data_8Y5I # _model_server_result.job_id sANMQ3Kg9j-rJOvZF53mLA _model_server_result.datetime_utc '2024-11-14 14:33:44' _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 8y5i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 8Y5I # _exptl.entry_id 8Y5I _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 8Y5I _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y5I _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 5 F N N ? 5 H 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 OE1 GLN 96 A GLN 96 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc2 D OE1 GLN 96 D GLN 96 1_555 I MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 H O1G ATP . D ATP 401 1_555 I MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _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 8Y5I _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 F 5 ATP A 1 401 401 ATP ATP . G 6 MG A 1 402 402 MG MG . H 5 ATP D 1 401 401 ATP ATP . I 6 MG D 1 402 402 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 . . . F 5 113.426 129.816 165.771 1 62.27 ? PG ATP 401 A 1 HETATM 2 O O1G ATP . . . F 5 113.675 128.438 165.218 1 62.94 ? O1G ATP 401 A 1 HETATM 3 O O2G ATP . . . F 5 111.951 130.111 165.742 1 62.52 ? O2G ATP 401 A 1 HETATM 4 O O3G ATP . . . F 5 113.935 129.881 167.182 1 61.86 ? O3G ATP 401 A 1 HETATM 5 P PB ATP . . . F 5 114.635 132.422 165.383 1 62.47 ? PB ATP 401 A 1 HETATM 6 O O1B ATP . . . F 5 114.15 132.609 166.8 1 62.61 ? O1B ATP 401 A 1 HETATM 7 O O2B ATP . . . F 5 116.135 132.564 165.332 1 63 ? O2B ATP 401 A 1 HETATM 8 O O3B ATP . . . F 5 114.215 130.926 164.85 1 61.76 ? O3B ATP 401 A 1 HETATM 9 P PA ATP . . . F 5 114.511 134.019 162.944 1 61.71 ? PA ATP 401 A 1 HETATM 10 O O1A ATP . . . F 5 114.304 132.912 161.951 1 62.68 ? O1A ATP 401 A 1 HETATM 11 O O2A ATP . . . F 5 115.979 134.333 163.047 1 62.33 ? O2A ATP 401 A 1 HETATM 12 O O3A ATP . . . F 5 113.935 133.561 164.418 1 62.37 ? O3A ATP 401 A 1 HETATM 13 O O5' ATP . . . F 5 113.687 135.361 162.444 1 62.63 ? O5' ATP 401 A 1 HETATM 14 C C5' ATP . . . F 5 112.539 135.727 163.171 1 62.99 ? C5' ATP 401 A 1 HETATM 15 C C4' ATP . . . F 5 111.544 136.379 162.268 1 62.49 ? C4' ATP 401 A 1 HETATM 16 O O4' ATP . . . F 5 112.105 136.714 161.145 1 62.99 ? O4' ATP 401 A 1 HETATM 17 C C3' ATP . . . F 5 110.321 135.316 161.903 1 62.45 ? C3' ATP 401 A 1 HETATM 18 O O3' ATP . . . F 5 109.026 135.988 162.116 1 62.83 ? O3' ATP 401 A 1 HETATM 19 C C2' ATP . . . F 5 110.447 135.031 160.708 1 62.34 ? C2' ATP 401 A 1 HETATM 20 O O2' ATP . . . F 5 109.098 134.787 160.097 1 63.25 ? O2' ATP 401 A 1 HETATM 21 C C1' ATP . . . F 5 111.094 136.352 160.097 1 62.4 ? C1' ATP 401 A 1 HETATM 22 N N9 ATP . . . F 5 111.697 136.108 158.956 1 62.25 ? N9 ATP 401 A 1 HETATM 23 C C8 ATP . . . F 5 112.697 135.234 158.989 1 62.51 ? C8 ATP 401 A 1 HETATM 24 N N7 ATP . . . F 5 113.183 135.12 157.753 1 62.89 ? N7 ATP 401 A 1 HETATM 25 C C5 ATP . . . F 5 112.478 135.929 156.961 1 62.82 ? C5 ATP 401 A 1 HETATM 26 C C6 ATP . . . F 5 112.554 136.192 155.617 1 63.45 ? C6 ATP 401 A 1 HETATM 27 N N6 ATP . . . F 5 113.454 135.664 154.605 1 63.17 ? N6 ATP 401 A 1 HETATM 28 N N1 ATP . . . F 5 111.723 137.05 155.059 1 63.64 ? N1 ATP 401 A 1 HETATM 29 C C2 ATP . . . F 5 110.79 137.668 155.814 1 63.09 ? C2 ATP 401 A 1 HETATM 30 N N3 ATP . . . F 5 110.712 137.408 157.135 1 62.45 ? N3 ATP 401 A 1 HETATM 31 C C4 ATP . . . F 5 111.56 136.536 157.701 1 62.43 ? C4 ATP 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 56 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #