data_6JON # _model_server_result.job_id a8_i_sf21FsDolPneI4hHg _model_server_result.datetime_utc '2025-02-26 02:57:38' _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 6jon # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6JON # _exptl.entry_id 6JON _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 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 96.06 _cell.angle_gamma 90 _cell.entry_id 6JON _cell.length_a 134.82 _cell.length_b 55.29 _cell.length_c 50.55 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JON _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,E _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 2 _struct_asym.id B _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 O THR 89 A THR 69 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc2 A O ASP 92 A ASP 72 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc3 A OD1 ASP 92 A ASP 72 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc4 A O PHE 94 A PHE 74 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? metalc ? metalc5 A OD1 ASP 98 A ASP 78 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc6 A OD1 ASP 100 A ASP 80 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc7 A O GLU 162 A GLU 142 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc8 B O2G DTP . A DTP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc9 B O2B DTP . A DTP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc10 B O2A DTP . A DTP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc11 C MG MG . A MG 402 1_555 E O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 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 DTP doub 83 n n PG O2G DTP sing 84 n n PG O3G DTP sing 85 n n PG O3B DTP sing 86 n n O2G HOG2 DTP sing 87 n n O3G HOG3 DTP sing 88 n n PB O1B DTP doub 89 n n PB O2B DTP sing 90 n n PB O3B DTP sing 91 n n PB O3A DTP sing 92 n n O2B HOB2 DTP sing 93 n n PA O1A DTP doub 94 n n PA O2A DTP sing 95 n n PA O3A DTP sing 96 n n PA O5' DTP sing 97 n n O2A HOA2 DTP sing 98 n n O5' C5' DTP sing 99 n n C5' C4' DTP sing 100 n n C5' "H5'1" DTP sing 101 n n C5' "H5'2" DTP sing 102 n n C4' O4' DTP sing 103 n n C4' C3' DTP sing 104 n n C4' H4' DTP sing 105 n n O4' C1' DTP sing 106 n n C3' O3' DTP sing 107 n n C3' C2' DTP sing 108 n n C3' H3' DTP sing 109 n n O3' HO3' DTP sing 110 n n C2' C1' DTP sing 111 n n C2' "H2'1" DTP sing 112 n n C2' "H2'2" DTP sing 113 n n C1' N9 DTP sing 114 n n C1' H1' DTP sing 115 n n N9 C8 DTP sing 116 n y N9 C4 DTP sing 117 n y C8 N7 DTP doub 118 n y C8 H8 DTP sing 119 n n N7 C5 DTP sing 120 n y C5 C6 DTP sing 121 n y C5 C4 DTP doub 122 n y C6 N6 DTP sing 123 n n C6 N1 DTP doub 124 n y N6 HN61 DTP sing 125 n n N6 HN62 DTP sing 126 n n N1 C2 DTP sing 127 n y C2 N3 DTP doub 128 n y C2 H2 DTP sing 129 n n N3 C4 DTP sing 130 n y # _atom_sites.entry_id 6JON _atom_sites.fract_transf_matrix[1][1] 0.007417 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000787 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018086 _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] 0.019894 _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 DTP A 1 401 1 DTP DAP . C 3 MG A 1 402 1 MG MG . D 3 MG A 1 403 2 MG MG . E 4 HOH A 1 501 1 HOH HOH . E 4 HOH A 2 502 2 HOH HOH . E 4 HOH A 3 503 8 HOH HOH . E 4 HOH A 4 504 5 HOH HOH . E 4 HOH A 5 505 9 HOH HOH . E 4 HOH A 6 506 4 HOH HOH . E 4 HOH A 7 507 7 HOH HOH . E 4 HOH A 8 508 6 HOH HOH . E 4 HOH A 9 509 10 HOH HOH . E 4 HOH A 10 510 3 HOH HOH . # 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 DTP . . . B 2 -12.407 24.203 3.459 1 75.4 ? PG DTP 401 A 1 HETATM 2 O O1G DTP . . . B 2 -11.377 24.856 2.555 1 76.43 ? O1G DTP 401 A 1 HETATM 3 O O2G DTP . . . B 2 -13.769 24.85 3.38 1 76.72 ? O2G DTP 401 A 1 HETATM 4 O O3G DTP . . . B 2 -11.925 24.072 4.893 1 78.45 ? O3G DTP 401 A 1 HETATM 5 P PB DTP . . . B 2 -13.781 22.134 1.696 1 72.34 ? PB DTP 401 A 1 HETATM 6 O O1B DTP . . . B 2 -13.485 20.858 0.961 1 74.33 ? O1B DTP 401 A 1 HETATM 7 O O2B DTP . . . B 2 -15.201 22.215 2.217 1 73.75 ? O2B DTP 401 A 1 HETATM 8 O O3B DTP . . . B 2 -12.687 22.54 2.739 1 76.46 ? O3B DTP 401 A 1 HETATM 9 P PA DTP . . . B 2 -14.758 24.464 -0.013 1 68.87 ? PA DTP 401 A 1 HETATM 10 O O1A DTP . . . B 2 -14.305 25.56 -0.935 1 69.43 ? O1A DTP 401 A 1 HETATM 11 O O2A DTP . . . B 2 -15.574 24.922 1.18 1 68.96 ? O2A DTP 401 A 1 HETATM 12 O O3A DTP . . . B 2 -13.81 23.256 0.217 1 72.13 ? O3A DTP 401 A 1 HETATM 13 O O5' DTP . . . B 2 -16.114 23.783 -1.136 1 69.03 ? O5' DTP 401 A 1 HETATM 14 C C5' DTP . . . B 2 -17.059 22.973 -0.597 1 68.27 ? C5' DTP 401 A 1 HETATM 15 C C4' DTP . . . B 2 -17.151 21.59 -1.414 1 68.58 ? C4' DTP 401 A 1 HETATM 16 O O4' DTP . . . B 2 -17.298 21.77 -2.831 1 69.08 ? O4' DTP 401 A 1 HETATM 17 C C3' DTP . . . B 2 -15.878 20.81 -1.185 1 68.16 ? C3' DTP 401 A 1 HETATM 18 O O3' DTP . . . B 2 -16.016 20.025 -0.014 1 67.88 ? O3' DTP 401 A 1 HETATM 19 C C2' DTP . . . B 2 -15.832 19.956 -2.482 1 69.11 ? C2' DTP 401 A 1 HETATM 20 C C1' DTP . . . B 2 -16.519 20.869 -3.57 1 70.51 ? C1' DTP 401 A 1 HETATM 21 N N9 DTP . . . B 2 -15.573 21.659 -4.505 1 73.46 ? N9 DTP 401 A 1 HETATM 22 C C8 DTP . . . B 2 -14.666 22.627 -4.039 1 74.66 ? C8 DTP 401 A 1 HETATM 23 N N7 DTP . . . B 2 -13.94 23.191 -5.037 1 75.92 ? N7 DTP 401 A 1 HETATM 24 C C5 DTP . . . B 2 -14.374 22.579 -6.238 1 76.56 ? C5 DTP 401 A 1 HETATM 25 C C6 DTP . . . B 2 -13.994 22.74 -7.632 1 79.17 ? C6 DTP 401 A 1 HETATM 26 N N6 DTP . . . B 2 -13.004 23.653 -8.061 1 83.82 ? N6 DTP 401 A 1 HETATM 27 N N1 DTP . . . B 2 -14.629 21.969 -8.569 1 78.8 ? N1 DTP 401 A 1 HETATM 28 C C2 DTP . . . B 2 -15.607 21.067 -8.151 1 78.23 ? C2 DTP 401 A 1 HETATM 29 N N3 DTP . . . B 2 -16.026 20.85 -6.878 1 76.85 ? N3 DTP 401 A 1 HETATM 30 C C4 DTP . . . B 2 -15.399 21.617 -5.913 1 75.67 ? C4 DTP 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 30 #