data_1EBM # _model_server_result.job_id '_rlncu06FE-aRsyVnDiuLg' _model_server_result.datetime_utc '2024-12-02 12:49:36' _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 1ebm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":17}' # _entry.id 1EBM # _exptl.entry_id 1EBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 1EBM _cell.length_a 92.357 _cell.length_b 92.357 _cell.length_c 212.872 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1EBM _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A O3' DA 7 C DA 24 1_555 A P 8OG 8 C 8OG 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? covale ? covale2 A O3' 8OG 8 C 8OG 25 1_555 A P DG 9 C DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? metalc ? metalc1 D CA CA . C CA 17 1_555 A OP2 DA 7 C DA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc2 D CA CA . C CA 17 1_555 E O HOH . C HOH 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc3 D CA CA . C CA 17 1_555 E O HOH . C HOH 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc4 D CA CA . C CA 17 1_555 E O HOH . C HOH 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? hydrog WATSON-CRICK hydrog1 A N1 DG 1 C DG 18 1_555 B N3 DC 15 D DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 1 C DG 18 1_555 B O2 DC 15 D DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 1 C DG 18 1_555 B N4 DC 15 D DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DC 2 C DC 19 1_555 B N1 DG 14 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 DC 2 C DC 19 1_555 B O6 DG 14 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 DC 2 C DC 19 1_555 B N2 DG 14 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 3 C DG 20 1_555 B N3 DC 13 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 3 C DG 20 1_555 B O2 DC 13 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 3 C DG 20 1_555 B N4 DC 13 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 DT 4 C DT 21 1_555 B N1 DA 12 D DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O4 DT 4 C DT 21 1_555 B N6 DA 12 D DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 5 C DC 22 1_555 B N1 DG 11 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 5 C DC 22 1_555 B O6 DG 11 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 5 C DC 22 1_555 B N2 DG 11 D DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DC 6 C DC 23 1_555 B N1 DG 10 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N4 DC 6 C DC 23 1_555 B O6 DG 10 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O2 DC 6 C DC 23 1_555 B N2 DG 10 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N1 DA 7 C DA 24 1_555 B N3 DT 9 D DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N6 DA 7 C DA 24 1_555 B O4 DT 9 D DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 DG 9 C DG 26 1_555 B N3 DC 7 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 DG 9 C DG 26 1_555 B O2 DC 7 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 DG 9 C DG 26 1_555 B N4 DC 7 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N3 DT 10 C DT 27 1_555 B N1 DA 6 D DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O4 DT 10 C DT 27 1_555 B N6 DA 6 D DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N3 DC 11 C DC 28 1_555 B N1 DG 5 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N4 DC 11 C DC 28 1_555 B O6 DG 5 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O2 DC 11 C DC 28 1_555 B N2 DG 5 D DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N3 DT 12 C DT 29 1_555 B N1 DA 4 D DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O4 DT 12 C DT 29 1_555 B N6 DA 4 D DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N1 DA 13 C DA 30 1_555 B N3 DT 3 D DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N6 DA 13 C DA 30 1_555 B O4 DT 3 D DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N3 DC 14 C DC 31 1_555 B N1 DG 2 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N4 DC 14 C DC 31 1_555 B O6 DG 2 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A O2 DC 14 C DC 31 1_555 B N2 DG 2 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N3 DC 15 C DC 32 1_555 B N1 DG 1 D DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A N4 DC 15 C DC 32 1_555 B O6 DG 1 D DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A O2 DC 15 C DC 32 1_555 B N2 DG 1 D DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1EBM _atom_sites.fract_transf_matrix[1][1] 0.010828 _atom_sites.fract_transf_matrix[1][2] 0.006251 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012503 _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] 0.004698 _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 D 4 CA C 1 17 17 CA CA . E 5 HOH C 1 1 1 HOH HOH . E 5 HOH C 2 36 36 HOH HOH . E 5 HOH C 3 62 62 HOH HOH . E 5 HOH C 4 63 63 HOH HOH . E 5 HOH C 5 86 86 HOH HOH . E 5 HOH C 6 117 117 HOH HOH . E 5 HOH C 7 146 146 HOH HOH . E 5 HOH C 8 149 149 HOH HOH . E 5 HOH C 9 159 159 HOH HOH . E 5 HOH C 10 166 166 HOH HOH . F 5 HOH D 1 55 55 HOH HOH . F 5 HOH D 2 158 158 HOH HOH . F 5 HOH D 3 174 174 HOH HOH . F 5 HOH D 4 180 180 HOH HOH . F 5 HOH D 5 181 181 HOH HOH . G 5 HOH A 1 326 4 HOH HOH . G 5 HOH A 2 327 5 HOH HOH . G 5 HOH A 3 328 6 HOH HOH . G 5 HOH A 4 329 7 HOH HOH . G 5 HOH A 5 330 9 HOH HOH . G 5 HOH A 6 331 11 HOH HOH . G 5 HOH A 7 332 14 HOH HOH . G 5 HOH A 8 333 19 HOH HOH . G 5 HOH A 9 334 20 HOH HOH . G 5 HOH A 10 335 25 HOH HOH . G 5 HOH A 11 336 28 HOH HOH . G 5 HOH A 12 337 29 HOH HOH . G 5 HOH A 13 338 34 HOH HOH . G 5 HOH A 14 339 35 HOH HOH . G 5 HOH A 15 340 37 HOH HOH . G 5 HOH A 16 341 38 HOH HOH . G 5 HOH A 17 342 42 HOH HOH . G 5 HOH A 18 343 43 HOH HOH . G 5 HOH A 19 344 44 HOH HOH . G 5 HOH A 20 345 48 HOH HOH . G 5 HOH A 21 346 57 HOH HOH . G 5 HOH A 22 347 58 HOH HOH . G 5 HOH A 23 348 61 HOH HOH . G 5 HOH A 24 349 64 HOH HOH . G 5 HOH A 25 350 68 HOH HOH . G 5 HOH A 26 351 70 HOH HOH . G 5 HOH A 27 352 71 HOH HOH . G 5 HOH A 28 353 72 HOH HOH . G 5 HOH A 29 354 73 HOH HOH . G 5 HOH A 30 355 77 HOH HOH . G 5 HOH A 31 356 79 HOH HOH . G 5 HOH A 32 357 80 HOH HOH . G 5 HOH A 33 358 87 HOH HOH . G 5 HOH A 34 359 92 HOH HOH . G 5 HOH A 35 360 93 HOH HOH . G 5 HOH A 36 361 95 HOH HOH . G 5 HOH A 37 362 96 HOH HOH . G 5 HOH A 38 363 97 HOH HOH . G 5 HOH A 39 364 98 HOH HOH . G 5 HOH A 40 365 99 HOH HOH . G 5 HOH A 41 366 100 HOH HOH . G 5 HOH A 42 367 102 HOH HOH . G 5 HOH A 43 368 103 HOH HOH . G 5 HOH A 44 369 104 HOH HOH . G 5 HOH A 45 370 105 HOH HOH . G 5 HOH A 46 371 106 HOH HOH . G 5 HOH A 47 372 107 HOH HOH . G 5 HOH A 48 373 108 HOH HOH . G 5 HOH A 49 374 109 HOH HOH . G 5 HOH A 50 375 110 HOH HOH . G 5 HOH A 51 376 111 HOH HOH . G 5 HOH A 52 377 112 HOH HOH . G 5 HOH A 53 378 113 HOH HOH . G 5 HOH A 54 379 114 HOH HOH . G 5 HOH A 55 380 115 HOH HOH . G 5 HOH A 56 381 116 HOH HOH . G 5 HOH A 57 382 118 HOH HOH . G 5 HOH A 58 383 119 HOH HOH . G 5 HOH A 59 384 120 HOH HOH . G 5 HOH A 60 385 121 HOH HOH . G 5 HOH A 61 386 122 HOH HOH . G 5 HOH A 62 387 123 HOH HOH . G 5 HOH A 63 388 124 HOH HOH . G 5 HOH A 64 389 125 HOH HOH . G 5 HOH A 65 390 126 HOH HOH . G 5 HOH A 66 391 127 HOH HOH . G 5 HOH A 67 392 128 HOH HOH . G 5 HOH A 68 393 129 HOH HOH . G 5 HOH A 69 394 130 HOH HOH . G 5 HOH A 70 395 132 HOH HOH . G 5 HOH A 71 396 133 HOH HOH . G 5 HOH A 72 397 134 HOH HOH . G 5 HOH A 73 398 137 HOH HOH . G 5 HOH A 74 399 138 HOH HOH . G 5 HOH A 75 400 139 HOH HOH . G 5 HOH A 76 401 140 HOH HOH . G 5 HOH A 77 402 141 HOH HOH . G 5 HOH A 78 403 142 HOH HOH . G 5 HOH A 79 404 143 HOH HOH . G 5 HOH A 80 405 144 HOH HOH . G 5 HOH A 81 406 145 HOH HOH . G 5 HOH A 82 407 147 HOH HOH . G 5 HOH A 83 408 148 HOH HOH . G 5 HOH A 84 409 150 HOH HOH . G 5 HOH A 85 410 153 HOH HOH . G 5 HOH A 86 411 154 HOH HOH . G 5 HOH A 87 412 155 HOH HOH . G 5 HOH A 88 413 156 HOH HOH . G 5 HOH A 89 414 157 HOH HOH . G 5 HOH A 90 415 160 HOH HOH . G 5 HOH A 91 416 161 HOH HOH . G 5 HOH A 92 417 162 HOH HOH . G 5 HOH A 93 418 163 HOH HOH . G 5 HOH A 94 419 164 HOH HOH . G 5 HOH A 95 420 165 HOH HOH . G 5 HOH A 96 421 167 HOH HOH . G 5 HOH A 97 422 168 HOH HOH . G 5 HOH A 98 423 169 HOH HOH . G 5 HOH A 99 424 170 HOH HOH . G 5 HOH A 100 425 171 HOH HOH . G 5 HOH A 101 426 172 HOH HOH . G 5 HOH A 102 427 173 HOH HOH . G 5 HOH A 103 428 175 HOH HOH . G 5 HOH A 104 429 177 HOH HOH . G 5 HOH A 105 430 178 HOH HOH . G 5 HOH A 106 431 179 HOH HOH . G 5 HOH A 107 432 182 HOH HOH . G 5 HOH A 108 433 183 HOH HOH . G 5 HOH A 109 434 184 HOH HOH . G 5 HOH A 110 435 185 HOH HOH . G 5 HOH A 111 436 186 HOH HOH . G 5 HOH A 112 437 187 HOH HOH . G 5 HOH A 113 438 188 HOH HOH . G 5 HOH A 114 439 189 HOH HOH . G 5 HOH A 115 440 190 HOH HOH . G 5 HOH A 116 441 191 HOH HOH . G 5 HOH A 117 442 192 HOH HOH . G 5 HOH A 118 443 193 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x 24.783 _atom_site.Cartn_y 32.406 _atom_site.Cartn_z 40.417 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 66.62 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 17 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #