data_5XMK # _model_server_result.job_id XBv2yDnii2NQDCfGWWcNSg _model_server_result.datetime_utc '2024-11-05 02:25:48' _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 5xmk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":501}' # _entry.id 5XMK # _exptl.entry_id 5XMK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 5 _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 5XMK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XMK _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 tetradecameric _pdbx_struct_assembly.oligomeric_count 14 _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,I,J,K,L,M,N,O,P,Q,R,S _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 O N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N # _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 5XMK _atom_sites.fract_transf_matrix[1][1] 0.003946 _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] 0.003946 _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] 0.003946 _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 O 3 ATP B 1 501 501 ATP ATP . P 3 ATP C 1 501 501 ATP ATP . Q 3 ATP D 1 501 501 ATP ATP . R 3 ATP E 1 501 501 ATP ATP . S 3 ATP F 1 501 501 ATP ATP . # 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 . . . R 3 143.279 150.218 114.438 1 202.08 ? PG ATP 501 E 1 HETATM 2 O O1G ATP . . . R 3 143.223 149.893 112.965 1 199.55 ? O1G ATP 501 E 1 HETATM 3 O O2G ATP . . . R 3 143.007 149.024 115.303 1 203.31 ? O2G ATP 501 E 1 HETATM 4 O O3G ATP . . . R 3 142.561 151.477 114.866 1 201.21 ? O3G ATP 501 E 1 HETATM 5 P PB ATP . . . R 3 145.649 151.522 113.741 1 204.46 ? PB ATP 501 E 1 HETATM 6 O O1B ATP . . . R 3 145.932 150.738 112.483 1 205.45 ? O1B ATP 501 E 1 HETATM 7 O O2B ATP . . . R 3 146.795 152.086 114.545 1 201.8 ? O2B ATP 501 E 1 HETATM 8 O O3B ATP . . . R 3 144.81 150.584 114.739 1 203.04 ? O3B ATP 501 E 1 HETATM 9 P PA ATP . . . R 3 145.368 154.11 112.857 1 216.85 ? PA ATP 501 E 1 HETATM 10 O O1A ATP . . . R 3 146.544 153.778 111.978 1 217.08 ? O1A ATP 501 E 1 HETATM 11 O O2A ATP . . . R 3 145.632 154.896 114.111 1 219.2 ? O2A ATP 501 E 1 HETATM 12 O O3A ATP . . . R 3 144.679 152.734 113.32 1 209.71 ? O3A ATP 501 E 1 HETATM 13 O O5' ATP . . . R 3 144.26 154.875 111.973 1 222.31 ? O5' ATP 501 E 1 HETATM 14 C C5' ATP . . . R 3 144.538 156.164 111.415 1 226.23 ? C5' ATP 501 E 1 HETATM 15 C C4' ATP . . . R 3 144.502 157.226 112.519 1 229.05 ? C4' ATP 501 E 1 HETATM 16 O O4' ATP . . . R 3 145.828 157.647 112.865 1 227.92 ? O4' ATP 501 E 1 HETATM 17 C C3' ATP . . . R 3 143.724 158.49 112.171 1 231.03 ? C3' ATP 501 E 1 HETATM 18 O O3' ATP . . . R 3 142.532 158.568 112.963 1 232 ? O3' ATP 501 E 1 HETATM 19 C C2' ATP . . . R 3 144.672 159.638 112.47 1 230.61 ? C2' ATP 501 E 1 HETATM 20 O O2' ATP . . . R 3 144.04 160.719 113.168 1 232.59 ? O2' ATP 501 E 1 HETATM 21 C C1' ATP . . . R 3 145.768 159.002 113.32 1 227.25 ? C1' ATP 501 E 1 HETATM 22 N N9 ATP . . . R 3 147.104 159.67 113.257 1 224.69 ? N9 ATP 501 E 1 HETATM 23 C C8 ATP . . . R 3 147.456 160.771 112.55 1 225.72 ? C8 ATP 501 E 1 HETATM 24 N N7 ATP . . . R 3 148.757 161.089 112.758 1 225.25 ? N7 ATP 501 E 1 HETATM 25 C C5 ATP . . . R 3 149.264 160.19 113.614 1 223.45 ? C5 ATP 501 E 1 HETATM 26 C C6 ATP . . . R 3 150.584 159.953 114.249 1 222.56 ? C6 ATP 501 E 1 HETATM 27 N N6 ATP . . . R 3 151.623 160.775 113.983 1 223.35 ? N6 ATP 501 E 1 HETATM 28 N N1 ATP . . . R 3 150.706 158.899 115.093 1 220.47 ? N1 ATP 501 E 1 HETATM 29 C C2 ATP . . . R 3 149.666 158.077 115.359 1 220.67 ? C2 ATP 501 E 1 HETATM 30 N N3 ATP . . . R 3 148.439 158.24 114.81 1 221.73 ? N3 ATP 501 E 1 HETATM 31 C C4 ATP . . . R 3 148.175 159.259 113.947 1 222.53 ? C4 ATP 501 E 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 66 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #