data_8WDB # _model_server_result.job_id bUKTeaYB0qAXlI4WXZlJQw _model_server_result.datetime_utc '2025-02-05 11:58:45' _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 8wdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 8WDB # _exptl.entry_id 8WDB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 90 _cell.entry_id 8WDB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,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 ? _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 ? 5 E N N ? 5 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 OG SER 49 D SER 49 1_555 G MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc2 A OE1 GLN 98 D GLN 98 1_555 G MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc3 A OG SER 331 D SER 331 1_555 H MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc4 A OE1 GLN 376 D GLN 376 1_555 H MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc5 E O1G ATP . D ATP 601 1_555 G MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc6 E O2B ATP . D ATP 601 1_555 G MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc7 F O3G ATP . D ATP 602 1_555 H MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc8 F O2B ATP . D ATP 602 1_555 H MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 8WDB _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 E 5 ATP D 1 601 1 ATP ATP . F 5 ATP D 1 602 2 ATP ATP . G 6 MG D 1 603 1 MG MG . H 6 MG D 1 604 2 MG MG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG ATP . . . E 5 161.547 148.787 109.505 1 43.52 ? PG ATP 601 D 1 HETATM 2 O O1G ATP . . . E 5 162.873 149.45 109.72 1 43.52 ? O1G ATP 601 D 1 HETATM 3 O O2G ATP . . . E 5 160.491 149.179 110.489 1 43.52 ? O2G ATP 601 D 1 HETATM 4 O O3G ATP . . . E 5 161.073 148.851 108.087 1 43.52 ? O3G ATP 601 D 1 HETATM 5 P PB ATP . . . E 5 163.144 146.541 110.268 1 43.52 ? PB ATP 601 D 1 HETATM 6 O O1B ATP . . . E 5 163.816 145.961 109.06 1 43.52 ? O1B ATP 601 D 1 HETATM 7 O O2B ATP . . . E 5 163.902 147.484 111.156 1 43.52 ? O2B ATP 601 D 1 HETATM 8 O O3B ATP . . . E 5 161.772 147.214 109.767 1 43.52 ? O3B ATP 601 D 1 HETATM 9 P PA ATP . . . E 5 163.297 145.008 112.601 1 43.52 ? PA ATP 601 D 1 HETATM 10 O O1A ATP . . . E 5 164.707 144.557 112.397 1 43.52 ? O1A ATP 601 D 1 HETATM 11 O O2A ATP . . . E 5 163.007 146.172 113.498 1 43.52 ? O2A ATP 601 D 1 HETATM 12 O O3A ATP . . . E 5 162.658 145.299 111.16 1 43.52 ? O3A ATP 601 D 1 HETATM 13 O O5' ATP . . . E 5 162.485 143.75 113.151 1 43.52 ? O5' ATP 601 D 1 HETATM 14 C C5' ATP . . . E 5 162.198 142.648 112.302 1 43.52 ? C5' ATP 601 D 1 HETATM 15 C C4' ATP . . . E 5 161.267 141.709 113.046 1 43.52 ? C4' ATP 601 D 1 HETATM 16 O O4' ATP . . . E 5 161.775 141.486 114.354 1 43.52 ? O4' ATP 601 D 1 HETATM 17 C C3' ATP . . . E 5 159.899 142.333 113.208 1 43.52 ? C3' ATP 601 D 1 HETATM 18 O O3' ATP . . . E 5 158.945 141.571 112.475 1 43.52 ? O3' ATP 601 D 1 HETATM 19 C C2' ATP . . . E 5 159.583 142.281 114.683 1 43.52 ? C2' ATP 601 D 1 HETATM 20 O O2' ATP . . . E 5 158.349 141.6 114.893 1 43.52 ? O2' ATP 601 D 1 HETATM 21 C C1' ATP . . . E 5 160.72 141.504 115.307 1 43.52 ? C1' ATP 601 D 1 HETATM 22 N N9 ATP . . . E 5 161.178 142.168 116.548 1 43.52 ? N9 ATP 601 D 1 HETATM 23 C C8 ATP . . . E 5 161.859 143.317 116.61 1 43.52 ? C8 ATP 601 D 1 HETATM 24 N N7 ATP . . . E 5 162.13 143.656 117.891 1 43.52 ? N7 ATP 601 D 1 HETATM 25 C C5 ATP . . . E 5 161.61 142.703 118.675 1 43.52 ? C5 ATP 601 D 1 HETATM 26 C C6 ATP . . . E 5 161.539 142.449 120.125 1 43.52 ? C6 ATP 601 D 1 HETATM 27 N N6 ATP . . . E 5 162.091 143.303 121.012 1 43.52 ? N6 ATP 601 D 1 HETATM 28 N N1 ATP . . . E 5 160.903 141.331 120.531 1 43.52 ? N1 ATP 601 D 1 HETATM 29 C C2 ATP . . . E 5 160.349 140.472 119.661 1 43.52 ? C2 ATP 601 D 1 HETATM 30 N N3 ATP . . . E 5 160.379 140.645 118.331 1 43.52 ? N3 ATP 601 D 1 HETATM 31 C C4 ATP . . . E 5 160.982 141.725 117.787 1 43.52 ? C4 ATP 601 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #