data_5LMZ # _model_server_result.job_id aQ-WTUdSu1QfviyxIWuzAw _model_server_result.datetime_utc '2024-11-05 01:02:03' _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 5lmz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 5LMZ # _exptl.entry_id 5LMZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 266.253 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-DEAZA-ADENOSINE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5LMZ _cell.length_a 125.92 _cell.length_b 125.92 _cell.length_c 125.92 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LMZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_454 -z-1/2,-x,y-1/2 0 0 -1 -1 0 0 0 1 0 -62.96 0 -62.96 3 'crystal symmetry operation' 10_554 -y,z+1/2,-x-1/2 0 -1 0 0 0 1 -1 0 0 0 62.96 -62.96 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N N # _chem_comp.formula 'C11 H14 N4 O4' _chem_comp.formula_weight 266.253 _chem_comp.id 1DA _chem_comp.mon_nstd_flag . _chem_comp.name 1-DEAZA-ADENOSINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O5' C5' 1DA sing 1 n n O5' HO5' 1DA sing 2 n n C5' C4' 1DA sing 3 n n C5' "H5'1" 1DA sing 4 n n C5' "H5'2" 1DA sing 5 n n C4' O4' 1DA sing 6 n n C4' C3' 1DA sing 7 n n C4' H4' 1DA sing 8 n n O4' C1' 1DA sing 9 n n C3' O3' 1DA sing 10 n n C3' C2' 1DA sing 11 n n C3' H3' 1DA sing 12 n n O3' HO3' 1DA sing 13 n n C2' O2' 1DA sing 14 n n C2' C1' 1DA sing 15 n n C2' H2' 1DA sing 16 n n O2' HO2' 1DA sing 17 n n C1' N9 1DA sing 18 n n C1' H1' 1DA sing 19 n n N9 C8 1DA sing 20 n y N9 C4 1DA sing 21 n y C8 N7 1DA doub 22 n y C8 H8 1DA sing 23 n n N7 C5 1DA sing 24 n y C5 C6 1DA sing 25 n y C5 C4 1DA doub 26 n y C6 N6 1DA sing 27 n n C6 C1 1DA doub 28 n y N6 HN61 1DA sing 29 n n N6 HN62 1DA sing 30 n n C1 C2 1DA sing 31 n y C1 H1 1DA sing 32 n n C2 N3 1DA doub 33 n y C2 H2 1DA sing 34 n n N3 C4 1DA sing 35 n y # _atom_sites.entry_id 5LMZ _atom_sites.fract_transf_matrix[1][1] 0.007942 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007942 _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] 0.007942 _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 C 2 1DA A 1 301 2 1DA 1DA . D 3 CL A 1 302 1 CL CL . E 4 GOL A 1 303 4 GOL GOL . F 2 1DA B 1 301 1 1DA 1DA . G 3 CL B 1 302 2 CL CL . H 3 CL B 1 303 3 CL CL . I 4 GOL B 1 304 5 GOL GOL . J 5 HOH A 1 401 212 HOH HOH . J 5 HOH A 2 402 122 HOH HOH . J 5 HOH A 3 403 34 HOH HOH . J 5 HOH A 4 404 161 HOH HOH . J 5 HOH A 5 405 149 HOH HOH . J 5 HOH A 6 406 221 HOH HOH . J 5 HOH A 7 407 80 HOH HOH . J 5 HOH A 8 408 119 HOH HOH . J 5 HOH A 9 409 5 HOH HOH . J 5 HOH A 10 410 178 HOH HOH . J 5 HOH A 11 411 59 HOH HOH . J 5 HOH A 12 412 45 HOH HOH . J 5 HOH A 13 413 131 HOH HOH . J 5 HOH A 14 414 160 HOH HOH . J 5 HOH A 15 415 11 HOH HOH . J 5 HOH A 16 416 171 HOH HOH . J 5 HOH A 17 417 156 HOH HOH . J 5 HOH A 18 418 1 HOH HOH . J 5 HOH A 19 419 40 HOH HOH . J 5 HOH A 20 420 213 HOH HOH . J 5 HOH A 21 421 23 HOH HOH . J 5 HOH A 22 422 83 HOH HOH . J 5 HOH A 23 423 141 HOH HOH . J 5 HOH A 24 424 73 HOH HOH . J 5 HOH A 25 425 52 HOH HOH . J 5 HOH A 26 426 71 HOH HOH . J 5 HOH A 27 427 38 HOH HOH . J 5 HOH A 28 428 25 HOH HOH . J 5 HOH A 29 429 74 HOH HOH . J 5 HOH A 30 430 72 HOH HOH . J 5 HOH A 31 431 22 HOH HOH . J 5 HOH A 32 432 57 HOH HOH . J 5 HOH A 33 433 81 HOH HOH . J 5 HOH A 34 434 88 HOH HOH . J 5 HOH A 35 435 19 HOH HOH . J 5 HOH A 36 436 26 HOH HOH . J 5 HOH A 37 437 126 HOH HOH . J 5 HOH A 38 438 158 HOH HOH . J 5 HOH A 39 439 139 HOH HOH . J 5 HOH A 40 440 164 HOH HOH . J 5 HOH A 41 441 108 HOH HOH . J 5 HOH A 42 442 129 HOH HOH . J 5 HOH A 43 443 7 HOH HOH . J 5 HOH A 44 444 10 HOH HOH . J 5 HOH A 45 445 56 HOH HOH . J 5 HOH A 46 446 203 HOH HOH . J 5 HOH A 47 447 132 HOH HOH . J 5 HOH A 48 448 50 HOH HOH . J 5 HOH A 49 449 154 HOH HOH . J 5 HOH A 50 450 130 HOH HOH . J 5 HOH A 51 451 121 HOH HOH . J 5 HOH A 52 452 109 HOH HOH . J 5 HOH A 53 453 37 HOH HOH . J 5 HOH A 54 454 192 HOH HOH . J 5 HOH A 55 455 12 HOH HOH . J 5 HOH A 56 456 112 HOH HOH . J 5 HOH A 57 457 99 HOH HOH . J 5 HOH A 58 458 6 HOH HOH . J 5 HOH A 59 459 15 HOH HOH . J 5 HOH A 60 460 46 HOH HOH . J 5 HOH A 61 461 60 HOH HOH . J 5 HOH A 62 462 117 HOH HOH . J 5 HOH A 63 463 84 HOH HOH . J 5 HOH A 64 464 105 HOH HOH . J 5 HOH A 65 465 66 HOH HOH . J 5 HOH A 66 466 98 HOH HOH . J 5 HOH A 67 467 118 HOH HOH . J 5 HOH A 68 468 48 HOH HOH . J 5 HOH A 69 469 76 HOH HOH . J 5 HOH A 70 470 58 HOH HOH . J 5 HOH A 71 471 128 HOH HOH . J 5 HOH A 72 472 87 HOH HOH . J 5 HOH A 73 473 78 HOH HOH . J 5 HOH A 74 474 136 HOH HOH . J 5 HOH A 75 475 31 HOH HOH . J 5 HOH A 76 476 198 HOH HOH . J 5 HOH A 77 477 152 HOH HOH . J 5 HOH A 78 478 114 HOH HOH . J 5 HOH A 79 479 91 HOH HOH . J 5 HOH A 80 480 35 HOH HOH . J 5 HOH A 81 481 133 HOH HOH . J 5 HOH A 82 482 54 HOH HOH . J 5 HOH A 83 483 208 HOH HOH . J 5 HOH A 84 484 111 HOH HOH . J 5 HOH A 85 485 29 HOH HOH . J 5 HOH A 86 486 179 HOH HOH . J 5 HOH A 87 487 183 HOH HOH . J 5 HOH A 88 488 209 HOH HOH . J 5 HOH A 89 489 140 HOH HOH . J 5 HOH A 90 490 218 HOH HOH . J 5 HOH A 91 491 33 HOH HOH . J 5 HOH A 92 492 175 HOH HOH . J 5 HOH A 93 493 145 HOH HOH . J 5 HOH A 94 494 92 HOH HOH . J 5 HOH A 95 495 150 HOH HOH . J 5 HOH A 96 496 142 HOH HOH . J 5 HOH A 97 497 185 HOH HOH . J 5 HOH A 98 498 159 HOH HOH . J 5 HOH A 99 499 188 HOH HOH . J 5 HOH A 100 500 153 HOH HOH . J 5 HOH A 101 501 199 HOH HOH . J 5 HOH A 102 502 169 HOH HOH . J 5 HOH A 103 503 207 HOH HOH . J 5 HOH A 104 504 138 HOH HOH . J 5 HOH A 105 505 223 HOH HOH . J 5 HOH A 106 506 197 HOH HOH . J 5 HOH A 107 507 93 HOH HOH . J 5 HOH A 108 508 196 HOH HOH . J 5 HOH A 109 509 146 HOH HOH . J 5 HOH A 110 510 137 HOH HOH . J 5 HOH A 111 511 206 HOH HOH . J 5 HOH A 112 512 201 HOH HOH . J 5 HOH A 113 513 190 HOH HOH . J 5 HOH A 114 514 225 HOH HOH . K 5 HOH B 1 401 163 HOH HOH . K 5 HOH B 2 402 205 HOH HOH . K 5 HOH B 3 403 102 HOH HOH . K 5 HOH B 4 404 3 HOH HOH . K 5 HOH B 5 405 27 HOH HOH . K 5 HOH B 6 406 113 HOH HOH . K 5 HOH B 7 407 186 HOH HOH . K 5 HOH B 8 408 115 HOH HOH . K 5 HOH B 9 409 165 HOH HOH . K 5 HOH B 10 410 96 HOH HOH . K 5 HOH B 11 411 100 HOH HOH . K 5 HOH B 12 412 55 HOH HOH . K 5 HOH B 13 413 53 HOH HOH . K 5 HOH B 14 414 106 HOH HOH . K 5 HOH B 15 415 166 HOH HOH . K 5 HOH B 16 416 124 HOH HOH . K 5 HOH B 17 417 49 HOH HOH . K 5 HOH B 18 418 104 HOH HOH . K 5 HOH B 19 419 43 HOH HOH . K 5 HOH B 20 420 90 HOH HOH . K 5 HOH B 21 421 77 HOH HOH . K 5 HOH B 22 422 13 HOH HOH . K 5 HOH B 23 423 147 HOH HOH . K 5 HOH B 24 424 155 HOH HOH . K 5 HOH B 25 425 62 HOH HOH . K 5 HOH B 26 426 16 HOH HOH . K 5 HOH B 27 427 226 HOH HOH . K 5 HOH B 28 428 69 HOH HOH . K 5 HOH B 29 429 125 HOH HOH . K 5 HOH B 30 430 20 HOH HOH . K 5 HOH B 31 431 67 HOH HOH . K 5 HOH B 32 432 41 HOH HOH . K 5 HOH B 33 433 4 HOH HOH . K 5 HOH B 34 434 174 HOH HOH . K 5 HOH B 35 435 95 HOH HOH . K 5 HOH B 36 436 32 HOH HOH . K 5 HOH B 37 437 97 HOH HOH . K 5 HOH B 38 438 162 HOH HOH . K 5 HOH B 39 439 82 HOH HOH . K 5 HOH B 40 440 222 HOH HOH . K 5 HOH B 41 441 89 HOH HOH . K 5 HOH B 42 442 24 HOH HOH . K 5 HOH B 43 443 30 HOH HOH . K 5 HOH B 44 444 70 HOH HOH . K 5 HOH B 45 445 63 HOH HOH . K 5 HOH B 46 446 127 HOH HOH . K 5 HOH B 47 447 42 HOH HOH . K 5 HOH B 48 448 107 HOH HOH . K 5 HOH B 49 449 123 HOH HOH . K 5 HOH B 50 450 14 HOH HOH . K 5 HOH B 51 451 64 HOH HOH . K 5 HOH B 52 452 21 HOH HOH . K 5 HOH B 53 453 18 HOH HOH . K 5 HOH B 54 454 120 HOH HOH . K 5 HOH B 55 455 65 HOH HOH . K 5 HOH B 56 456 219 HOH HOH . K 5 HOH B 57 457 182 HOH HOH . K 5 HOH B 58 458 28 HOH HOH . K 5 HOH B 59 459 47 HOH HOH . K 5 HOH B 60 460 134 HOH HOH . K 5 HOH B 61 461 94 HOH HOH . K 5 HOH B 62 462 79 HOH HOH . K 5 HOH B 63 463 191 HOH HOH . K 5 HOH B 64 464 51 HOH HOH . K 5 HOH B 65 465 184 HOH HOH . K 5 HOH B 66 466 148 HOH HOH . K 5 HOH B 67 467 143 HOH HOH . K 5 HOH B 68 468 75 HOH HOH . K 5 HOH B 69 469 103 HOH HOH . K 5 HOH B 70 470 189 HOH HOH . K 5 HOH B 71 471 9 HOH HOH . K 5 HOH B 72 472 151 HOH HOH . K 5 HOH B 73 473 17 HOH HOH . K 5 HOH B 74 474 2 HOH HOH . K 5 HOH B 75 475 217 HOH HOH . K 5 HOH B 76 476 210 HOH HOH . K 5 HOH B 77 477 177 HOH HOH . K 5 HOH B 78 478 8 HOH HOH . K 5 HOH B 79 479 101 HOH HOH . K 5 HOH B 80 480 224 HOH HOH . K 5 HOH B 81 481 193 HOH HOH . K 5 HOH B 82 482 172 HOH HOH . K 5 HOH B 83 483 135 HOH HOH . K 5 HOH B 84 484 36 HOH HOH . K 5 HOH B 85 485 173 HOH HOH . K 5 HOH B 86 486 216 HOH HOH . K 5 HOH B 87 487 157 HOH HOH . K 5 HOH B 88 488 144 HOH HOH . K 5 HOH B 89 489 176 HOH HOH . K 5 HOH B 90 490 181 HOH HOH . K 5 HOH B 91 491 116 HOH HOH . K 5 HOH B 92 492 204 HOH HOH . K 5 HOH B 93 493 110 HOH HOH . K 5 HOH B 94 494 195 HOH HOH . K 5 HOH B 95 495 215 HOH HOH . K 5 HOH B 96 496 39 HOH HOH . K 5 HOH B 97 497 220 HOH HOH . K 5 HOH B 98 498 168 HOH HOH . K 5 HOH B 99 499 44 HOH HOH . K 5 HOH B 100 500 211 HOH HOH . K 5 HOH B 101 501 202 HOH HOH . K 5 HOH B 102 502 85 HOH HOH . K 5 HOH B 103 503 187 HOH HOH . K 5 HOH B 104 504 194 HOH HOH . K 5 HOH B 105 505 86 HOH HOH . K 5 HOH B 106 506 170 HOH HOH . K 5 HOH B 107 507 214 HOH HOH . K 5 HOH B 108 508 61 HOH HOH . K 5 HOH B 109 509 200 HOH HOH . K 5 HOH B 110 510 68 HOH HOH . K 5 HOH B 111 511 180 HOH HOH . K 5 HOH B 112 512 167 HOH HOH . # 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 O O5' 1DA . . . F 2 -29.855 57.179 -19.025 1 33.28 ? O5' 1DA 301 B 1 HETATM 2 C C5' 1DA . . . F 2 -30.166 55.899 -19.554 1 24.91 ? C5' 1DA 301 B 1 HETATM 3 C C4' 1DA . . . F 2 -29.813 55.825 -21.011 1 24.13 ? C4' 1DA 301 B 1 HETATM 4 O O4' 1DA . . . F 2 -28.467 55.344 -21.152 1 25.3 ? O4' 1DA 301 B 1 HETATM 5 C C3' 1DA . . . F 2 -30.647 54.858 -21.83 1 25.43 ? C3' 1DA 301 B 1 HETATM 6 O O3' 1DA . . . F 2 -31.786 55.532 -22.368 1 22.82 ? O3' 1DA 301 B 1 HETATM 7 C C2' 1DA . . . F 2 -29.699 54.447 -22.968 1 26.19 ? C2' 1DA 301 B 1 HETATM 8 O O2' 1DA . . . F 2 -30.024 55.003 -24.226 1 27.85 ? O2' 1DA 301 B 1 HETATM 9 C C1' 1DA . . . F 2 -28.308 54.916 -22.48 1 27.85 ? C1' 1DA 301 B 1 HETATM 10 N N9 1DA . . . F 2 -27.295 53.871 -22.558 1 23.63 ? N9 1DA 301 B 1 HETATM 11 C C8 1DA . . . F 2 -27.261 52.679 -21.947 1 27 ? C8 1DA 301 B 1 HETATM 12 N N7 1DA . . . F 2 -26.195 51.993 -22.351 1 18.79 ? N7 1DA 301 B 1 HETATM 13 C C5 1DA . . . F 2 -25.532 52.715 -23.253 1 16.36 ? C5 1DA 301 B 1 HETATM 14 C C6 1DA . . . F 2 -24.37 52.495 -23.997 1 16.43 ? C6 1DA 301 B 1 HETATM 15 N N6 1DA . . . F 2 -23.608 51.294 -23.889 1 22.06 ? N6 1DA 301 B 1 HETATM 16 C C1 1DA . . . F 2 -23.963 53.496 -24.873 1 15.04 ? C1 1DA 301 B 1 HETATM 17 C C2 1DA . . . F 2 -24.693 54.643 -24.982 1 17.56 ? C2 1DA 301 B 1 HETATM 18 N N3 1DA . . . F 2 -25.799 54.846 -24.266 1 19.04 ? N3 1DA 301 B 1 HETATM 19 C C4 1DA . . . F 2 -26.221 53.918 -23.414 1 19.35 ? C4 1DA 301 B 1 HETATM 20 H HO5' 1DA . . . F 2 -30.312 57.31 -18.287 1 39.94 ? HO5' 1DA 301 B 1 HETATM 21 H "H5'1" 1DA . . . F 2 -31.11 55.732 -19.449 1 29.89 ? "H5'1" 1DA 301 B 1 HETATM 22 H "H5'2" 1DA . . . F 2 -29.667 55.222 -19.068 1 29.89 ? "H5'2" 1DA 301 B 1 HETATM 23 H H4' 1DA . . . F 2 -29.876 56.705 -21.398 1 28.96 ? H4' 1DA 301 B 1 HETATM 24 H H3' 1DA . . . F 2 -30.919 54.071 -21.286 1 30.51 ? H3' 1DA 301 B 1 HETATM 25 H H2' 1DA . . . F 2 -29.697 53.483 -23.043 1 31.43 ? H2' 1DA 301 B 1 HETATM 26 H HO2' 1DA . . . F 2 -30.335 54.368 -24.758 1 33.42 ? HO2' 1DA 301 B 1 HETATM 27 H H1' 1DA . . . F 2 -28.028 55.659 -23.014 1 33.42 ? H1' 1DA 301 B 1 HETATM 28 H H8 1DA . . . F 2 -27.905 52.37 -21.288 1 32.4 ? H8 1DA 301 B 1 HETATM 29 H HN61 1DA . . . F 2 -23.948 50.575 -23.437 1 26.48 ? HN61 1DA 301 B 1 HETATM 30 H HN62 1DA . . . F 2 -22.78 51.243 -24.271 1 26.48 ? HN62 1DA 301 B 1 HETATM 31 H H1 1DA . . . F 2 -23.155 53.379 -25.406 1 18.05 ? H1 1DA 301 B 1 HETATM 32 H H2 1DA . . . F 2 -24.396 55.333 -25.596 1 21.08 ? H2 1DA 301 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #