data_5DGK # _model_server_result.job_id X-xrqvTj7_ctVYDbIorOOw _model_server_result.datetime_utc '2025-08-31 16:31:09' _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 5dgk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":702}' # _entry.id 5DGK # _exptl.entry_id 5DGK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _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 120 _cell.entry_id 5DGK _cell.length_a 110.14 _cell.length_b 110.14 _cell.length_c 302.755 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DGK _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 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 _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' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 55.07 95.384038 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -55.07 95.384038 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 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 C ARG 35 A ARG 35 1_555 A N MSE 36 A MSE 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C MSE 36 A MSE 36 1_555 A N ALA 37 A ALA 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C LEU 102 A LEU 102 1_555 A N MSE 103 A MSE 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 103 A MSE 103 1_555 A N ARG 104 A ARG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C ASN 165 A ASN 165 1_555 A N MSE 166 A MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C MSE 166 A MSE 166 1_555 A N TYR 167 A TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C ARG 395 A ARG 395 1_555 A N MSE 396 A MSE 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C MSE 396 A MSE 396 1_555 A N PHE 397 A PHE 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 A C ASN 467 A ASN 467 1_555 A N MSE 468 A MSE 468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 A C MSE 468 A MSE 468 1_555 A N PHE 469 A PHE 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale11 A C GLN 493 A GLN 493 1_555 A N MSE 494 A MSE 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 A C MSE 494 A MSE 494 1_555 A N LEU 495 A LEU 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 B C ARG 35 B ARG 35 1_555 B N MSE 36 B MSE 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 B C MSE 36 B MSE 36 1_555 B N ALA 37 B ALA 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 B C LEU 102 B LEU 102 1_555 B N MSE 103 B MSE 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale16 B C MSE 103 B MSE 103 1_555 B N ARG 104 B ARG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 B C ASN 165 B ASN 165 1_555 B N MSE 166 B MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale18 B C MSE 166 B MSE 166 1_555 B N TYR 167 B TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale19 B C ARG 395 B ARG 395 1_555 B N MSE 396 B MSE 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale20 B C MSE 396 B MSE 396 1_555 B N PHE 397 B PHE 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale21 B C ASN 467 B ASN 467 1_555 B N MSE 468 B MSE 468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale22 B C MSE 468 B MSE 468 1_555 B N PHE 469 B PHE 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale23 B C GLN 493 B GLN 493 1_555 B N MSE 494 B MSE 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale24 B C MSE 494 B MSE 494 1_555 B N LEU 495 B LEU 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OG SER 217 A SER 217 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 C O1G ANP . A ANP 701 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc3 C O1B ANP . A ANP 701 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc4 D MG MG . A MG 702 1_555 G O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc5 D MG MG . A MG 702 1_555 G O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc6 D MG MG . A MG 702 1_555 G O HOH . A HOH 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc7 B OG SER 217 B SER 217 1_555 F MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc8 E O1G ANP . B ANP 701 1_555 F MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc9 E O1B ANP . B ANP 701 1_555 F MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc10 F MG MG . B MG 702 1_555 H O HOH . B HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc11 F MG MG . B MG 702 1_555 H O HOH . B HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc12 F MG MG . B MG 702 1_555 H O HOH . B HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5DGK _atom_sites.fract_transf_matrix[1][1] 0.009079 _atom_sites.fract_transf_matrix[1][2] 0.005242 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010484 _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] 0.003303 _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 ANP A 1 701 2 ANP ANP . D 3 MG A 1 702 3 MG MG . E 2 ANP B 1 701 4 ANP ANP . F 3 MG B 1 702 5 MG MG . G 4 HOH A 1 801 5 HOH HOH . G 4 HOH A 2 802 4 HOH HOH . G 4 HOH A 3 803 7 HOH HOH . G 4 HOH A 4 804 6 HOH HOH . G 4 HOH A 5 805 5 HOH HOH . G 4 HOH A 6 806 2 HOH HOH . G 4 HOH A 7 807 1 HOH HOH . H 4 HOH B 1 801 6 HOH HOH . H 4 HOH B 2 802 13 HOH HOH . H 4 HOH B 3 803 7 HOH HOH . H 4 HOH B 4 804 8 HOH HOH . H 4 HOH B 5 805 6 HOH HOH . H 4 HOH B 6 806 14 HOH HOH . H 4 HOH B 7 807 4 HOH HOH . H 4 HOH B 8 808 8 HOH HOH . H 4 HOH B 9 809 3 HOH HOH . H 4 HOH B 10 810 12 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id F _atom_site.label_entity_id 3 _atom_site.Cartn_x 10.827 _atom_site.Cartn_y 32.981 _atom_site.Cartn_z 192.441 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 39.52 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 702 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 481 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #