data_6KBD # _model_server_result.job_id 2v7CH71U9QsDhaDDin8IOA _model_server_result.datetime_utc '2025-07-14 16:21:34' _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 6kbd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":902}' # _entry.id 6KBD # _exptl.entry_id 6KBD _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.78 _cell.angle_gamma 90 _cell.entry_id 6KBD _cell.length_a 57.801 _cell.length_b 53.317 _cell.length_c 124.134 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C 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 disulf ? disulf1 A SG CYS 217 A CYS 217 1_555 A SG CYS 227 A CYS 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc1 A OD1 ASP 522 A ASP 555 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc2 A OD2 ASP 522 A ASP 555 1_555 E MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc3 A O VAL 523 A VAL 556 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc4 A OD1 ASP 594 A ASP 627 1_555 E MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc5 A OD2 ASP 595 A ASP 628 1_555 E MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc6 C O1G DTP . A DTP 902 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? metalc ? metalc7 C O1B DTP . A DTP 902 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc8 C O2A DTP . A DTP 902 1_555 E MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? # _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 6KBD _atom_sites.fract_transf_matrix[1][1] 0.017301 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002364 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018756 _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] 0.008131 _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 1 901 1 DTP DTP . C 2 DTP A 1 902 2 DTP DTP . D 3 MG A 1 903 1 MG MG . E 3 MG A 1 904 2 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 DTP . . . C 2 -37.922 -2.524 -34.339 1 63.76 ? PG DTP 902 A 1 HETATM 2 O O1G DTP . . . C 2 -36.887 -1.642 -34.931 1 54.01 ? O1G DTP 902 A 1 HETATM 3 O O2G DTP . . . C 2 -38.068 -3.774 -35.159 1 77.84 ? O2G DTP 902 A 1 HETATM 4 O O3G DTP . . . C 2 -39.237 -1.866 -33.955 1 66.37 ? O3G DTP 902 A 1 HETATM 5 P PB DTP . . . C 2 -36.14 -2.061 -32.222 1 55.46 ? PB DTP 902 A 1 HETATM 6 O O1B DTP . . . C 2 -34.91 -2.217 -33.025 1 65.03 ? O1B DTP 902 A 1 HETATM 7 O O2B DTP . . . C 2 -35.896 -2.434 -30.824 1 52.97 ? O2B DTP 902 A 1 HETATM 8 O O3B DTP . . . C 2 -37.256 -2.977 -32.923 1 76.44 ? O3B DTP 902 A 1 HETATM 9 P PA DTP . . . C 2 -35.686 0.632 -32.817 1 77.54 ? PA DTP 902 A 1 HETATM 10 O O1A DTP . . . C 2 -35.064 0.339 -34.177 1 63.85 ? O1A DTP 902 A 1 HETATM 11 O O2A DTP . . . C 2 -36.356 1.97 -32.527 1 72.61 ? O2A DTP 902 A 1 HETATM 12 O O3A DTP . . . C 2 -36.707 -0.568 -32.407 1 67.47 ? O3A DTP 902 A 1 HETATM 13 O O5' DTP . . . C 2 -34.505 0.454 -31.74 1 83.11 ? O5' DTP 902 A 1 HETATM 14 C C5' DTP . . . C 2 -34.306 1.392 -30.686 1 75.89 ? C5' DTP 902 A 1 HETATM 15 C C4' DTP . . . C 2 -33.924 0.691 -29.411 1 67.19 ? C4' DTP 902 A 1 HETATM 16 O O4' DTP . . . C 2 -32.577 0.314 -29.491 1 62.52 ? O4' DTP 902 A 1 HETATM 17 C C3' DTP . . . C 2 -34.062 1.625 -28.217 1 71.45 ? C3' DTP 902 A 1 HETATM 18 O O3' DTP . . . C 2 -35.043 1.105 -27.288 1 101.28 ? O3' DTP 902 A 1 HETATM 19 C C2' DTP . . . C 2 -32.709 1.775 -27.559 1 74.09 ? C2' DTP 902 A 1 HETATM 20 C C1' DTP . . . C 2 -31.838 0.838 -28.366 1 72.55 ? C1' DTP 902 A 1 HETATM 21 N N9 DTP . . . C 2 -30.64 1.543 -28.859 1 65.92 ? N9 DTP 902 A 1 HETATM 22 C C8 DTP . . . C 2 -30.513 2.094 -30.072 1 57.42 ? C8 DTP 902 A 1 HETATM 23 N N7 DTP . . . C 2 -29.281 2.646 -30.213 1 55.56 ? N7 DTP 902 A 1 HETATM 24 C C5 DTP . . . C 2 -28.601 2.429 -29.08 1 56.33 ? C5 DTP 902 A 1 HETATM 25 C C6 DTP . . . C 2 -27.233 2.715 -28.589 1 55.35 ? C6 DTP 902 A 1 HETATM 26 N N6 DTP . . . C 2 -26.333 3.374 -29.351 1 56.14 ? N6 DTP 902 A 1 HETATM 27 N N1 DTP . . . C 2 -26.916 2.324 -27.334 1 56.86 ? N1 DTP 902 A 1 HETATM 28 C C2 DTP . . . C 2 -27.828 1.675 -26.547 1 60.83 ? C2 DTP 902 A 1 HETATM 29 N N3 DTP . . . C 2 -29.084 1.365 -26.944 1 51.75 ? N3 DTP 902 A 1 HETATM 30 C C4 DTP . . . C 2 -29.508 1.712 -28.173 1 55.45 ? C4 DTP 902 A 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #