data_5YGI # _model_server_result.job_id zi3fFofQWoOeDxWLcKOOOw _model_server_result.datetime_utc '2024-11-05 08:10:52' _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 5ygi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":505}' # _entry.id 5YGI # _exptl.entry_id 5YGI _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 3 _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 5YGI _cell.length_a 111.743 _cell.length_b 111.743 _cell.length_c 66.191 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YGI _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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,H _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 ? 3 D N N ? 3 E 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 metalc ? metalc1 A OD2 ASP 98 A ASP 103 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc2 A OD1 ASP 98 A ASP 103 1_555 F MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc3 A OD2 ASP 102 A ASP 107 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc4 A OD2 ASP 102 A ASP 107 1_555 F MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc5 A OD2 ASP 238 A ASP 243 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc6 D MG MG . A MG 503 1_555 G O7 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc7 D MG MG . A MG 503 1_555 G O3 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc8 D MG MG . A MG 503 1_555 H O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc9 D MG MG . A MG 503 1_555 H O HOH . A HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc10 D MG MG . A MG 503 1_555 H O HOH . A HOH 635 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 E MG MG . A MG 504 1_555 G O9 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc12 E MG MG . A MG 504 1_555 G O4 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc13 E MG MG . A MG 504 1_555 H O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc14 E MG MG . A MG 504 1_555 H O HOH . A HOH 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc15 F MG MG . A MG 505 1_555 G O9 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc16 F MG MG . A MG 505 1_555 H O HOH . A HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc17 F MG MG . A MG 505 1_555 H O HOH . A HOH 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc18 F MG MG . A MG 505 1_555 H O HOH . A HOH 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? # _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 5YGI _atom_sites.fract_transf_matrix[1][1] 0.008949 _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] 0.008949 _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] 0.015108 _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 PO4 A 1 501 501 PO4 PO4 . C 2 PO4 A 1 502 502 PO4 PO4 . D 3 MG A 1 503 601 MG MG . E 3 MG A 1 504 602 MG MG . F 3 MG A 1 505 603 MG MG . G 4 T93 A 1 506 701 T93 T93 . H 5 HOH A 1 601 835 HOH HOH . H 5 HOH A 2 602 851 HOH HOH . H 5 HOH A 3 603 820 HOH HOH . H 5 HOH A 4 604 838 HOH HOH . H 5 HOH A 5 605 810 HOH HOH . H 5 HOH A 6 606 832 HOH HOH . H 5 HOH A 7 607 837 HOH HOH . H 5 HOH A 8 608 815 HOH HOH . H 5 HOH A 9 609 812 HOH HOH . H 5 HOH A 10 610 850 HOH HOH . H 5 HOH A 11 611 831 HOH HOH . H 5 HOH A 12 612 808 HOH HOH . H 5 HOH A 13 613 806 HOH HOH . H 5 HOH A 14 614 849 HOH HOH . H 5 HOH A 15 615 846 HOH HOH . H 5 HOH A 16 616 814 HOH HOH . H 5 HOH A 17 617 809 HOH HOH . H 5 HOH A 18 618 852 HOH HOH . H 5 HOH A 19 619 821 HOH HOH . H 5 HOH A 20 620 834 HOH HOH . H 5 HOH A 21 621 853 HOH HOH . H 5 HOH A 22 622 825 HOH HOH . H 5 HOH A 23 623 848 HOH HOH . H 5 HOH A 24 624 804 HOH HOH . H 5 HOH A 25 625 807 HOH HOH . H 5 HOH A 26 626 818 HOH HOH . H 5 HOH A 27 627 816 HOH HOH . H 5 HOH A 28 628 822 HOH HOH . H 5 HOH A 29 629 802 HOH HOH . H 5 HOH A 30 630 844 HOH HOH . H 5 HOH A 31 631 847 HOH HOH . H 5 HOH A 32 632 841 HOH HOH . H 5 HOH A 33 633 803 HOH HOH . H 5 HOH A 34 634 805 HOH HOH . H 5 HOH A 35 635 819 HOH HOH . H 5 HOH A 36 636 827 HOH HOH . H 5 HOH A 37 637 801 HOH HOH . H 5 HOH A 38 638 829 HOH HOH . H 5 HOH A 39 639 833 HOH HOH . H 5 HOH A 40 640 823 HOH HOH . H 5 HOH A 41 641 817 HOH HOH . H 5 HOH A 42 642 811 HOH HOH . H 5 HOH A 43 643 813 HOH HOH . H 5 HOH A 44 644 845 HOH HOH . H 5 HOH A 45 645 840 HOH HOH . H 5 HOH A 46 646 839 HOH HOH . H 5 HOH A 47 647 842 HOH HOH . H 5 HOH A 48 648 843 HOH HOH . H 5 HOH A 49 649 828 HOH HOH . H 5 HOH A 50 650 826 HOH HOH . H 5 HOH A 51 651 824 HOH HOH . H 5 HOH A 52 652 830 HOH HOH . H 5 HOH A 53 653 836 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 -19.328 _atom_site.Cartn_y 32.565 _atom_site.Cartn_z -7.504 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 24.32 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 505 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #