data_3LDS # _model_server_result.job_id ku5jzODCHdjL_s5pfuei8g _model_server_result.datetime_utc '2025-01-25 08:13:37' _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 3lds # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":904}' # _entry.id 3LDS # _exptl.entry_id 3LDS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 4 _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 90 _cell.angle_gamma 90 _cell.entry_id 3LDS _cell.length_a 81.011 _cell.length_b 121.002 _cell.length_c 128.668 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LDS _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H,I,J,K _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 4 _struct_asym.id D _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 covale ? covale1 B O3' DA 13 P DA 113 1_555 B P DDG 14 P DDG 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? covale ? covale2 C O3' DA 2 T DA 2 1_555 C P 8OG 3 T 8OG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? covale ? covale3 C O3' 8OG 3 T 8OG 3 1_555 C P DC 4 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? metalc ? metalc1 A OD2 ASP 114 A ASP 114 1_555 G MN MN . A MN 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc2 A OE2 GLU 116 A GLU 116 1_555 G MN MN . A MN 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc3 A OD2 ASP 411 A ASP 411 1_555 E MN MN . A MN 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc4 A OD1 ASP 411 A ASP 411 1_555 F MN MN . A MN 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc5 A O LEU 412 A LEU 412 1_555 F MN MN . A MN 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc6 A OD1 ASP 623 A ASP 623 1_555 E MN MN . A MN 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc7 A OD2 ASP 623 A ASP 623 1_555 F MN MN . A MN 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc8 D O2A DTP . A DTP 904 1_555 E MN MN . A MN 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc9 D O3G DTP . A DTP 904 1_555 F MN MN . A MN 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc10 D O2A DTP . A DTP 904 1_555 F MN MN . A MN 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc11 D O2B DTP . A DTP 904 1_555 F MN MN . A MN 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc12 E MN MN . A MN 906 1_555 J O HOH . A HOH 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? hydrog 'DG-DC PAIR' hydrog1 B N1 DG 1 P DG 101 1_555 C O2 DC 17 T DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N3 DC 2 P DC 102 1_555 C N1 DG 16 T DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N4 DC 2 P DC 102 1_555 C O6 DG 16 T DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O2 DC 2 P DC 102 1_555 C N2 DG 16 T DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DG 3 P DG 103 1_555 C N3 DC 15 T DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N2 DG 3 P DG 103 1_555 C O2 DC 15 T DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O6 DG 3 P DG 103 1_555 C N4 DC 15 T DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DG 4 P DG 104 1_555 C N3 DC 14 T DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N2 DG 4 P DG 104 1_555 C O2 DC 14 T DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O6 DG 4 P DG 104 1_555 C N4 DC 14 T DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 5 P DC 105 1_555 C N1 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 5 P DC 105 1_555 C O6 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 5 P DC 105 1_555 C N2 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DT 6 P DT 106 1_555 C N1 DA 12 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O4 DT 6 P DT 106 1_555 C N6 DA 12 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 7 P DG 107 1_555 C N3 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 7 P DG 107 1_555 C O2 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 7 P DG 107 1_555 C N4 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 8 P DT 108 1_555 C N1 DA 10 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 8 P DT 108 1_555 C N6 DA 10 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DC 9 P DC 109 1_555 C N1 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 DC 9 P DC 109 1_555 C O6 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 DC 9 P DC 109 1_555 C N2 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DA MISPAIR' hydrog24 B N6 DA 10 P DA 110 1_555 C N1 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N1 DA 10 P DA 110 1_555 C N3 DT 8 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N6 DA 10 P DA 110 1_555 C O4 DT 8 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N3 DT 11 P DT 111 1_555 C N1 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O4 DT 11 P DT 111 1_555 C N6 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N1 DA 12 P DA 112 1_555 C N3 DT 6 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N6 DA 12 P DA 112 1_555 C O4 DT 6 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N1 DA 13 P DA 113 1_555 C N3 DT 5 T DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B N6 DA 13 P DA 113 1_555 C O4 DT 5 T DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N1 DDG 14 P DDG 114 1_555 C N3 DC 4 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B N2 DDG 14 P DDG 114 1_555 C O2 DC 4 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B O6 DDG 14 P DDG 114 1_555 C N4 DC 4 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 310 n n PG O2G DTP sing 311 n n PG O3G DTP sing 312 n n PG O3B DTP sing 313 n n O2G HOG2 DTP sing 314 n n O3G HOG3 DTP sing 315 n n PB O1B DTP doub 316 n n PB O2B DTP sing 317 n n PB O3B DTP sing 318 n n PB O3A DTP sing 319 n n O2B HOB2 DTP sing 320 n n PA O1A DTP doub 321 n n PA O2A DTP sing 322 n n PA O3A DTP sing 323 n n PA O5' DTP sing 324 n n O2A HOA2 DTP sing 325 n n O5' C5' DTP sing 326 n n C5' C4' DTP sing 327 n n C5' "H5'1" DTP sing 328 n n C5' "H5'2" DTP sing 329 n n C4' O4' DTP sing 330 n n C4' C3' DTP sing 331 n n C4' H4' DTP sing 332 n n O4' C1' DTP sing 333 n n C3' O3' DTP sing 334 n n C3' C2' DTP sing 335 n n C3' H3' DTP sing 336 n n O3' HO3' DTP sing 337 n n C2' C1' DTP sing 338 n n C2' "H2'1" DTP sing 339 n n C2' "H2'2" DTP sing 340 n n C1' N9 DTP sing 341 n n C1' H1' DTP sing 342 n n N9 C8 DTP sing 343 n y N9 C4 DTP sing 344 n y C8 N7 DTP doub 345 n y C8 H8 DTP sing 346 n n N7 C5 DTP sing 347 n y C5 C6 DTP sing 348 n y C5 C4 DTP doub 349 n y C6 N6 DTP sing 350 n n C6 N1 DTP doub 351 n y N6 HN61 DTP sing 352 n n N6 HN62 DTP sing 353 n n N1 C2 DTP sing 354 n y C2 N3 DTP doub 355 n y C2 H2 DTP sing 356 n n N3 C4 DTP sing 357 n y # _atom_sites.entry_id 3LDS _atom_sites.fract_transf_matrix[1][1] 0.012344 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008264 _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] 0.007772 _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 D 4 DTP A 1 904 1 DTP DTP . E 5 MN A 1 906 906 MN MN . F 5 MN A 1 907 907 MN MN . G 5 MN A 1 908 908 MN MN . H 6 SO4 P 1 2 2 SO4 SO4 . I 6 SO4 T 1 19 1 SO4 SO4 . J 7 HOH A 1 905 2 HOH HOH . J 7 HOH A 2 909 3 HOH HOH . J 7 HOH A 3 910 4 HOH HOH . J 7 HOH A 4 911 1 HOH HOH . J 7 HOH A 5 912 2 HOH HOH . J 7 HOH A 6 913 4 HOH HOH . J 7 HOH A 7 914 5 HOH HOH . J 7 HOH A 8 915 6 HOH HOH . J 7 HOH A 9 916 7 HOH HOH . J 7 HOH A 10 917 9 HOH HOH . K 7 HOH P 1 8 8 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 . . . D 4 3.522 -14.446 -50.805 1 47.87 ? PG DTP 904 A 1 HETATM 2 O O1G DTP . . . D 4 4.763 -15.037 -51.442 1 44.89 ? O1G DTP 904 A 1 HETATM 3 O O2G DTP . . . D 4 3.105 -15.165 -49.543 1 41.51 ? O2G DTP 904 A 1 HETATM 4 O O3G DTP . . . D 4 2.395 -14.17 -51.763 1 44.87 ? O3G DTP 904 A 1 HETATM 5 P PB DTP . . . D 4 3.081 -11.761 -49.94 1 44.45 ? PB DTP 904 A 1 HETATM 6 O O1B DTP . . . D 4 3.968 -10.873 -49.074 1 43.26 ? O1B DTP 904 A 1 HETATM 7 O O2B DTP . . . D 4 2.535 -11.274 -51.258 1 43.14 ? O2B DTP 904 A 1 HETATM 8 O O3B DTP . . . D 4 4.05 -12.982 -50.366 1 43.89 ? O3B DTP 904 A 1 HETATM 9 P PA DTP . . . D 4 0.42 -12.064 -49.137 1 47.89 ? PA DTP 904 A 1 HETATM 10 O O1A DTP . . . D 4 -0.355 -12.593 -47.939 1 46.12 ? O1A DTP 904 A 1 HETATM 11 O O2A DTP . . . D 4 -0.006 -12.451 -50.538 1 45.13 ? O2A DTP 904 A 1 HETATM 12 O O3A DTP . . . D 4 1.964 -12.444 -49.007 1 40.98 ? O3A DTP 904 A 1 HETATM 13 O O5' DTP . . . D 4 0.491 -10.47 -48.966 1 46.62 ? O5' DTP 904 A 1 HETATM 14 C C5' DTP . . . D 4 -0.052 -9.548 -49.898 1 44.35 ? C5' DTP 904 A 1 HETATM 15 C C4' DTP . . . D 4 0.5 -8.199 -49.474 1 44.72 ? C4' DTP 904 A 1 HETATM 16 O O4' DTP . . . D 4 -0.264 -7.682 -48.381 1 47.22 ? O4' DTP 904 A 1 HETATM 17 C C3' DTP . . . D 4 1.903 -8.334 -48.939 1 45.06 ? C3' DTP 904 A 1 HETATM 18 O O3' DTP . . . D 4 2.845 -8.235 -50.016 1 41.37 ? O3' DTP 904 A 1 HETATM 19 C C2' DTP . . . D 4 1.987 -7.204 -47.933 1 43.69 ? C2' DTP 904 A 1 HETATM 20 C C1' DTP . . . D 4 0.563 -7.061 -47.398 1 49.12 ? C1' DTP 904 A 1 HETATM 21 N N9 DTP . . . D 4 0.569 -7.833 -46.129 1 52.63 ? N9 DTP 904 A 1 HETATM 22 C C8 DTP . . . D 4 0.109 -9.095 -45.968 1 52.29 ? C8 DTP 904 A 1 HETATM 23 N N7 DTP . . . D 4 0.308 -9.541 -44.7 1 55.45 ? N7 DTP 904 A 1 HETATM 24 C C5 DTP . . . D 4 0.926 -8.549 -44.029 1 55.24 ? C5 DTP 904 A 1 HETATM 25 C C6 DTP . . . D 4 1.424 -8.364 -42.651 1 55.15 ? C6 DTP 904 A 1 HETATM 26 N N6 DTP . . . D 4 1.278 -9.373 -41.766 1 54.19 ? N6 DTP 904 A 1 HETATM 27 N N1 DTP . . . D 4 2.004 -7.175 -42.331 1 56.07 ? N1 DTP 904 A 1 HETATM 28 C C2 DTP . . . D 4 2.139 -6.183 -43.243 1 53.34 ? C2 DTP 904 A 1 HETATM 29 N N3 DTP . . . D 4 1.705 -6.286 -44.514 1 51.4 ? N3 DTP 904 A 1 HETATM 30 C C4 DTP . . . D 4 1.098 -7.419 -44.963 1 53.26 ? C4 DTP 904 A 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #