data_1NJJ # _model_server_result.job_id 9noCMiokoELD5_iF7kypRA _model_server_result.datetime_utc '2024-12-03 11:48:31' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1njj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 1NJJ # _exptl.entry_id 1NJJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 496.552 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GENETICIN _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.03 _cell.angle_gamma 90 _cell.entry_id 1NJJ _cell.length_a 67.818 _cell.length_b 88.54 _cell.length_c 150.445 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NJJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,L,M 1 1 C,D,I,J,K,N,O 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N # _chem_comp.formula 'C20 H40 N4 O10' _chem_comp.formula_weight 496.552 _chem_comp.id GET _chem_comp.mon_nstd_flag . _chem_comp.name GENETICIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms G418 # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C11 O11 GET sing 83 n n C11 C21 GET sing 84 n n C11 O51 GET sing 85 n n C11 H111 GET sing 86 n n O11 C42 GET sing 87 n n C21 N21 GET sing 88 n n C21 C31 GET sing 89 n n C21 H21 GET sing 90 n n N21 H211 GET sing 91 n n N21 H212 GET sing 92 n n C31 O31 GET sing 93 n n C31 C41 GET sing 94 n n C31 H311 GET sing 95 n n O31 H31 GET sing 96 n n C41 O41 GET sing 97 n n C41 C51 GET sing 98 n n C41 H411 GET sing 99 n n O41 H41 GET sing 100 n n C51 O51 GET sing 101 n n C51 C61 GET sing 102 n n C51 H511 GET sing 103 n n C61 O61 GET sing 104 n n C61 C71 GET sing 105 n n C61 H611 GET sing 106 n n O61 H61 GET sing 107 n n C71 H711 GET sing 108 n n C71 H712 GET sing 109 n n C71 H713 GET sing 110 n n C12 N12 GET sing 111 n n C12 C22 GET sing 112 n n C12 C62 GET sing 113 n n C12 H12 GET sing 114 n n N12 H121 GET sing 115 n n N12 H122 GET sing 116 n n C22 C32 GET sing 117 n n C22 H221 GET sing 118 n n C22 H222 GET sing 119 n n C32 N32 GET sing 120 n n C32 C42 GET sing 121 n n C32 H32 GET sing 122 n n N32 H321 GET sing 123 n n N32 H322 GET sing 124 n n C42 C52 GET sing 125 n n C42 H421 GET sing 126 n n C52 O52 GET sing 127 n n C52 C62 GET sing 128 n n C52 H521 GET sing 129 n n O52 H52 GET sing 130 n n C62 O62 GET sing 131 n n C62 H621 GET sing 132 n n O62 C13 GET sing 133 n n C13 C23 GET sing 134 n n C13 O53 GET sing 135 n n C13 H131 GET sing 136 n n C23 O23 GET sing 137 n n C23 C33 GET sing 138 n n C23 H231 GET sing 139 n n O23 H23 GET sing 140 n n C33 N33 GET sing 141 n n C33 C43 GET sing 142 n n C33 H331 GET sing 143 n n N33 C93 GET sing 144 n n N33 H33 GET sing 145 n n C93 H931 GET sing 146 n n C93 H932 GET sing 147 n n C93 H933 GET sing 148 n n C43 O43 GET sing 149 n n C43 C83 GET sing 150 n n C43 C53 GET sing 151 n n O43 H43 GET sing 152 n n C83 H831 GET sing 153 n n C83 H832 GET sing 154 n n C83 H833 GET sing 155 n n C53 O53 GET sing 156 n n C53 H531 GET sing 157 n n C53 H532 GET sing 158 n n # _atom_sites.entry_id 1NJJ _atom_sites.fract_transf_matrix[1][1] 0.014745 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000008 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011294 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006647 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 GET A 1 601 600 GET GFO . F 3 ORX A 1 602 4 ORX PDO . G 2 GET B 1 602 600 GET GFO . H 3 ORX B 1 603 4 ORX PDO . I 2 GET C 1 603 600 GET GFO . J 3 ORX C 1 604 4 ORX PDO . K 3 ORX D 1 426 4 ORX PDO . L 4 HOH A 1 603 9 HOH WAT . L 4 HOH A 2 604 10 HOH WAT . L 4 HOH A 3 605 14 HOH WAT . L 4 HOH A 4 606 20 HOH WAT . L 4 HOH A 5 607 28 HOH WAT . L 4 HOH A 6 608 31 HOH WAT . L 4 HOH A 7 609 48 HOH WAT . L 4 HOH A 8 610 51 HOH WAT . L 4 HOH A 9 611 53 HOH WAT . L 4 HOH A 10 612 55 HOH WAT . L 4 HOH A 11 613 57 HOH WAT . L 4 HOH A 12 614 61 HOH WAT . L 4 HOH A 13 615 65 HOH WAT . L 4 HOH A 14 616 79 HOH WAT . L 4 HOH A 15 617 80 HOH WAT . L 4 HOH A 16 618 88 HOH WAT . L 4 HOH A 17 619 90 HOH WAT . L 4 HOH A 18 620 95 HOH WAT . L 4 HOH A 19 621 97 HOH WAT . L 4 HOH A 20 622 102 HOH WAT . L 4 HOH A 21 623 111 HOH WAT . L 4 HOH A 22 624 114 HOH WAT . L 4 HOH A 23 625 124 HOH WAT . L 4 HOH A 24 626 131 HOH WAT . L 4 HOH A 25 627 145 HOH WAT . L 4 HOH A 26 628 146 HOH WAT . L 4 HOH A 27 629 147 HOH WAT . L 4 HOH A 28 630 148 HOH WAT . L 4 HOH A 29 631 149 HOH WAT . L 4 HOH A 30 632 150 HOH WAT . L 4 HOH A 31 633 154 HOH WAT . L 4 HOH A 32 634 155 HOH WAT . L 4 HOH A 33 635 157 HOH WAT . L 4 HOH A 34 636 164 HOH WAT . L 4 HOH A 35 637 168 HOH WAT . L 4 HOH A 36 638 169 HOH WAT . L 4 HOH A 37 639 174 HOH WAT . L 4 HOH A 38 640 176 HOH WAT . L 4 HOH A 39 641 178 HOH WAT . L 4 HOH A 40 642 185 HOH WAT . L 4 HOH A 41 643 189 HOH WAT . L 4 HOH A 42 644 193 HOH WAT . L 4 HOH A 43 645 200 HOH WAT . L 4 HOH A 44 646 206 HOH WAT . L 4 HOH A 45 647 209 HOH WAT . L 4 HOH A 46 648 213 HOH WAT . L 4 HOH A 47 649 237 HOH WAT . L 4 HOH A 48 650 238 HOH WAT . L 4 HOH A 49 651 239 HOH WAT . L 4 HOH A 50 652 252 HOH WAT . L 4 HOH A 51 653 253 HOH WAT . M 4 HOH B 1 604 3 HOH WAT . M 4 HOH B 2 605 11 HOH WAT . M 4 HOH B 3 606 12 HOH WAT . M 4 HOH B 4 607 17 HOH WAT . M 4 HOH B 5 608 18 HOH WAT . M 4 HOH B 6 609 21 HOH WAT . M 4 HOH B 7 610 22 HOH WAT . M 4 HOH B 8 611 25 HOH WAT . M 4 HOH B 9 612 30 HOH WAT . M 4 HOH B 10 613 44 HOH WAT . M 4 HOH B 11 614 45 HOH WAT . M 4 HOH B 12 615 46 HOH WAT . M 4 HOH B 13 616 52 HOH WAT . M 4 HOH B 14 617 58 HOH WAT . M 4 HOH B 15 618 59 HOH WAT . M 4 HOH B 16 619 64 HOH WAT . M 4 HOH B 17 620 67 HOH WAT . M 4 HOH B 18 621 78 HOH WAT . M 4 HOH B 19 622 84 HOH WAT . M 4 HOH B 20 623 91 HOH WAT . M 4 HOH B 21 624 94 HOH WAT . M 4 HOH B 22 625 113 HOH WAT . M 4 HOH B 23 626 119 HOH WAT . M 4 HOH B 24 627 130 HOH WAT . M 4 HOH B 25 628 142 HOH WAT . M 4 HOH B 26 629 143 HOH WAT . M 4 HOH B 27 630 156 HOH WAT . M 4 HOH B 28 631 175 HOH WAT . M 4 HOH B 29 632 194 HOH WAT . M 4 HOH B 30 633 195 HOH WAT . M 4 HOH B 31 634 196 HOH WAT . M 4 HOH B 32 635 203 HOH WAT . M 4 HOH B 33 636 205 HOH WAT . M 4 HOH B 34 637 217 HOH WAT . M 4 HOH B 35 638 218 HOH WAT . M 4 HOH B 36 639 219 HOH WAT . M 4 HOH B 37 640 220 HOH WAT . M 4 HOH B 38 641 221 HOH WAT . M 4 HOH B 39 642 223 HOH WAT . M 4 HOH B 40 643 232 HOH WAT . M 4 HOH B 41 644 233 HOH WAT . M 4 HOH B 42 645 234 HOH WAT . M 4 HOH B 43 646 235 HOH WAT . M 4 HOH B 44 647 236 HOH WAT . M 4 HOH B 45 648 255 HOH WAT . M 4 HOH B 46 649 256 HOH WAT . M 4 HOH B 47 650 268 HOH WAT . M 4 HOH B 48 651 271 HOH WAT . N 4 HOH C 1 605 1 HOH WAT . N 4 HOH C 2 606 4 HOH WAT . N 4 HOH C 3 607 7 HOH WAT . N 4 HOH C 4 608 8 HOH WAT . N 4 HOH C 5 609 23 HOH WAT . N 4 HOH C 6 610 33 HOH WAT . N 4 HOH C 7 611 34 HOH WAT . N 4 HOH C 8 612 36 HOH WAT . N 4 HOH C 9 613 37 HOH WAT . N 4 HOH C 10 614 40 HOH WAT . N 4 HOH C 11 615 49 HOH WAT . N 4 HOH C 12 616 60 HOH WAT . N 4 HOH C 13 617 62 HOH WAT . N 4 HOH C 14 618 68 HOH WAT . N 4 HOH C 15 619 74 HOH WAT . N 4 HOH C 16 620 76 HOH WAT . N 4 HOH C 17 621 77 HOH WAT . N 4 HOH C 18 622 81 HOH WAT . N 4 HOH C 19 623 101 HOH WAT . N 4 HOH C 20 624 105 HOH WAT . N 4 HOH C 21 625 108 HOH WAT . N 4 HOH C 22 626 121 HOH WAT . N 4 HOH C 23 627 127 HOH WAT . N 4 HOH C 24 628 132 HOH WAT . N 4 HOH C 25 629 133 HOH WAT . N 4 HOH C 26 630 134 HOH WAT . N 4 HOH C 27 631 135 HOH WAT . N 4 HOH C 28 632 136 HOH WAT . N 4 HOH C 29 633 137 HOH WAT . N 4 HOH C 30 634 138 HOH WAT . N 4 HOH C 31 635 139 HOH WAT . N 4 HOH C 32 636 140 HOH WAT . N 4 HOH C 33 637 141 HOH WAT . N 4 HOH C 34 638 160 HOH WAT . N 4 HOH C 35 639 161 HOH WAT . N 4 HOH C 36 640 177 HOH WAT . N 4 HOH C 37 641 179 HOH WAT . N 4 HOH C 38 642 190 HOH WAT . N 4 HOH C 39 643 191 HOH WAT . N 4 HOH C 40 644 198 HOH WAT . N 4 HOH C 41 645 202 HOH WAT . N 4 HOH C 42 646 204 HOH WAT . N 4 HOH C 43 647 212 HOH WAT . N 4 HOH C 44 648 240 HOH WAT . N 4 HOH C 45 649 241 HOH WAT . N 4 HOH C 46 650 242 HOH WAT . N 4 HOH C 47 651 243 HOH WAT . N 4 HOH C 48 652 245 HOH WAT . N 4 HOH C 49 653 247 HOH WAT . N 4 HOH C 50 654 248 HOH WAT . N 4 HOH C 51 655 249 HOH WAT . N 4 HOH C 52 656 250 HOH WAT . N 4 HOH C 53 657 258 HOH WAT . N 4 HOH C 54 658 259 HOH WAT . N 4 HOH C 55 659 260 HOH WAT . N 4 HOH C 56 660 262 HOH WAT . N 4 HOH C 57 661 263 HOH WAT . N 4 HOH C 58 662 270 HOH WAT . N 4 HOH C 59 663 273 HOH WAT . O 4 HOH D 1 427 2 HOH WAT . O 4 HOH D 2 428 6 HOH WAT . O 4 HOH D 3 429 16 HOH WAT . O 4 HOH D 4 430 19 HOH WAT . O 4 HOH D 5 431 32 HOH WAT . O 4 HOH D 6 432 35 HOH WAT . O 4 HOH D 7 433 39 HOH WAT . O 4 HOH D 8 434 42 HOH WAT . O 4 HOH D 9 435 43 HOH WAT . O 4 HOH D 10 436 50 HOH WAT . O 4 HOH D 11 437 54 HOH WAT . O 4 HOH D 12 438 56 HOH WAT . O 4 HOH D 13 439 63 HOH WAT . O 4 HOH D 14 440 69 HOH WAT . O 4 HOH D 15 441 70 HOH WAT . O 4 HOH D 16 442 72 HOH WAT . O 4 HOH D 17 443 75 HOH WAT . O 4 HOH D 18 444 83 HOH WAT . O 4 HOH D 19 445 92 HOH WAT . O 4 HOH D 20 446 93 HOH WAT . O 4 HOH D 21 447 100 HOH WAT . O 4 HOH D 22 448 112 HOH WAT . O 4 HOH D 23 449 118 HOH WAT . O 4 HOH D 24 450 123 HOH WAT . O 4 HOH D 25 451 125 HOH WAT . O 4 HOH D 26 452 126 HOH WAT . O 4 HOH D 27 453 129 HOH WAT . O 4 HOH D 28 454 151 HOH WAT . O 4 HOH D 29 455 152 HOH WAT . O 4 HOH D 30 456 166 HOH WAT . O 4 HOH D 31 457 170 HOH WAT . O 4 HOH D 32 458 173 HOH WAT . O 4 HOH D 33 459 181 HOH WAT . O 4 HOH D 34 460 182 HOH WAT . O 4 HOH D 35 461 184 HOH WAT . O 4 HOH D 36 462 188 HOH WAT . O 4 HOH D 37 463 197 HOH WAT . O 4 HOH D 38 464 199 HOH WAT . O 4 HOH D 39 465 207 HOH WAT . O 4 HOH D 40 466 211 HOH WAT . O 4 HOH D 41 467 214 HOH WAT . O 4 HOH D 42 468 225 HOH WAT . O 4 HOH D 43 469 226 HOH WAT . O 4 HOH D 44 470 228 HOH WAT . O 4 HOH D 45 471 229 HOH WAT . O 4 HOH D 46 472 261 HOH WAT . O 4 HOH D 47 473 266 HOH WAT . O 4 HOH D 48 474 267 HOH WAT . O 4 HOH D 49 475 272 HOH WAT . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C11 GET . . . E 2 76.654 85.365 121.589 1 100.09 ? C11 GET 601 A 1 HETATM 2 O O11 GET . . . E 2 77.334 84.099 121.4 1 100.1 ? O11 GET 601 A 1 HETATM 3 C C21 GET . . . E 2 76.36 85.99 120.206 1 100.05 ? C21 GET 601 A 1 HETATM 4 N N21 GET . . . E 2 77.622 86.175 119.466 1 100.17 ? N21 GET 601 A 1 HETATM 5 C C31 GET . . . E 2 75.644 87.336 120.365 1 100.29 ? C31 GET 601 A 1 HETATM 6 O O31 GET . . . E 2 74.361 87.116 120.963 1 101.29 ? O31 GET 601 A 1 HETATM 7 C C41 GET . . . E 2 76.442 88.317 121.237 1 100.32 ? C41 GET 601 A 1 HETATM 8 O O41 GET . . . E 2 77.506 88.835 120.461 1 100.2 ? O41 GET 601 A 1 HETATM 9 C C51 GET . . . E 2 77.031 87.667 122.536 1 100.01 ? C51 GET 601 A 1 HETATM 10 O O51 GET . . . E 2 77.46 86.254 122.428 1 100.12 ? O51 GET 601 A 1 HETATM 11 C C61 GET . . . E 2 76.027 87.853 123.701 1 99.49 ? C61 GET 601 A 1 HETATM 12 O O61 GET . . . E 2 76.432 87.027 124.846 1 99.36 ? O61 GET 601 A 1 HETATM 13 C C71 GET . . . E 2 75.989 89.334 124.143 1 99.22 ? C71 GET 601 A 1 HETATM 14 C C12 GET . . . E 2 75.775 80.044 120.81 1 102.66 ? C12 GET 601 A 1 HETATM 15 N N12 GET . . . E 2 74.674 79.071 120.931 1 102.71 ? N12 GET 601 A 1 HETATM 16 C C22 GET . . . E 2 76.151 80.558 122.234 1 101.74 ? C22 GET 601 A 1 HETATM 17 C C32 GET . . . E 2 77.088 81.79 122.197 1 101.12 ? C32 GET 601 A 1 HETATM 18 N N32 GET . . . E 2 77.359 82.235 123.572 1 100.64 ? N32 GET 601 A 1 HETATM 19 C C42 GET . . . E 2 76.45 82.944 121.381 1 100.99 ? C42 GET 601 A 1 HETATM 20 C C52 GET . . . E 2 76.188 82.478 119.911 1 101.65 ? C52 GET 601 A 1 HETATM 21 O O52 GET . . . E 2 75.484 83.484 119.189 1 100.95 ? O52 GET 601 A 1 HETATM 22 C C62 GET . . . E 2 75.342 81.18 119.814 1 102.64 ? C62 GET 601 A 1 HETATM 23 O O62 GET . . . E 2 75.457 80.7 118.468 1 103.73 ? O62 GET 601 A 1 HETATM 24 C C13 GET . . . E 2 74.16 80.582 117.877 1 104.64 ? C13 GET 601 A 1 HETATM 25 C C23 GET . . . E 2 73.888 79.161 117.314 1 105.11 ? C23 GET 601 A 1 HETATM 26 O O23 GET . . . E 2 75.033 78.739 116.567 1 105.32 ? O23 GET 601 A 1 HETATM 27 C C33 GET . . . E 2 72.632 79.088 116.372 1 105.73 ? C33 GET 601 A 1 HETATM 28 N N33 GET . . . E 2 71.599 78.274 117.07 1 105.59 ? N33 GET 601 A 1 HETATM 29 C C93 GET . . . E 2 71.859 76.833 116.842 1 105.1 ? C93 GET 601 A 1 HETATM 30 C C43 GET . . . E 2 71.967 80.449 115.859 1 106.04 ? C43 GET 601 A 1 HETATM 31 O O43 GET . . . E 2 70.663 80.535 116.393 1 106.54 ? O43 GET 601 A 1 HETATM 32 C C83 GET . . . E 2 71.854 80.378 114.323 1 106.29 ? C83 GET 601 A 1 HETATM 33 C C53 GET . . . E 2 72.742 81.767 116.235 1 105.45 ? C53 GET 601 A 1 HETATM 34 O O53 GET . . . E 2 74.071 81.532 116.79 1 104.73 ? O53 GET 601 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 34 #