data_4PHG # _model_server_result.job_id VXfUf6qBwu3r8x2Sb2qjrA _model_server_result.datetime_utc '2024-10-19 19:35:09' _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 4phg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 4PHG # _exptl.entry_id 4PHG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.906 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'YTTRIUM (III) ION' _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 106.35 _cell.angle_gamma 90 _cell.entry_id 4PHG _cell.length_a 32.97 _cell.length_b 53.16 _cell.length_c 46.91 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PHG _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N 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 SG CYS 37 A CYS 35 1_555 C CAA 2UJ . A 2UJ 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.652 ? metalc ? metalc1 A OG1 THR 24 A THR 22 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc2 A OD1 ASP 33 A ASP 31 1_555 D Y YT3 . A YT3 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc3 A OD2 ASP 33 A ASP 31 1_555 D Y YT3 . A YT3 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc4 A OG1 THR 42 A THR 40 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc5 A OD1 ASP 46 A ASP 44 1_555 F Y YT3 . A YT3 205 2_646 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc6 A OD2 ASP 46 A ASP 44 1_555 F Y YT3 . A YT3 205 2_646 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc7 A OE2 GLU 51 A GLU 49 1_555 E Y YT3 . A YT3 204 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc8 A OE1 GLU 71 A GLU 69 1_555 E Y YT3 . A YT3 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc9 A OE2 GLU 71 A GLU 69 1_555 E Y YT3 . A YT3 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc10 A OD1 ASN 101 A ASN 99 1_555 D Y YT3 . A YT3 203 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc11 A OE1 GLU 108 A GLU 106 1_555 E Y YT3 . A YT3 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc12 A OE2 GLU 108 A GLU 106 1_555 E Y YT3 . A YT3 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc13 A OE1 GLU 119 A GLU 117 1_555 F Y YT3 . A YT3 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc14 A OE1 GLU 133 A GLU 131 1_555 F Y YT3 . A YT3 205 1_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc15 A OE2 GLU 133 A GLU 131 1_555 F Y YT3 . A YT3 205 1_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc16 B MG MG . A MG 201 1_555 C O2B 2UJ . A 2UJ 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc17 B MG MG . A MG 201 1_555 C O2G 2UJ . A 2UJ 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc18 B MG MG . A MG 201 1_555 G O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc19 B MG MG . A MG 201 1_555 G O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc20 D Y YT3 . A YT3 203 1_555 G O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc21 D Y YT3 . A YT3 203 1_555 G O HOH . A HOH 317 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc22 E Y YT3 . A YT3 204 1_555 G O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc23 E Y YT3 . A YT3 204 1_555 G O HOH . A HOH 310 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc24 E Y YT3 . A YT3 204 1_555 G O HOH . A HOH 318 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc25 F Y YT3 . A YT3 205 1_555 G O HOH . A HOH 320 2_656 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? # _chem_comp.formula 'Y 3' _chem_comp.formula_weight 88.906 _chem_comp.id YT3 _chem_comp.mon_nstd_flag . _chem_comp.name 'YTTRIUM (III) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4PHG _atom_sites.fract_transf_matrix[1][1] 0.030331 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0089 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018811 _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] 0.022216 _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 B 2 MG A 1 201 500 MG MG . C 3 2UJ A 1 202 400 2UJ aGT . D 4 YT3 A 1 203 1 YT3 YT3 . E 4 YT3 A 1 204 2 YT3 YT3 . F 4 YT3 A 1 205 3 YT3 YT3 . G 5 HOH A 1 301 47 HOH HOH . G 5 HOH A 2 302 43 HOH HOH . G 5 HOH A 3 303 28 HOH HOH . G 5 HOH A 4 304 51 HOH HOH . G 5 HOH A 5 305 45 HOH HOH . G 5 HOH A 6 306 46 HOH HOH . G 5 HOH A 7 307 53 HOH HOH . G 5 HOH A 8 308 54 HOH HOH . G 5 HOH A 9 309 6 HOH HOH . G 5 HOH A 10 310 48 HOH HOH . G 5 HOH A 11 311 49 HOH HOH . G 5 HOH A 12 312 4 HOH HOH . G 5 HOH A 13 313 39 HOH HOH . G 5 HOH A 14 314 30 HOH HOH . G 5 HOH A 15 315 33 HOH HOH . G 5 HOH A 16 316 13 HOH HOH . G 5 HOH A 17 317 44 HOH HOH . G 5 HOH A 18 318 50 HOH HOH . G 5 HOH A 19 319 10 HOH HOH . G 5 HOH A 20 320 52 HOH HOH . G 5 HOH A 21 321 16 HOH HOH . G 5 HOH A 22 322 42 HOH HOH . G 5 HOH A 23 323 15 HOH HOH . G 5 HOH A 24 324 1 HOH HOH . G 5 HOH A 25 325 2 HOH HOH . G 5 HOH A 26 326 3 HOH HOH . G 5 HOH A 27 327 5 HOH HOH . G 5 HOH A 28 328 7 HOH HOH . G 5 HOH A 29 329 8 HOH HOH . G 5 HOH A 30 330 9 HOH HOH . G 5 HOH A 31 331 11 HOH HOH . G 5 HOH A 32 332 12 HOH HOH . G 5 HOH A 33 333 14 HOH HOH . G 5 HOH A 34 334 17 HOH HOH . G 5 HOH A 35 335 18 HOH HOH . G 5 HOH A 36 336 19 HOH HOH . G 5 HOH A 37 337 20 HOH HOH . G 5 HOH A 38 338 21 HOH HOH . G 5 HOH A 39 339 22 HOH HOH . G 5 HOH A 40 340 23 HOH HOH . G 5 HOH A 41 341 24 HOH HOH . G 5 HOH A 42 342 25 HOH HOH . G 5 HOH A 43 343 26 HOH HOH . G 5 HOH A 44 344 29 HOH HOH . G 5 HOH A 45 345 35 HOH HOH . G 5 HOH A 46 346 36 HOH HOH . G 5 HOH A 47 347 37 HOH HOH . G 5 HOH A 48 348 38 HOH HOH . G 5 HOH A 49 349 40 HOH HOH . G 5 HOH A 50 350 41 HOH HOH . G 5 HOH A 51 351 55 HOH HOH . G 5 HOH A 52 352 56 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol Y _atom_site.label_atom_id Y _atom_site.label_comp_id YT3 _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 4 _atom_site.Cartn_x -3.223 _atom_site.Cartn_y -13.106 _atom_site.Cartn_z 14.636 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 31.1 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id Y _atom_site.auth_comp_id YT3 _atom_site.auth_seq_id 204 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #