclinic C 1 2 1