data_3U9D # _model_server_result.job_id UtznkLfcjL4R6Z4JMPB6cg _model_server_result.datetime_utc '2024-11-25 06:30:08' _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 3u9d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 3U9D # _exptl.entry_id 3U9D _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 90.03 _cell.angle_gamma 90 _cell.entry_id 3U9D _cell.length_a 45.698 _cell.length_b 75.738 _cell.length_c 128.518 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U9D _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 author_and_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 O1B ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc2 E O3G ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc3 C OD1 ASP 11 C ASP 11 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? metalc ? metalc4 G O3G ATP . C ATP 501 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc5 G O1B ATP . C ATP 501 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc6 G O1G ATP . C ATP 501 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? # _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 3U9D _atom_sites.fract_transf_matrix[1][1] 0.021883 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000011 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013203 _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] 0.007781 _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 -12.731 -32.263 -52.322 1 33.56 ? PG ATP 501 C 1 HETATM 2 O O1G ATP . . . G 3 -13.073 -30.984 -51.569 1 35.03 ? O1G ATP 501 C 1 HETATM 3 O O2G ATP . . . G 3 -13.499 -32.494 -53.628 1 34.92 ? O2G ATP 501 C 1 HETATM 4 O O3G ATP . . . G 3 -11.24 -32.542 -52.397 1 31.97 ? O3G ATP 501 C 1 HETATM 5 P PB ATP . . . G 3 -12.204 -34.157 -50.489 1 28.22 ? PB ATP 501 C 1 HETATM 6 O O1B ATP . . . G 3 -10.893 -33.411 -50.699 1 27.68 ? O1B ATP 501 C 1 HETATM 7 O O2B ATP . . . G 3 -12.739 -34.49 -49.135 1 21.86 ? O2B ATP 501 C 1 HETATM 8 O O3B ATP . . . G 3 -13.327 -33.396 -51.344 1 29.3 ? O3B ATP 501 C 1 HETATM 9 P PA ATP . . . G 3 -11.279 -36.643 -50.718 1 26.68 ? PA ATP 501 C 1 HETATM 10 O O1A ATP . . . G 3 -9.898 -36.643 -51.293 1 23.36 ? O1A ATP 501 C 1 HETATM 11 O O2A ATP . . . G 3 -11.657 -36.303 -49.306 1 30.11 ? O2A ATP 501 C 1 HETATM 12 O O3A ATP . . . G 3 -12.095 -35.486 -51.383 1 29 ? O3A ATP 501 C 1 HETATM 13 O O5' ATP . . . G 3 -11.984 -38.028 -51.105 1 26.33 ? O5' ATP 501 C 1 HETATM 14 C C5' ATP . . . G 3 -12.356 -38.931 -50.093 1 23.13 ? C5' ATP 501 C 1 HETATM 15 C C4' ATP . . . G 3 -13.034 -40.1 -50.768 1 23.09 ? C4' ATP 501 C 1 HETATM 16 O O4' ATP . . . G 3 -12.102 -40.932 -51.496 1 24.2 ? O4' ATP 501 C 1 HETATM 17 C C3' ATP . . . G 3 -13.618 -40.958 -49.674 1 23.04 ? C3' ATP 501 C 1 HETATM 18 O O3' ATP . . . G 3 -15.006 -41.167 -49.92 1 23.63 ? O3' ATP 501 C 1 HETATM 19 C C2' ATP . . . G 3 -12.932 -42.293 -49.791 1 22.69 ? C2' ATP 501 C 1 HETATM 20 O O2' ATP . . . G 3 -13.984 -43.212 -49.546 1 22.85 ? O2' ATP 501 C 1 HETATM 21 C C1' ATP . . . G 3 -12.409 -42.312 -51.229 1 22.53 ? C1' ATP 501 C 1 HETATM 22 N N9 ATP . . . G 3 -11.293 -43.282 -51.439 1 21.7 ? N9 ATP 501 C 1 HETATM 23 C C8 ATP . . . G 3 -10.103 -43.29 -50.818 1 23.37 ? C8 ATP 501 C 1 HETATM 24 N N7 ATP . . . G 3 -9.32 -44.33 -51.232 1 24.46 ? N7 ATP 501 C 1 HETATM 25 C C5 ATP . . . G 3 -10.027 -45.036 -52.148 1 23.34 ? C5 ATP 501 C 1 HETATM 26 C C6 ATP . . . G 3 -9.818 -46.264 -52.981 1 23.77 ? C6 ATP 501 C 1 HETATM 27 N N6 ATP . . . G 3 -8.668 -46.993 -52.96 1 23.24 ? N6 ATP 501 C 1 HETATM 28 N N1 ATP . . . G 3 -10.834 -46.642 -53.794 1 24.06 ? N1 ATP 501 C 1 HETATM 29 C C2 ATP . . . G 3 -11.988 -45.94 -53.855 1 22.74 ? C2 ATP 501 C 1 HETATM 30 N N3 ATP . . . G 3 -12.229 -44.844 -53.121 1 21.37 ? N3 ATP 501 C 1 HETATM 31 C C4 ATP . . . G 3 -11.319 -44.336 -52.27 1 21.47 ? C4 ATP 501 C 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #