data_3U8X # _model_server_result.job_id zj5r1JAxrvD5uW2AJcNUEQ _model_server_result.datetime_utc '2024-11-16 01:26:12' _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 3u8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 3U8X # _exptl.entry_id 3U8X _exptl.method 'X-RAY DIFFRACTION' # _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 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 3U8X _cell.length_a 46.011 _cell.length_b 75.326 _cell.length_c 128.866 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F 1 1 C,D,G,H 2 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 E N N ? 3 G 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 E O3G ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc2 E O1G ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc3 E O1B ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc4 C OD2 ASP 154 C ASP 154 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? # _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 3U8X _atom_sites.fract_transf_matrix[1][1] 0.021734 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000002 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013276 _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] 0.00776 _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 3 ATP A 1 501 501 ATP ATP . F 4 MG A 1 502 502 MG MG . G 3 ATP C 1 501 501 ATP ATP . H 4 MG C 1 502 502 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 . . . G 3 8.568 -32.623 13.1 1 32.83 ? PG ATP 501 C 1 HETATM 2 O O1G ATP . . . G 3 9.057 -31.908 14.373 1 31.84 ? O1G ATP 501 C 1 HETATM 3 O O2G ATP . . . G 3 7.08 -33.013 13.274 1 23.98 ? O2G ATP 501 C 1 HETATM 4 O O3G ATP . . . G 3 9.446 -32.046 11.849 1 10.95 ? O3G ATP 501 C 1 HETATM 5 P PB ATP . . . G 3 10.403 -34.152 14.084 1 13.4 ? PB ATP 501 C 1 HETATM 6 O O1B ATP . . . G 3 11.415 -33.314 13.399 1 14.83 ? O1B ATP 501 C 1 HETATM 7 O O2B ATP . . . G 3 10.241 -34.236 15.604 1 12.62 ? O2B ATP 501 C 1 HETATM 8 O O3B ATP . . . G 3 9.004 -34.094 13.458 1 14.81 ? O3B ATP 501 C 1 HETATM 9 P PA ATP . . . G 3 11.885 -36.595 13.352 1 13.53 ? PA ATP 501 C 1 HETATM 10 O O1A ATP . . . G 3 12.515 -36.254 12.019 1 9.06 ? O1A ATP 501 C 1 HETATM 11 O O2A ATP . . . G 3 12.635 -36.388 14.593 1 14.45 ? O2A ATP 501 C 1 HETATM 12 O O3A ATP . . . G 3 10.569 -35.708 13.505 1 11.48 ? O3A ATP 501 C 1 HETATM 13 O O5' ATP . . . G 3 11.191 -38.019 13.146 1 11.97 ? O5' ATP 501 C 1 HETATM 14 C C5' ATP . . . G 3 10.47 -38.656 14.157 1 12.35 ? C5' ATP 501 C 1 HETATM 15 C C4' ATP . . . G 3 9.682 -39.741 13.463 1 7.1 ? C4' ATP 501 C 1 HETATM 16 O O4' ATP . . . G 3 10.647 -40.587 12.871 1 10.21 ? O4' ATP 501 C 1 HETATM 17 C C3' ATP . . . G 3 8.98 -40.605 14.476 1 9.19 ? C3' ATP 501 C 1 HETATM 18 O O3' ATP . . . G 3 7.656 -40.874 14.092 1 3.76 ? O3' ATP 501 C 1 HETATM 19 C C2' ATP . . . G 3 9.76 -41.927 14.447 1 11.83 ? C2' ATP 501 C 1 HETATM 20 O O2' ATP . . . G 3 9.026 -43.119 14.766 1 13.3 ? O2' ATP 501 C 1 HETATM 21 C C1' ATP . . . G 3 10.146 -41.929 12.989 1 11.91 ? C1' ATP 501 C 1 HETATM 22 N N9 ATP . . . G 3 11.253 -42.823 12.762 1 13.42 ? N9 ATP 501 C 1 HETATM 23 C C8 ATP . . . G 3 12.42 -42.737 13.381 1 14.4 ? C8 ATP 501 C 1 HETATM 24 N N7 ATP . . . G 3 13.253 -43.683 12.917 1 12.67 ? N7 ATP 501 C 1 HETATM 25 C C5 ATP . . . G 3 12.581 -44.365 11.999 1 10.56 ? C5 ATP 501 C 1 HETATM 26 C C6 ATP . . . G 3 12.905 -45.513 11.173 1 11.72 ? C6 ATP 501 C 1 HETATM 27 N N6 ATP . . . G 3 14.178 -46.083 11.278 1 12.82 ? N6 ATP 501 C 1 HETATM 28 N N1 ATP . . . G 3 11.928 -45.931 10.311 1 8.67 ? N1 ATP 501 C 1 HETATM 29 C C2 ATP . . . G 3 10.7 -45.376 10.271 1 13.08 ? C2 ATP 501 C 1 HETATM 30 N N3 ATP . . . G 3 10.342 -44.291 10.986 1 10.04 ? N3 ATP 501 C 1 HETATM 31 C C4 ATP . . . G 3 11.258 -43.794 11.875 1 12.39 ? C4 ATP 501 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #