data_5XMK # _model_server_result.job_id k524mWyhqLI-W_d95u8v4w _model_server_result.datetime_utc '2024-11-05 02:21:35' _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 5xmk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","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 . . . S 3 154.788 123.955 110.776 1 193.62 ? PG ATP 501 F 1 HETATM 2 O O1G ATP . . . S 3 154.953 124.303 109.317 1 195.18 ? O1G ATP 501 F 1 HETATM 3 O O2G ATP . . . S 3 154.509 122.495 111.041 1 194.85 ? O2G ATP 501 F 1 HETATM 4 O O3G ATP . . . S 3 153.906 124.91 111.541 1 196.09 ? O3G ATP 501 F 1 HETATM 5 P PB ATP . . . S 3 157.555 123.426 110.882 1 198.74 ? PB ATP 501 F 1 HETATM 6 O O1B ATP . . . S 3 157.207 122.472 109.763 1 198.99 ? O1B ATP 501 F 1 HETATM 7 O O2B ATP . . . S 3 158.291 122.902 112.092 1 199.62 ? O2B ATP 501 F 1 HETATM 8 O O3B ATP . . . S 3 156.246 124.196 111.414 1 195.28 ? O3B ATP 501 F 1 HETATM 9 P PA ATP . . . S 3 160.001 124.447 110.082 1 229.21 ? PA ATP 501 F 1 HETATM 10 O O1A ATP . . . S 3 160.225 123.097 109.451 1 229.08 ? O1A ATP 501 F 1 HETATM 11 O O2A ATP . . . S 3 160.659 124.775 111.4 1 227.94 ? O2A ATP 501 F 1 HETATM 12 O O3A ATP . . . S 3 158.415 124.634 110.26 1 213.99 ? O3A ATP 501 F 1 HETATM 13 O O5' ATP . . . S 3 160.414 125.575 109.014 1 242.59 ? O5' ATP 501 F 1 HETATM 14 C C5' ATP . . . S 3 161.788 125.906 108.815 1 254.65 ? C5' ATP 501 F 1 HETATM 15 C C4' ATP . . . S 3 162.2 127.006 109.8 1 264.3 ? C4' ATP 501 F 1 HETATM 16 O O4' ATP . . . S 3 163.123 126.475 110.758 1 267.94 ? O4' ATP 501 F 1 HETATM 17 C C3' ATP . . . S 3 162.891 128.193 109.139 1 271.06 ? C3' ATP 501 F 1 HETATM 18 O O3' ATP . . . S 3 162.363 129.423 109.652 1 274.4 ? O3' ATP 501 F 1 HETATM 19 C C2' ATP . . . S 3 164.361 128.031 109.477 1 272.49 ? C2' ATP 501 F 1 HETATM 20 O O2' ATP . . . S 3 165.019 129.287 109.689 1 272.48 ? O2' ATP 501 F 1 HETATM 21 C C1' ATP . . . S 3 164.373 127.179 110.743 1 273.4 ? C1' ATP 501 F 1 HETATM 22 N N9 ATP . . . S 3 165.52 126.221 110.828 1 277.07 ? N9 ATP 501 F 1 HETATM 23 C C8 ATP . . . S 3 166.707 126.292 110.181 1 279.43 ? C8 ATP 501 F 1 HETATM 24 N N7 ATP . . . S 3 167.509 125.247 110.514 1 278.47 ? N7 ATP 501 F 1 HETATM 25 C C5 ATP . . . S 3 166.842 124.485 111.394 1 277.04 ? C5 ATP 501 F 1 HETATM 26 C C6 ATP . . . S 3 167.102 123.235 112.152 1 274.67 ? C6 ATP 501 F 1 HETATM 27 N N6 ATP . . . S 3 168.264 122.563 112.035 1 272.85 ? N6 ATP 501 F 1 HETATM 28 N N1 ATP . . . S 3 166.134 122.771 112.977 1 276.12 ? N1 ATP 501 F 1 HETATM 29 C C2 ATP . . . S 3 164.957 123.411 113.122 1 278.79 ? C2 ATP 501 F 1 HETATM 30 N N3 ATP . . . S 3 164.655 124.55 112.463 1 279.8 ? N3 ATP 501 F 1 HETATM 31 C C4 ATP . . . S 3 165.536 125.132 111.603 1 278.72 ? C4 ATP 501 F 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #