data_5DRD # _model_server_result.job_id Und7yH31N46TA_CcMXOrGA _model_server_result.datetime_utc '2024-10-10 09:23:05' _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 5drd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5DRD # _exptl.entry_id 5DRD _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 5DRD _cell.length_a 81.61 _cell.length_b 81.61 _cell.length_c 166.45 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DRD _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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 138 A ASN 261 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc2 A OD2 ASP 151 A ASP 274 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc3 B MG MG . A MG 401 1_555 C O2B ATP . A ATP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc4 B MG MG . A MG 401 1_555 C O1A ATP . A ATP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? # _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 5DRD _atom_sites.fract_transf_matrix[1][1] 0.012253 _atom_sites.fract_transf_matrix[1][2] 0.007075 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014149 _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] 0.006008 _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 1 401 1 MG MG . C 3 ATP A 1 402 1 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 . . . C 3 -13.363 -22.574 7.778 1 91.98 ? PG ATP 402 A 1 HETATM 2 O O1G ATP . . . C 3 -13.435 -21.211 7.101 1 87.39 ? O1G ATP 402 A 1 HETATM 3 O O2G ATP . . . C 3 -14.533 -23.442 7.385 1 69.97 ? O2G ATP 402 A 1 HETATM 4 O O3G ATP . . . C 3 -13.072 -22.261 9.273 1 64.69 ? O3G ATP 402 A 1 HETATM 5 P PB ATP . . . C 3 -11.44 -23.75 5.731 1 46.36 ? PB ATP 402 A 1 HETATM 6 O O1B ATP . . . C 3 -10.878 -22.605 4.957 1 52.49 ? O1B ATP 402 A 1 HETATM 7 O O2B ATP . . . C 3 -12.214 -24.838 5.103 1 37.39 ? O2B ATP 402 A 1 HETATM 8 O O3B ATP . . . C 3 -12.047 -23.384 7.192 1 53.52 ? O3B ATP 402 A 1 HETATM 9 P PA ATP . . . C 3 -9.917 -26.025 6.751 1 40.88 ? PA ATP 402 A 1 HETATM 10 O O1A ATP . . . C 3 -11.132 -26.792 6.335 1 41.43 ? O1A ATP 402 A 1 HETATM 11 O O2A ATP . . . C 3 -9.616 -26.024 8.259 1 48.09 ? O2A ATP 402 A 1 HETATM 12 O O3A ATP . . . C 3 -10.08 -24.512 6.217 1 46.25 ? O3A ATP 402 A 1 HETATM 13 O O5' ATP . . . C 3 -8.61 -26.637 6.093 1 43.41 ? O5' ATP 402 A 1 HETATM 14 C C5' ATP . . . C 3 -8.357 -26.409 4.671 1 45.07 ? C5' ATP 402 A 1 HETATM 15 C C4' ATP . . . C 3 -7.724 -27.618 4.017 1 41.45 ? C4' ATP 402 A 1 HETATM 16 O O4' ATP . . . C 3 -6.382 -27.781 4.476 1 48.25 ? O4' ATP 402 A 1 HETATM 17 C C3' ATP . . . C 3 -8.385 -28.922 4.426 1 42.28 ? C3' ATP 402 A 1 HETATM 18 O O3' ATP . . . C 3 -9.527 -29.255 3.633 1 41.75 ? O3' ATP 402 A 1 HETATM 19 C C2' ATP . . . C 3 -7.216 -29.879 4.386 1 42.24 ? C2' ATP 402 A 1 HETATM 20 O O2' ATP . . . C 3 -6.892 -30.206 3.052 1 50.61 ? O2' ATP 402 A 1 HETATM 21 C C1' ATP . . . C 3 -6.026 -29.12 4.855 1 41.81 ? C1' ATP 402 A 1 HETATM 22 N N9 ATP . . . C 3 -5.865 -29.255 6.338 1 40.75 ? N9 ATP 402 A 1 HETATM 23 C C8 ATP . . . C 3 -6.516 -28.505 7.277 1 43.15 ? C8 ATP 402 A 1 HETATM 24 N N7 ATP . . . C 3 -6.16 -28.872 8.581 1 38.58 ? N7 ATP 402 A 1 HETATM 25 C C5 ATP . . . C 3 -5.32 -29.895 8.462 1 35.35 ? C5 ATP 402 A 1 HETATM 26 C C6 ATP . . . C 3 -4.603 -30.725 9.402 1 37.19 ? C6 ATP 402 A 1 HETATM 27 N N6 ATP . . . C 3 -4.732 -30.563 10.778 1 37.94 ? N6 ATP 402 A 1 HETATM 28 N N1 ATP . . . C 3 -3.814 -31.643 8.883 1 35.95 ? N1 ATP 402 A 1 HETATM 29 C C2 ATP . . . C 3 -3.68 -31.826 7.57 1 42.23 ? C2 ATP 402 A 1 HETATM 30 N N3 ATP . . . C 3 -4.313 -31.092 6.681 1 36.62 ? N3 ATP 402 A 1 HETATM 31 C C4 ATP . . . C 3 -5.121 -30.126 7.008 1 35.2 ? C4 ATP 402 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #