data_1R9S # _model_server_result.job_id Y68zqisXcWb44WX62xwr4w _model_server_result.datetime_utc '2025-02-28 08:32:00' _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 1r9s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":3000}' # _entry.id 1R9S # _exptl.entry_id 1R9S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 14 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 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 101.67 _cell.angle_gamma 90 _cell.entry_id 1R9S _cell.length_a 169.647 _cell.length_b 222.338 _cell.length_c 194.316 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1R9S _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 ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W _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 14 _struct_asym.id N _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 A O3' A 10 R A 10 1_555 N O2A UTP . R UTP 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc1 A O3' A 10 R A 10 1_555 M MG MG . R MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.799 ? metalc ? metalc2 A O2' A 10 R A 10 1_555 M MG MG . R MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc3 M MG MG . R MG 2001 1_555 N O2A UTP . R UTP 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc4 M MG MG . R MG 2001 1_555 N O5' UTP . R UTP 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc5 M MG MG . R MG 2001 1_555 N O1A UTP . R UTP 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? metalc ? metalc6 N O1G UTP . R UTP 3000 1_555 Q MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc7 N O3G UTP . R UTP 3000 1_555 Q MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.047 ? metalc ? metalc8 C SG CYS 67 A CYS 67 1_555 P ZN ZN . A ZN 1735 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc9 C SG CYS 70 A CYS 70 1_555 P ZN ZN . A ZN 1735 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 C NE2 HIS 80 A HIS 80 1_555 P ZN ZN . A ZN 1735 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc11 C SG CYS 110 A CYS 110 1_555 O ZN ZN . A ZN 1734 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc12 C SG CYS 167 A CYS 167 1_555 O ZN ZN . A ZN 1734 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc13 C OD1 ASP 483 A ASP 483 1_555 Q MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc14 D SG CYS 1163 B CYS 1163 1_555 R ZN ZN . B ZN 1307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc15 D SG CYS 1166 B CYS 1166 1_555 R ZN ZN . B ZN 1307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc16 D SG CYS 1182 B CYS 1182 1_555 R ZN ZN . B ZN 1307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc17 D SG CYS 1185 B CYS 1185 1_555 R ZN ZN . B ZN 1307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc18 E SG CYS 86 C CYS 86 1_555 S ZN ZN . C ZN 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc19 E SG CYS 88 C CYS 88 1_555 S ZN ZN . C ZN 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc20 E SG CYS 92 C CYS 92 1_555 S ZN ZN . C ZN 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc21 E SG CYS 95 C CYS 95 1_555 S ZN ZN . C ZN 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc22 I SG CYS 7 I CYS 7 1_555 T ZN ZN . I ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc23 I SG CYS 10 I CYS 10 1_555 T ZN ZN . I ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc24 I SG CYS 29 I CYS 29 1_555 T ZN ZN . I ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc25 I SG CYS 32 I CYS 32 1_555 T ZN ZN . I ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.893 ? metalc ? metalc26 I SG CYS 75 I CYS 75 1_555 U ZN ZN . I ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? metalc ? metalc27 I SG CYS 78 I CYS 78 1_555 U ZN ZN . I ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc28 I SG CYS 103 I CYS 103 1_555 U ZN ZN . I ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc29 I SG CYS 106 I CYS 106 1_555 U ZN ZN . I ZN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc30 J SG CYS 7 J CYS 7 1_555 V ZN ZN . J ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc31 J SG CYS 10 J CYS 10 1_555 V ZN ZN . J ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc32 J SG CYS 45 J CYS 45 1_555 V ZN ZN . J ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc33 J SG CYS 46 J CYS 46 1_555 V ZN ZN . J ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc34 L SG CYS 31 L CYS 31 1_555 W ZN ZN . L ZN 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc35 L SG CYS 34 L CYS 34 1_555 W ZN ZN . L ZN 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.721 ? metalc ? metalc36 L SG CYS 48 L CYS 48 1_555 W ZN ZN . L ZN 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc37 L SG CYS 51 L CYS 51 1_555 W ZN ZN . L ZN 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? hydrog WATSON-CRICK hydrog1 A N1 G 4 R G 4 1_555 B N3 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 4 R G 4 1_555 B O2 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 4 R G 4 1_555 B N4 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 A 5 R A 5 1_555 B N3 DT 10 T DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 A 5 R A 5 1_555 B O4 DT 10 T DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 A 7 R A 7 1_555 B N3 DT 8 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 A 7 R A 7 1_555 B O4 DT 8 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 G 8 R G 8 1_555 B N3 DC 7 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N2 G 8 R G 8 1_555 B O2 DC 7 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O6 G 8 R G 8 1_555 B N4 DC 7 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-DT MISPAIR' hydrog11 A N1 G 8 R G 8 1_555 B O4 DT 8 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 G 9 R G 9 1_555 B N3 DC 6 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 G 9 R G 9 1_555 B O2 DC 6 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 G 9 R G 9 1_555 B N4 DC 6 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 A 10 R A 10 1_555 B N3 DT 5 T DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 A 10 R A 10 1_555 B O4 DT 5 T DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-DC MISPAIR' hydrog17 A N6 A 10 R A 10 1_555 B N3 DC 6 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 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 PA O1A UTP doub 655 n n PA O2A UTP sing 656 n n PA O3A UTP sing 657 n n PA O5' UTP sing 658 n n O2A H2A UTP sing 659 n n O3A PB UTP sing 660 n n O5' C5' UTP sing 661 n n PB O1B UTP sing 662 n n PB O2B UTP doub 663 n n PB O3B UTP sing 664 n n O1B H1B UTP sing 665 n n O3B PG UTP sing 666 n n PG O1G UTP sing 667 n n PG O2G UTP doub 668 n n PG O3G UTP sing 669 n n O1G H1G UTP sing 670 n n O3G H3G UTP sing 671 n n C5' C4' UTP sing 672 n n C5' "H5'1" UTP sing 673 n n C5' "H5'2" UTP sing 674 n n C4' O4' UTP sing 675 n n C4' C3' UTP sing 676 n n C4' H4' UTP sing 677 n n O4' C1' UTP sing 678 n n C1' C2' UTP sing 679 n n C1' N1 UTP sing 680 n n C1' H1' UTP sing 681 n n C2' O2' UTP sing 682 n n C2' C3' UTP sing 683 n n C2' H2' UTP sing 684 n n O2' HA UTP sing 685 n n C3' O3' UTP sing 686 n n C3' H3' UTP sing 687 n n O3' HB UTP sing 688 n n N1 C6 UTP sing 689 n y N1 C2 UTP sing 690 n y C6 C5 UTP doub 691 n y C6 H6 UTP sing 692 n n C2 O2 UTP doub 693 n n C2 N3 UTP sing 694 n y N3 C4 UTP sing 695 n y N3 H3 UTP sing 696 n n C4 O4 UTP doub 697 n n C4 C5 UTP sing 698 n y C5 H5 UTP sing 699 n n # _atom_sites.entry_id 1R9S _atom_sites.fract_transf_matrix[1][1] 0.005985 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001066 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00452 _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] 0.005244 _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 M 13 MG R 1 2001 2001 MG MG . N 14 UTP R 1 3000 3000 UTP UTP . O 15 ZN A 1 1734 1506 ZN ZN . P 15 ZN A 1 1735 1508 ZN ZN . Q 13 MG A 1 2002 2002 MG MG . R 15 ZN B 1 1307 1307 ZN ZN . S 15 ZN C 1 319 302 ZN ZN . T 15 ZN I 1 203 203 ZN ZN . U 15 ZN I 1 204 204 ZN ZN . V 15 ZN J 1 101 101 ZN ZN . W 15 ZN L 1 105 105 ZN ZN . # 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 PA UTP . . . N 14 2.061 0.048 48.517 1 78.71 ? PA UTP 3000 R 1 HETATM 2 O O1A UTP . . . N 14 3.317 0.667 48.022 1 78.71 ? O1A UTP 3000 R 1 HETATM 3 O O2A UTP . . . N 14 0.866 -0.026 47.633 1 78.71 ? O2A UTP 3000 R 1 HETATM 4 O O3A UTP . . . N 14 1.61 0.738 49.913 1 78.71 ? O3A UTP 3000 R 1 HETATM 5 O O5' UTP . . . N 14 2.349 -1.401 49.085 1 78.71 ? O5' UTP 3000 R 1 HETATM 6 P PB UTP . . . N 14 0.249 0.699 50.718 1 78.71 ? PB UTP 3000 R 1 HETATM 7 O O1B UTP . . . N 14 -0.883 1.366 50.094 1 78.71 ? O1B UTP 3000 R 1 HETATM 8 O O2B UTP . . . N 14 0.607 1.076 52.059 1 78.71 ? O2B UTP 3000 R 1 HETATM 9 O O3B UTP . . . N 14 -0.044 -0.865 50.633 1 78.71 ? O3B UTP 3000 R 1 HETATM 10 P PG UTP . . . N 14 -1.27 -1.718 51.157 1 78.71 ? PG UTP 3000 R 1 HETATM 11 O O1G UTP . . . N 14 -1.269 -3.034 50.372 1 78.71 ? O1G UTP 3000 R 1 HETATM 12 O O2G UTP . . . N 14 -0.967 -1.889 52.624 1 78.71 ? O2G UTP 3000 R 1 HETATM 13 O O3G UTP . . . N 14 -2.554 -0.936 50.922 1 78.71 ? O3G UTP 3000 R 1 HETATM 14 C C5' UTP . . . N 14 3.437 -2.156 48.579 1 78.71 ? C5' UTP 3000 R 1 HETATM 15 C C4' UTP . . . N 14 5.052 -1.783 48.334 1 78.71 ? C4' UTP 3000 R 1 HETATM 16 O O4' UTP . . . N 14 6.083 -1.374 47.565 1 78.71 ? O4' UTP 3000 R 1 HETATM 17 C C1' UTP . . . N 14 7.17 -1.203 48.467 1 78.71 ? C1' UTP 3000 R 1 HETATM 18 C C2' UTP . . . N 14 6.743 -1.527 49.833 1 78.71 ? C2' UTP 3000 R 1 HETATM 19 O O2' UTP . . . N 14 7.071 -3.038 49.885 1 78.71 ? O2' UTP 3000 R 1 HETATM 20 C C3' UTP . . . N 14 5.191 -1.454 49.672 1 78.71 ? C3' UTP 3000 R 1 HETATM 21 O O3' UTP . . . N 14 4.893 -2.416 50.53 1 78.71 ? O3' UTP 3000 R 1 HETATM 22 N N1 UTP . . . N 14 7.361 0.37 48.732 1 78.71 ? N1 UTP 3000 R 1 HETATM 23 C C6 UTP . . . N 14 6.243 1.17 48.683 1 78.71 ? C6 UTP 3000 R 1 HETATM 24 C C2 UTP . . . N 14 8.607 0.907 49.024 1 78.71 ? C2 UTP 3000 R 1 HETATM 25 O O2 UTP . . . N 14 9.629 0.241 49.024 1 78.71 ? O2 UTP 3000 R 1 HETATM 26 N N3 UTP . . . N 14 8.611 2.255 49.305 1 78.71 ? N3 UTP 3000 R 1 HETATM 27 C C4 UTP . . . N 14 7.522 3.108 49.302 1 78.71 ? C4 UTP 3000 R 1 HETATM 28 O O4 UTP . . . N 14 7.667 4.286 49.652 1 78.71 ? O4 UTP 3000 R 1 HETATM 29 C C5 UTP . . . N 14 6.279 2.484 48.948 1 78.71 ? C5 UTP 3000 R 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #