data_8GML # _model_server_result.job_id DALzX-ZOGsFHKqdrQzk56g _model_server_result.datetime_utc '2025-01-10 08:16:59' _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 8gml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 8GML # _exptl.entry_id 8GML _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 486.132 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-5-fluorouridine 5'-(tetrahydrogen 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 8GML _cell.length_a 98.822 _cell.length_b 98.822 _cell.length_c 81.184 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GML _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall 'P 61' _symmetry.space_group_name_H-M 'P 61' # _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 _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 metalc ? metalc1 A OD1 ASP 13 A ASP 13 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc2 A OD2 ASP 13 A ASP 13 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc3 D O11 B7P . A B7P 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc4 D O20 B7P . A B7P 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc5 E CA CA . A CA 502 1_555 F O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? hydrog WATSON-CRICK hydrog1 B N3 DC 5 T DC 5 1_555 C N1 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 5 T DC 5 1_555 C O6 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 5 T DC 5 1_555 C N2 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 6 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 7 T DC 7 1_555 C N1 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 7 T DC 7 1_555 C O6 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 7 T DC 7 1_555 C N2 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 10 T DA 10 1_555 C N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 10 T DA 10 1_555 C O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 11 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 11 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 11 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 12 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 12 T DT 12 1_555 C N6 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H14 F N2 O14 P3' _chem_comp.formula_weight 486.132 _chem_comp.id B7P _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-FdUTP # 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 O29 C28 B7P doub 70 n n C28 N27 B7P sing 71 n n C28 N21 B7P sing 72 n n N27 C25 B7P sing 73 n n C03 C04 B7P sing 74 n n C03 C02 B7P sing 75 n n C04 N21 B7P sing 76 n n C04 O05 B7P sing 77 n n N21 C22 B7P sing 78 n n O01 C02 B7P sing 79 n n C25 O26 B7P doub 80 n n C25 C23 B7P sing 81 n n C02 C06 B7P sing 82 n n O05 C06 B7P sing 83 n n C22 C23 B7P doub 84 n n C06 C07 B7P sing 85 n n C23 F24 B7P sing 86 n n O15 P13 B7P doub 87 n n C07 O08 B7P sing 88 n n O08 P09 B7P sing 89 n n P13 O12 B7P sing 90 n n P13 O14 B7P sing 91 n n P13 O16 B7P sing 92 n n O12 P09 B7P sing 93 n n O16 P17 B7P sing 94 n n P09 O10 B7P doub 95 n n P09 O11 B7P sing 96 n n P17 O19 B7P doub 97 n n P17 O18 B7P sing 98 n n P17 O20 B7P sing 99 n n C22 H1 B7P sing 100 n n O01 H2 B7P sing 101 n n C02 H3 B7P sing 102 n n C03 H4 B7P sing 103 n n C03 H5 B7P sing 104 n n C04 H6 B7P sing 105 n n C06 H7 B7P sing 106 n n C07 H8 B7P sing 107 n n C07 H9 B7P sing 108 n n O11 H10 B7P sing 109 n n O14 H11 B7P sing 110 n n O18 H12 B7P sing 111 n n O20 H13 B7P sing 112 n n N27 H14 B7P sing 113 n n # _atom_sites.entry_id 8GML _atom_sites.fract_transf_matrix[1][1] 0.010119 _atom_sites.fract_transf_matrix[1][2] 0.005842 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011685 _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] 0.012318 _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 B7P A 1 501 501 B7P B7P . E 5 CA A 1 502 1 CA CA . F 6 HOH A 1 601 21 HOH HOH . F 6 HOH A 2 602 44 HOH HOH . F 6 HOH A 3 603 15 HOH HOH . F 6 HOH A 4 604 2 HOH HOH . F 6 HOH A 5 605 32 HOH HOH . F 6 HOH A 6 606 45 HOH HOH . F 6 HOH A 7 607 41 HOH HOH . F 6 HOH A 8 608 46 HOH HOH . F 6 HOH A 9 609 4 HOH HOH . F 6 HOH A 10 610 37 HOH HOH . F 6 HOH A 11 611 8 HOH HOH . F 6 HOH A 12 612 27 HOH HOH . F 6 HOH A 13 613 42 HOH HOH . F 6 HOH A 14 614 17 HOH HOH . F 6 HOH A 15 615 12 HOH HOH . F 6 HOH A 16 616 43 HOH HOH . F 6 HOH A 17 617 3 HOH HOH . F 6 HOH A 18 618 22 HOH HOH . F 6 HOH A 19 619 39 HOH HOH . F 6 HOH A 20 620 26 HOH HOH . F 6 HOH A 21 621 20 HOH HOH . F 6 HOH A 22 622 1 HOH HOH . F 6 HOH A 23 623 30 HOH HOH . F 6 HOH A 24 624 29 HOH HOH . F 6 HOH A 25 625 7 HOH HOH . F 6 HOH A 26 626 6 HOH HOH . F 6 HOH A 27 627 25 HOH HOH . F 6 HOH A 28 628 5 HOH HOH . F 6 HOH A 29 629 36 HOH HOH . F 6 HOH A 30 630 23 HOH HOH . F 6 HOH A 31 631 38 HOH HOH . F 6 HOH A 32 632 11 HOH HOH . F 6 HOH A 33 633 16 HOH HOH . F 6 HOH A 34 634 18 HOH HOH . F 6 HOH A 35 635 31 HOH HOH . F 6 HOH A 36 636 9 HOH HOH . F 6 HOH A 37 637 13 HOH HOH . F 6 HOH A 38 638 33 HOH HOH . F 6 HOH A 39 639 14 HOH HOH . F 6 HOH A 40 640 48 HOH HOH . F 6 HOH A 41 641 35 HOH HOH . F 6 HOH A 42 642 47 HOH HOH . F 6 HOH A 43 643 40 HOH HOH . F 6 HOH A 44 644 19 HOH HOH . F 6 HOH A 45 645 34 HOH HOH . G 6 HOH T 1 101 10 HOH HOH . H 6 HOH P 1 101 28 HOH HOH . H 6 HOH P 2 102 24 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 C C22 B7P . . . D 4 -20.978 42.495 -5.178 1 73.98 ? C22 B7P 501 A 1 HETATM 2 C C28 B7P . . . D 4 -18.643 42.176 -6.039 1 73.75 ? C28 B7P 501 A 1 HETATM 3 O O01 B7P . . . D 4 -19.216 47.709 -4.716 1 53.51 ? O01 B7P 501 A 1 HETATM 4 C C02 B7P . . . D 4 -19.563 46.234 -4.689 1 60.51 ? C02 B7P 501 A 1 HETATM 5 C C03 B7P . . . D 4 -18.414 45.192 -4.822 1 57.39 ? C03 B7P 501 A 1 HETATM 6 C C04 B7P . . . D 4 -19.005 43.893 -4.152 1 67.54 ? C04 B7P 501 A 1 HETATM 7 O O05 B7P . . . D 4 -19.901 44.323 -3.282 1 69.08 ? O05 B7P 501 A 1 HETATM 8 C C06 B7P . . . D 4 -20.127 45.909 -3.559 1 65.88 ? C06 B7P 501 A 1 HETATM 9 C C07 B7P . . . D 4 -21.588 46.251 -3.727 1 70.96 ? C07 B7P 501 A 1 HETATM 10 O O08 B7P . . . D 4 -22.456 45.149 -3.873 1 78.43 ? O08 B7P 501 A 1 HETATM 11 P P09 B7P . . . D 4 -23.761 45.37 -4.898 1 89.04 ? P09 B7P 501 A 1 HETATM 12 O O10 B7P . . . D 4 -24.104 44.08 -5.639 1 77.95 -1 O10 B7P 501 A 1 HETATM 13 O O11 B7P . . . D 4 -25.008 45.688 -4.101 1 77.43 ? O11 B7P 501 A 1 HETATM 14 O O12 B7P . . . D 4 -23.469 46.621 -6.006 1 93.04 ? O12 B7P 501 A 1 HETATM 15 P P13 B7P . . . D 4 -23.069 48.273 -5.902 1 94.02 ? P13 B7P 501 A 1 HETATM 16 O O14 B7P . . . D 4 -22.975 48.802 -4.459 1 67.64 -1 O14 B7P 501 A 1 HETATM 17 O O15 B7P . . . D 4 -21.652 48.385 -6.482 1 73.3 ? O15 B7P 501 A 1 HETATM 18 O O16 B7P . . . D 4 -24.188 49.226 -6.755 1 76.89 ? O16 B7P 501 A 1 HETATM 19 P P17 B7P . . . D 4 -25.4 48.841 -7.847 1 82.86 ? P17 B7P 501 A 1 HETATM 20 O O18 B7P . . . D 4 -26.331 50.027 -8.051 1 73.34 -1 O18 B7P 501 A 1 HETATM 21 O O19 B7P . . . D 4 -24.798 48.458 -9.192 1 78.12 -1 O19 B7P 501 A 1 HETATM 22 O O20 B7P . . . D 4 -26.22 47.674 -7.339 1 82.82 ? O20 B7P 501 A 1 HETATM 23 N N21 B7P . . . D 4 -19.568 42.873 -5.097 1 72.65 ? N21 B7P 501 A 1 HETATM 24 C C23 B7P . . . D 4 -21.501 41.465 -6.15 1 72.83 ? C23 B7P 501 A 1 HETATM 25 F F24 B7P . . . D 4 -22.834 41.115 -6.212 1 71.37 ? F24 B7P 501 A 1 HETATM 26 C C25 B7P . . . D 4 -20.573 40.773 -7.086 1 72.96 ? C25 B7P 501 A 1 HETATM 27 O O26 B7P . . . D 4 -20.984 39.948 -7.861 1 75.28 ? O26 B7P 501 A 1 HETATM 28 N N27 B7P . . . D 4 -19.156 41.145 -7.02 1 73.51 ? N27 B7P 501 A 1 HETATM 29 O O29 B7P . . . D 4 -17.485 42.441 -6.005 1 76.04 ? O29 B7P 501 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #