data_1ZYD # _model_server_result.job_id qQqtG5c3jowQPlQWZBFPYg _model_server_result.datetime_utc '2024-11-25 02:24:09' _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 1zyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":306}' # _entry.id 1ZYD # _exptl.entry_id 1ZYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _entity.pdbx_number_of_molecules 4 _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 1ZYD _cell.length_a 82.11 _cell.length_b 175.21 _cell.length_c 47.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 D N N ? 2 F N N ? 2 G 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 E O2G ATP . A ATP 303 1_555 C MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc2 E O3B ATP . A ATP 303 1_555 C MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? metalc ? metalc3 E O3G ATP . A ATP 303 1_555 C MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? metalc ? metalc4 E O1A ATP . A ATP 303 1_555 C MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 E O3B ATP . A ATP 303 1_555 D MG MG . A MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc6 C MG MG . A MG 305 1_555 A OD1 ASP 159 A ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc7 C MG MG . A MG 305 1_555 A OD2 ASP 159 A ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc8 D MG MG . A MG 306 1_555 A OD1 ASN 146 A ASN 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc9 D MG MG . A MG 306 1_555 A OD2 ASP 159 A ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc10 H O3G ATP . B ATP 304 1_555 F MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc11 H O2G ATP . B ATP 304 1_555 F MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.115 ? metalc ? metalc12 H O3B ATP . B ATP 304 1_555 F MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.049 ? metalc ? metalc13 H O1A ATP . B ATP 304 1_555 F MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc14 H O3B ATP . B ATP 304 1_555 G MG MG . B MG 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc15 F MG MG . B MG 307 1_555 B OD1 ASP 159 B ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc16 F MG MG . B MG 307 1_555 B OD2 ASP 159 B ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc17 G MG MG . B MG 308 1_555 B OD1 ASN 146 B ASN 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc18 G MG MG . B MG 308 1_555 B OD2 ASP 159 B ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? # _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 1ZYD _atom_sites.fract_transf_matrix[1][1] 0.012179 _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] 0.005707 _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] 0.021022 _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 MG A 1 305 305 MG MG2 . D 2 MG A 1 306 306 MG MG2 . E 3 ATP A 1 303 304 ATP ATP . F 2 MG B 1 307 305 MG MG2 . G 2 MG B 1 308 306 MG MG2 . H 3 ATP B 1 304 304 ATP ATP . I 4 HOH A 1 1 1 HOH HOH . I 4 HOH A 2 2 2 HOH HOH . I 4 HOH A 3 3 3 HOH HOH . I 4 HOH A 4 4 4 HOH HOH . I 4 HOH A 5 5 5 HOH HOH . I 4 HOH A 6 6 6 HOH HOH . I 4 HOH A 7 7 7 HOH HOH . I 4 HOH A 8 10 10 HOH HOH . I 4 HOH A 9 11 11 HOH HOH . I 4 HOH A 10 16 16 HOH HOH . I 4 HOH A 11 17 17 HOH HOH . I 4 HOH A 12 18 18 HOH HOH . I 4 HOH A 13 23 23 HOH HOH . I 4 HOH A 14 28 28 HOH HOH . I 4 HOH A 15 29 29 HOH HOH . I 4 HOH A 16 32 32 HOH HOH . I 4 HOH A 17 35 35 HOH HOH . I 4 HOH A 18 36 36 HOH HOH . I 4 HOH A 19 43 43 HOH HOH . I 4 HOH A 20 44 44 HOH HOH . I 4 HOH A 21 49 49 HOH HOH . I 4 HOH A 22 51 51 HOH HOH . I 4 HOH A 23 54 54 HOH HOH . I 4 HOH A 24 55 55 HOH HOH . I 4 HOH A 25 57 57 HOH HOH . I 4 HOH A 26 58 58 HOH HOH . I 4 HOH A 27 60 60 HOH HOH . I 4 HOH A 28 61 61 HOH HOH . I 4 HOH A 29 62 62 HOH HOH . I 4 HOH A 30 64 64 HOH HOH . I 4 HOH A 31 65 65 HOH HOH . I 4 HOH A 32 66 66 HOH HOH . I 4 HOH A 33 68 68 HOH HOH . I 4 HOH A 34 69 69 HOH HOH . I 4 HOH A 35 70 70 HOH HOH . I 4 HOH A 36 71 71 HOH HOH . I 4 HOH A 37 73 73 HOH HOH . J 4 HOH B 1 8 8 HOH HOH . J 4 HOH B 2 9 9 HOH HOH . J 4 HOH B 3 12 12 HOH HOH . J 4 HOH B 4 13 13 HOH HOH . J 4 HOH B 5 14 14 HOH HOH . J 4 HOH B 6 15 15 HOH HOH . J 4 HOH B 7 20 20 HOH HOH . J 4 HOH B 8 21 21 HOH HOH . J 4 HOH B 9 22 22 HOH HOH . J 4 HOH B 10 24 24 HOH HOH . J 4 HOH B 11 25 25 HOH HOH . J 4 HOH B 12 26 26 HOH HOH . J 4 HOH B 13 27 27 HOH HOH . J 4 HOH B 14 31 31 HOH HOH . J 4 HOH B 15 33 33 HOH HOH . J 4 HOH B 16 34 34 HOH HOH . J 4 HOH B 17 37 37 HOH HOH . J 4 HOH B 18 38 38 HOH HOH . J 4 HOH B 19 39 39 HOH HOH . J 4 HOH B 20 40 40 HOH HOH . J 4 HOH B 21 41 41 HOH HOH . J 4 HOH B 22 42 42 HOH HOH . J 4 HOH B 23 45 45 HOH HOH . J 4 HOH B 24 47 47 HOH HOH . J 4 HOH B 25 48 48 HOH HOH . J 4 HOH B 26 52 52 HOH HOH . J 4 HOH B 27 53 53 HOH HOH . J 4 HOH B 28 56 56 HOH HOH . J 4 HOH B 29 63 63 HOH HOH . J 4 HOH B 30 67 67 HOH HOH . J 4 HOH B 31 72 72 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 D _atom_site.label_entity_id 2 _atom_site.Cartn_x 2.477 _atom_site.Cartn_y 62.517 _atom_site.Cartn_z 11.485 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 26.61 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 306 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #