data_3DY7 # _model_server_result.job_id pyDHMeplo6HRZZ0LZRJTUQ _model_server_result.datetime_utc '2024-11-07 12:39:17' _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 3dy7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":9000}' # _entry.id 3DY7 # _exptl.entry_id 3DY7 _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 1 _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 120 _cell.entry_id 3DY7 _cell.length_a 81.754 _cell.length_b 81.754 _cell.length_c 128.893 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DY7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _pdbx_struct_assembly.method_details PISA _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD1 ASN 135 A ASN 195 1_555 B MG MG . A MG 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc2 A OD1 ASP 148 A ASP 208 1_555 B MG MG . A MG 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.791 ? metalc ? metalc3 C O1B ATP . A ATP 9000 1_555 B MG MG . A MG 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc4 C O2A ATP . A ATP 9000 1_555 B MG MG . A MG 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? # _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 107 n n PG O2G ATP sing 108 n n PG O3G ATP sing 109 n n PG O3B ATP sing 110 n n O2G HOG2 ATP sing 111 n n O3G HOG3 ATP sing 112 n n PB O1B ATP doub 113 n n PB O2B ATP sing 114 n n PB O3B ATP sing 115 n n PB O3A ATP sing 116 n n O2B HOB2 ATP sing 117 n n PA O1A ATP doub 118 n n PA O2A ATP sing 119 n n PA O3A ATP sing 120 n n PA O5' ATP sing 121 n n O2A HOA2 ATP sing 122 n n O5' C5' ATP sing 123 n n C5' C4' ATP sing 124 n n C5' "H5'1" ATP sing 125 n n C5' "H5'2" ATP sing 126 n n C4' O4' ATP sing 127 n n C4' C3' ATP sing 128 n n C4' H4' ATP sing 129 n n O4' C1' ATP sing 130 n n C3' O3' ATP sing 131 n n C3' C2' ATP sing 132 n n C3' H3' ATP sing 133 n n O3' HO3' ATP sing 134 n n C2' O2' ATP sing 135 n n C2' C1' ATP sing 136 n n C2' H2' ATP sing 137 n n O2' HO2' ATP sing 138 n n C1' N9 ATP sing 139 n n C1' H1' ATP sing 140 n n N9 C8 ATP sing 141 n y N9 C4 ATP sing 142 n y C8 N7 ATP doub 143 n y C8 H8 ATP sing 144 n n N7 C5 ATP sing 145 n y C5 C6 ATP sing 146 n y C5 C4 ATP doub 147 n y C6 N6 ATP sing 148 n n C6 N1 ATP doub 149 n y N6 HN61 ATP sing 150 n n N6 HN62 ATP sing 151 n n N1 C2 ATP sing 152 n y C2 N3 ATP doub 153 n y C2 H2 ATP sing 154 n n N3 C4 ATP sing 155 n y # _atom_sites.entry_id 3DY7 _atom_sites.fract_transf_matrix[1][1] 0.012232 _atom_sites.fract_transf_matrix[1][2] 0.007062 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014124 _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] 0.007758 _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 MG A 1 9001 9001 MG MG . C 3 ATP A 1 9000 9000 ATP ATP . D 4 1CX A 1 9002 9002 1CX 1CX . # 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 . . . C 3 45.314 -6.623 2.29 1 58.6 ? PG ATP 9000 A 1 HETATM 2 O O1G ATP . . . C 3 44.281 -6.755 3.39 1 59.84 ? O1G ATP 9000 A 1 HETATM 3 O O2G ATP . . . C 3 45.622 -5.216 1.839 1 59.68 ? O2G ATP 9000 A 1 HETATM 4 O O3G ATP . . . C 3 45.093 -7.627 1.192 1 59.93 ? O3G ATP 9000 A 1 HETATM 5 P PB ATP . . . C 3 47.079 -7.981 4.1 1 55.41 ? PB ATP 9000 A 1 HETATM 6 O O1B ATP . . . C 3 46.504 -9.348 3.773 1 56.36 ? O1B ATP 9000 A 1 HETATM 7 O O2B ATP . . . C 3 48.542 -7.763 4.384 1 53.95 ? O2B ATP 9000 A 1 HETATM 8 O O3B ATP . . . C 3 46.771 -6.987 2.873 1 57.8 ? O3B ATP 9000 A 1 HETATM 9 P PA ATP . . . C 3 45.916 -8.457 6.488 1 56.34 ? PA ATP 9000 A 1 HETATM 10 O O1A ATP . . . C 3 45.217 -7.771 7.628 1 57.07 ? O1A ATP 9000 A 1 HETATM 11 O O2A ATP . . . C 3 45.272 -9.673 5.855 1 57.04 ? O2A ATP 9000 A 1 HETATM 12 O O3A ATP . . . C 3 46.205 -7.406 5.314 1 55.92 ? O3A ATP 9000 A 1 HETATM 13 O O5' ATP . . . C 3 47.455 -8.749 6.854 1 57.16 ? O5' ATP 9000 A 1 HETATM 14 C C5' ATP . . . C 3 47.975 -8.577 8.17 1 57.83 ? C5' ATP 9000 A 1 HETATM 15 C C4' ATP . . . C 3 49.501 -8.607 8.146 1 57.53 ? C4' ATP 9000 A 1 HETATM 16 O O4' ATP . . . C 3 49.933 -9.184 9.383 1 58.4 ? O4' ATP 9000 A 1 HETATM 17 C C3' ATP . . . C 3 50.075 -9.457 7.023 1 56.69 ? C3' ATP 9000 A 1 HETATM 18 O O3' ATP . . . C 3 50.794 -8.622 6.111 1 56.6 ? O3' ATP 9000 A 1 HETATM 19 C C2' ATP . . . C 3 51.058 -10.375 7.7 1 56.38 ? C2' ATP 9000 A 1 HETATM 20 O O2' ATP . . . C 3 52.338 -9.748 7.621 1 55.87 ? O2' ATP 9000 A 1 HETATM 21 C C1' ATP . . . C 3 50.663 -10.386 9.161 1 56.23 ? C1' ATP 9000 A 1 HETATM 22 N N9 ATP . . . C 3 49.808 -11.55 9.484 1 54.75 ? N9 ATP 9000 A 1 HETATM 23 C C8 ATP . . . C 3 48.528 -11.737 9.127 1 54.78 ? C8 ATP 9000 A 1 HETATM 24 N N7 ATP . . . C 3 48.057 -12.929 9.602 1 55.17 ? N7 ATP 9000 A 1 HETATM 25 C C5 ATP . . . C 3 49.064 -13.52 10.294 1 55.78 ? C5 ATP 9000 A 1 HETATM 26 C C6 ATP . . . C 3 49.282 -14.787 11.058 1 56.05 ? C6 ATP 9000 A 1 HETATM 27 N N6 ATP . . . C 3 48.307 -15.727 11.212 1 55.64 ? N6 ATP 9000 A 1 HETATM 28 N N1 ATP . . . C 3 50.508 -14.992 11.602 1 56.31 ? N1 ATP 9000 A 1 HETATM 29 C C2 ATP . . . C 3 51.513 -14.104 11.477 1 55.06 ? C2 ATP 9000 A 1 HETATM 30 N N3 ATP . . . C 3 51.385 -12.948 10.807 1 55.44 ? N3 ATP 9000 A 1 HETATM 31 C C4 ATP . . . C 3 50.212 -12.601 10.207 1 55.59 ? C4 ATP 9000 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #