data_9CIQ # _model_server_result.job_id qHp_psl1vwLU1DwW1g0y1Q _model_server_result.datetime_utc '2024-11-23 21:38:20' _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 9ciq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 9CIQ # _exptl.entry_id 9CIQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'A1ANT is incoming nucleotide, threofuranosyl thymine nucleoside triphosphate (tTTP)' _entity.formula_weight 468.142 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3~{S},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate' _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 9CIQ _cell.length_a 99.478 _cell.length_b 99.478 _cell.length_c 81.218 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CIQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _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,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 metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc2 A O MET 17 A MET 14 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc3 A OD1 ASP 118 A ASP 115 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc4 A OD2 ASP 118 A ASP 115 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc5 A OE2 GLU 119 A GLU 116 1_555 H CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? metalc ? metalc6 D O3 A1ANT . A A1ANT 501 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc7 D O5 A1ANT . A A1ANT 501 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc8 D O7 A1ANT . A A1ANT 501 1_555 G CA CA . A CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc9 D O3 A1ANT . A A1ANT 501 1_555 H CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.048 ? metalc ? metalc10 H CA CA . A CA 505 1_555 C O3' DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? hydrog WATSON-CRICK hydrog1 B N1 DA 5 T DA 5 1_555 C N3 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 5 T DA 5 1_555 C O4 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O4 DT 6 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DG 7 T DG 7 1_555 C N3 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N2 DG 7 T DG 7 1_555 C O2 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O6 DG 7 T DG 7 1_555 C N4 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 10 T DG 10 1_555 C N3 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 10 T DG 10 1_555 C O2 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 10 T DG 10 1_555 C N4 DC 3 P DC 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 H15 N2 O14 P3' _chem_comp.formula_weight 468.142 _chem_comp.id A1ANT _chem_comp.mon_nstd_flag . _chem_comp.name '[(3~{S},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate' _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 O1 C1 A1ANT sing 1 n n C1 C2 A1ANT sing 2 n n C2 O2 A1ANT sing 3 n n O2 P1 A1ANT sing 4 n n P1 O3 A1ANT sing 5 n n P1 O4 A1ANT sing 6 n n O4 P2 A1ANT sing 7 n n P2 O5 A1ANT sing 8 n n P2 O6 A1ANT sing 9 n n O6 P3 A1ANT sing 10 n n P3 O7 A1ANT sing 11 n n P3 O8 A1ANT sing 12 n n P3 O9 A1ANT doub 13 n n P2 O10 A1ANT doub 14 n n P1 O11 A1ANT doub 15 n n C2 C3 A1ANT sing 16 n n C3 O12 A1ANT sing 17 n n O12 C4 A1ANT sing 18 n n C4 N1 A1ANT sing 19 n n N1 C5 A1ANT sing 20 n n C5 N2 A1ANT sing 21 n n C5 O13 A1ANT doub 22 n n N1 C6 A1ANT sing 23 n n C6 C7 A1ANT doub 24 n n C7 C8 A1ANT sing 25 n n C7 C9 A1ANT sing 26 n n C9 O14 A1ANT doub 27 n n C1 C4 A1ANT sing 28 n n N2 C9 A1ANT sing 29 n n C1 H2 A1ANT sing 30 n n C2 H3 A1ANT sing 31 n n C3 H5 A1ANT sing 32 n n C3 H4 A1ANT sing 33 n n C4 H6 A1ANT sing 34 n n C6 H8 A1ANT sing 35 n n N2 H7 A1ANT sing 36 n n O1 H1 A1ANT sing 37 n n C8 H11 A1ANT sing 38 n n C8 H9 A1ANT sing 39 n n C8 H10 A1ANT sing 40 n n O3 H12 A1ANT sing 41 n n O5 H13 A1ANT sing 42 n n O7 H14 A1ANT sing 43 n n O8 H15 A1ANT sing 44 n n # _atom_sites.entry_id 9CIQ _atom_sites.fract_transf_matrix[1][1] 0.010052 _atom_sites.fract_transf_matrix[1][2] 0.005804 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011608 _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] 0.012313 _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 A1ANT A 1 501 501 A1ANT QTT . E 5 PEG A 1 502 502 PEG PEG . F 5 PEG A 1 503 503 PEG PEG . G 6 CA A 1 504 1 CA CA . H 6 CA A 1 505 2 CA CA . I 7 HOH A 1 601 4 HOH HOH . I 7 HOH A 2 602 14 HOH HOH . I 7 HOH A 3 603 1 HOH HOH . I 7 HOH A 4 604 24 HOH HOH . I 7 HOH A 5 605 30 HOH HOH . I 7 HOH A 6 606 16 HOH HOH . I 7 HOH A 7 607 25 HOH HOH . I 7 HOH A 8 608 23 HOH HOH . I 7 HOH A 9 609 11 HOH HOH . I 7 HOH A 10 610 2 HOH HOH . I 7 HOH A 11 611 27 HOH HOH . I 7 HOH A 12 612 9 HOH HOH . I 7 HOH A 13 613 36 HOH HOH . I 7 HOH A 14 614 35 HOH HOH . I 7 HOH A 15 615 8 HOH HOH . I 7 HOH A 16 616 19 HOH HOH . I 7 HOH A 17 617 17 HOH HOH . I 7 HOH A 18 618 6 HOH HOH . I 7 HOH A 19 619 13 HOH HOH . I 7 HOH A 20 620 5 HOH HOH . I 7 HOH A 21 621 37 HOH HOH . I 7 HOH A 22 622 3 HOH HOH . I 7 HOH A 23 623 15 HOH HOH . I 7 HOH A 24 624 7 HOH HOH . I 7 HOH A 25 625 33 HOH HOH . I 7 HOH A 26 626 12 HOH HOH . I 7 HOH A 27 627 31 HOH HOH . I 7 HOH A 28 628 34 HOH HOH . I 7 HOH A 29 629 29 HOH HOH . I 7 HOH A 30 630 20 HOH HOH . I 7 HOH A 31 631 18 HOH HOH . I 7 HOH A 32 632 22 HOH HOH . I 7 HOH A 33 633 26 HOH HOH . J 7 HOH T 1 101 28 HOH HOH . K 7 HOH P 1 101 10 HOH HOH . K 7 HOH P 2 102 32 HOH HOH . K 7 HOH P 3 103 21 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 C1 A1ANT . . . D 4 -21.199 44.946 -4.927 1 32.51 ? C1 A1ANT 501 A 1 HETATM 2 C C2 A1ANT . . . D 4 -21.287 43.749 -5.551 1 32.45 ? C2 A1ANT 501 A 1 HETATM 3 C C3 A1ANT . . . D 4 -21.704 44.153 -7.072 1 42.19 ? C3 A1ANT 501 A 1 HETATM 4 C C4 A1ANT . . . D 4 -22.195 45.875 -5.651 1 29.89 ? C4 A1ANT 501 A 1 HETATM 5 C C5 A1ANT . . . D 4 -23.685 47.505 -5.137 1 33.47 ? C5 A1ANT 501 A 1 HETATM 6 C C6 A1ANT . . . D 4 -23.869 45.443 -4.127 1 41.02 ? C6 A1ANT 501 A 1 HETATM 7 C C7 A1ANT . . . D 4 -24.985 45.923 -3.437 1 37.89 ? C7 A1ANT 501 A 1 HETATM 8 N N1 A1ANT . . . D 4 -23.253 46.286 -4.96 1 35.59 ? N1 A1ANT 501 A 1 HETATM 9 N N2 A1ANT . . . D 4 -24.756 47.974 -4.475 1 34.77 ? N2 A1ANT 501 A 1 HETATM 10 O O1 A1ANT . . . D 4 -19.855 45.419 -5.276 1 39.78 ? O1 A1ANT 501 A 1 HETATM 11 C C8 A1ANT . . . D 4 -25.735 44.998 -2.452 1 36.31 ? C8 A1ANT 501 A 1 HETATM 12 C C9 A1ANT . . . D 4 -25.43 47.226 -3.621 1 41.35 ? C9 A1ANT 501 A 1 HETATM 13 O O10 A1ANT . . . D 4 -18.443 42.714 -1.802 1 27.29 ? O10 A1ANT 501 A 1 HETATM 14 O O11 A1ANT . . . D 4 -23.086 41.907 -2.766 1 33.63 ? O11 A1ANT 501 A 1 HETATM 15 O O12 A1ANT . . . D 4 -22.654 45.057 -6.93 1 38.47 ? O12 A1ANT 501 A 1 HETATM 16 O O13 A1ANT . . . D 4 -23.116 48.231 -5.913 1 34.64 ? O13 A1ANT 501 A 1 HETATM 17 O O14 A1ANT . . . D 4 -26.392 47.642 -3.032 1 44.19 ? O14 A1ANT 501 A 1 HETATM 18 O O2 A1ANT . . . D 4 -22.308 42.916 -5.002 1 40.48 ? O2 A1ANT 501 A 1 HETATM 19 O O3 A1ANT . . . D 4 -21.531 40.542 -4.244 1 29.39 ? O3 A1ANT 501 A 1 HETATM 20 O O4 A1ANT . . . D 4 -20.644 42.593 -3.06 1 37.56 ? O4 A1ANT 501 A 1 HETATM 21 O O5 A1ANT . . . D 4 -18.576 41.265 -3.854 1 32.22 ? O5 A1ANT 501 A 1 HETATM 22 O O6 A1ANT . . . D 4 -19.757 40.546 -1.595 1 36.21 ? O6 A1ANT 501 A 1 HETATM 23 O O7 A1ANT . . . D 4 -19.189 38.543 -3.176 1 27.33 ? O7 A1ANT 501 A 1 HETATM 24 O O8 A1ANT . . . D 4 -18.206 38.609 -0.88 1 39.66 ? O8 A1ANT 501 A 1 HETATM 25 O O9 A1ANT . . . D 4 -20.625 38.258 -1.191 1 46.45 ? O9 A1ANT 501 A 1 HETATM 26 P P1 A1ANT . . . D 4 -21.931 41.912 -3.779 1 25.79 ? P1 A1ANT 501 A 1 HETATM 27 P P2 A1ANT . . . D 4 -19.276 41.765 -2.617 1 33.58 ? P2 A1ANT 501 A 1 HETATM 28 P P3 A1ANT . . . D 4 -19.414 38.95 -1.728 1 43.12 ? P3 A1ANT 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #