data_8PMD # _model_server_result.job_id 3OI4q2ameVZuYQe8wawT3A _model_server_result.datetime_utc '2024-11-04 22:45:35' _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 8pmd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1501}' # _entry.id 8PMD # _exptl.entry_id 8PMD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _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 8PMD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PMD _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 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 _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 B N N ? 2 C 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 462 A SER 462 1_555 E MG MG . A MG 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc2 A OE1 GLN 503 A GLN 503 1_555 E MG MG . A MG 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc3 A OG SER 1120 A SER 1120 1_555 D MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc4 A OE1 GLN 1161 A GLN 1161 1_555 D MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc5 B O2G ATP . A ATP 1501 1_555 D MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc6 B O1B ATP . A ATP 1501 1_555 D MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc7 C O3G ATP . A ATP 1502 1_555 E MG MG . A MG 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc8 C O2B ATP . A ATP 1502 1_555 E MG MG . A MG 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc9 D MG MG . A MG 1503 1_555 F O HOH . A HOH 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc10 E MG MG . A MG 1504 1_555 F O HOH . A HOH 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? # _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 8PMD _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 B 2 ATP A 1 1501 1501 ATP ATP . C 2 ATP A 1 1502 1701 ATP ATP . D 3 MG A 1 1503 1303 MG MG . E 3 MG A 1 1504 1 MG MG . F 4 HOH A 1 1601 2 HOH HOH . F 4 HOH A 2 1602 4 HOH HOH . # 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 . . . B 2 117.98 125.283 177.36 1 28.56 ? PG ATP 1501 A 1 HETATM 2 O O1G ATP . . . B 2 117.464 125.733 178.679 1 32.61 ? O1G ATP 1501 A 1 HETATM 3 O O2G ATP . . . B 2 117.455 126.096 176.188 1 21.39 ? O2G ATP 1501 A 1 HETATM 4 O O3G ATP . . . B 2 119.504 125.225 177.301 1 31.23 ? O3G ATP 1501 A 1 HETATM 5 P PB ATP . . . B 2 116.208 123.002 176.624 1 18.64 ? PB ATP 1501 A 1 HETATM 6 O O1B ATP . . . B 2 115.205 123.889 176.01 1 30.01 ? O1B ATP 1501 A 1 HETATM 7 O O2B ATP . . . B 2 115.745 122.217 177.844 1 27.92 ? O2B ATP 1501 A 1 HETATM 8 O O3B ATP . . . B 2 117.509 123.793 177.051 1 28.68 ? O3B ATP 1501 A 1 HETATM 9 P PA ATP . . . B 2 116.419 121.467 174.11 1 19.5 ? PA ATP 1501 A 1 HETATM 10 O O1A ATP . . . B 2 115.032 120.972 174.013 1 34.01 ? O1A ATP 1501 A 1 HETATM 11 O O2A ATP . . . B 2 116.752 122.611 173.16 1 33.09 ? O2A ATP 1501 A 1 HETATM 12 O O3A ATP . . . B 2 116.782 121.953 175.575 1 20.32 ? O3A ATP 1501 A 1 HETATM 13 O O5' ATP . . . B 2 117.455 120.307 173.847 1 30.8 ? O5' ATP 1501 A 1 HETATM 14 C C5' ATP . . . B 2 117.635 119.23 174.788 1 22.03 ? C5' ATP 1501 A 1 HETATM 15 C C4' ATP . . . B 2 118.778 118.362 174.319 1 29.45 ? C4' ATP 1501 A 1 HETATM 16 O O4' ATP . . . B 2 118.609 118.044 172.92 1 28.71 ? O4' ATP 1501 A 1 HETATM 17 C C3' ATP . . . B 2 120.166 118.984 174.443 1 28.92 ? C3' ATP 1501 A 1 HETATM 18 O O3' ATP . . . B 2 121.141 118.003 174.773 1 28.67 ? O3' ATP 1501 A 1 HETATM 19 C C2' ATP . . . B 2 120.394 119.577 173.051 1 26.57 ? C2' ATP 1501 A 1 HETATM 20 O O2' ATP . . . B 2 121.78 119.666 172.742 1 35.71 ? O2' ATP 1501 A 1 HETATM 21 C C1' ATP . . . B 2 119.698 118.544 172.166 1 21.42 ? C1' ATP 1501 A 1 HETATM 22 N N9 ATP . . . B 2 119.172 119.084 170.919 1 18.2 ? N9 ATP 1501 A 1 HETATM 23 C C8 ATP . . . B 2 118.447 120.235 170.761 1 26.24 ? C8 ATP 1501 A 1 HETATM 24 N N7 ATP . . . B 2 118.088 120.477 169.525 1 31.1 ? N7 ATP 1501 A 1 HETATM 25 C C5 ATP . . . B 2 118.611 119.407 168.817 1 24.87 ? C5 ATP 1501 A 1 HETATM 26 C C6 ATP . . . B 2 118.58 119.065 167.452 1 19.88 ? C6 ATP 1501 A 1 HETATM 27 N N6 ATP . . . B 2 117.975 119.8 166.514 1 23.81 ? N6 ATP 1501 A 1 HETATM 28 N N1 ATP . . . B 2 119.2 117.926 167.075 1 25.7 ? N1 ATP 1501 A 1 HETATM 29 C C2 ATP . . . B 2 119.806 117.186 168.006 1 25.96 ? C2 ATP 1501 A 1 HETATM 30 N N3 ATP . . . B 2 119.9 117.407 169.319 1 25.95 ? N3 ATP 1501 A 1 HETATM 31 C C4 ATP . . . B 2 119.28 118.539 169.664 1 23.96 ? C4 ATP 1501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #