data_7RKH # _model_server_result.job_id 1F2qF1pmgTfq1Aa2IhDtWw _model_server_result.datetime_utc '2025-07-04 17:15:46' _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 7rkh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":602}' # _entry.id 7RKH # _exptl.entry_id 7RKH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 484.141 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 7RKH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RKH _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? _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 E N N ? 2 I N N ? 2 N N N ? 2 R 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 metalc ? metalc1 A OD1 ASP 70 D ASP 70 1_555 G MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc2 A OD2 ASP 70 D ASP 70 1_555 G MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc3 E O2B UTP . D UTP 601 1_555 Q MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc4 F O3G ATP . D ATP 602 1_555 G MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc5 F O1B ATP . D ATP 602 1_555 G MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc6 H MG MG . D MG 604 1_555 R O1B UTP . C UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc7 B OD1 ASP 70 A ASP 70 1_555 K MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc8 B OD2 ASP 70 A ASP 70 1_555 K MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc9 I O1B UTP . A UTP 601 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc10 J O3G ATP . A ATP 602 1_555 K MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc11 J O1B ATP . A ATP 602 1_555 K MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc12 L MG MG . A MG 604 1_555 N O2B UTP . B UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc13 C OD1 ASP 70 B ASP 70 1_555 P MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc14 C OD2 ASP 70 B ASP 70 1_555 P MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc15 O O3G ATP . B ATP 603 1_555 P MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.997 ? metalc ? metalc16 O O1B ATP . B ATP 603 1_555 P MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.924 ? metalc ? metalc17 D OD1 ASP 70 C ASP 70 1_555 T MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc18 D OD2 ASP 70 C ASP 70 1_555 T MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc19 S O3G ATP . C ATP 603 1_555 T MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc20 S O1B ATP . C ATP 603 1_555 T MG MG . C MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? # _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 405 n n PA O2A UTP sing 406 n n PA O3A UTP sing 407 n n PA O5' UTP sing 408 n n O2A H2A UTP sing 409 n n O3A PB UTP sing 410 n n O5' C5' UTP sing 411 n n PB O1B UTP sing 412 n n PB O2B UTP doub 413 n n PB O3B UTP sing 414 n n O1B H1B UTP sing 415 n n O3B PG UTP sing 416 n n PG O1G UTP sing 417 n n PG O2G UTP doub 418 n n PG O3G UTP sing 419 n n O1G H1G UTP sing 420 n n O3G H3G UTP sing 421 n n C5' C4' UTP sing 422 n n C5' "H5'1" UTP sing 423 n n C5' "H5'2" UTP sing 424 n n C4' O4' UTP sing 425 n n C4' C3' UTP sing 426 n n C4' H4' UTP sing 427 n n O4' C1' UTP sing 428 n n C1' C2' UTP sing 429 n n C1' N1 UTP sing 430 n n C1' H1' UTP sing 431 n n C2' O2' UTP sing 432 n n C2' C3' UTP sing 433 n n C2' H2' UTP sing 434 n n O2' HA UTP sing 435 n n C3' O3' UTP sing 436 n n C3' H3' UTP sing 437 n n O3' HB UTP sing 438 n n N1 C6 UTP sing 439 n y N1 C2 UTP sing 440 n y C6 C5 UTP doub 441 n y C6 H6 UTP sing 442 n n C2 O2 UTP doub 443 n n C2 N3 UTP sing 444 n y N3 C4 UTP sing 445 n y N3 H3 UTP sing 446 n n C4 O4 UTP doub 447 n n C4 C5 UTP sing 448 n y C5 H5 UTP sing 449 n n # _atom_sites.entry_id 7RKH _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 E 2 UTP D 1 601 602 UTP UTP . F 3 ATP D 1 602 601 ATP ATP . G 4 MG D 1 603 603 MG MG . H 4 MG D 1 604 604 MG MG . I 2 UTP A 1 601 602 UTP UTP . J 3 ATP A 1 602 601 ATP ATP . K 4 MG A 1 603 603 MG MG . L 4 MG A 1 604 604 MG MG . M 4 MG B 1 601 604 MG MG . N 2 UTP B 1 602 602 UTP UTP . O 3 ATP B 1 603 601 ATP ATP . P 4 MG B 1 604 603 MG MG . Q 4 MG C 1 601 604 MG MG . R 2 UTP C 1 602 602 UTP UTP . S 3 ATP C 1 603 601 ATP ATP . T 4 MG C 1 604 603 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 PA UTP . . . N 2 183.948 169.617 155.038 1 33.26 ? PA UTP 602 B 1 HETATM 2 O O1A UTP . . . N 2 184.893 169.118 154.004 1 33.26 ? O1A UTP 602 B 1 HETATM 3 O O2A UTP . . . N 2 183.304 168.647 155.967 1 33.26 ? O2A UTP 602 B 1 HETATM 4 O O3A UTP . . . N 2 184.657 170.762 155.886 1 33.26 ? O3A UTP 602 B 1 HETATM 5 O O5' UTP . . . N 2 182.833 170.489 154.316 1 33.26 ? O5' UTP 602 B 1 HETATM 6 P PB UTP . . . N 2 184.521 172.351 155.885 1 33.26 ? PB UTP 602 B 1 HETATM 7 O O1B UTP . . . N 2 183.47 172.741 156.858 1 33.26 ? O1B UTP 602 B 1 HETATM 8 O O2B UTP . . . N 2 184.461 172.872 154.494 1 33.26 ? O2B UTP 602 B 1 HETATM 9 O O3B UTP . . . N 2 185.951 172.723 156.488 1 33.26 ? O3B UTP 602 B 1 HETATM 10 P PG UTP . . . N 2 186.836 172.125 157.683 1 33.26 ? PG UTP 602 B 1 HETATM 11 O O1G UTP . . . N 2 188.138 172.869 157.597 1 33.26 ? O1G UTP 602 B 1 HETATM 12 O O2G UTP . . . N 2 186.99 170.652 157.454 1 33.26 ? O2G UTP 602 B 1 HETATM 13 O O3G UTP . . . N 2 186.072 172.433 158.934 1 33.26 ? O3G UTP 602 B 1 HETATM 14 C C5' UTP . . . N 2 182.936 170.536 152.882 1 33.26 ? C5' UTP 602 B 1 HETATM 15 C C4' UTP . . . N 2 181.861 169.672 152.28 1 33.26 ? C4' UTP 602 B 1 HETATM 16 O O4' UTP . . . N 2 182.452 168.708 151.378 1 33.26 ? O4' UTP 602 B 1 HETATM 17 C C1' UTP . . . N 2 181.607 167.579 151.273 1 33.26 ? C1' UTP 602 B 1 HETATM 18 C C2' UTP . . . N 2 180.389 167.892 152.143 1 33.26 ? C2' UTP 602 B 1 HETATM 19 O O2' UTP . . . N 2 179.511 168.561 151.261 1 33.26 ? O2' UTP 602 B 1 HETATM 20 C C3' UTP . . . N 2 181.068 168.754 153.223 1 33.26 ? C3' UTP 602 B 1 HETATM 21 O O3' UTP . . . N 2 180.269 169.536 154.102 1 33.26 ? O3' UTP 602 B 1 HETATM 22 N N1 UTP . . . N 2 182.318 166.336 151.673 1 33.26 ? N1 UTP 602 B 1 HETATM 23 C C6 UTP . . . N 2 183.427 166.308 152.488 1 33.26 ? C6 UTP 602 B 1 HETATM 24 C C2 UTP . . . N 2 181.795 165.171 151.157 1 33.26 ? C2 UTP 602 B 1 HETATM 25 O O2 UTP . . . N 2 180.806 165.162 150.436 1 33.26 ? O2 UTP 602 B 1 HETATM 26 N N3 UTP . . . N 2 182.473 164.036 151.509 1 33.26 ? N3 UTP 602 B 1 HETATM 27 C C4 UTP . . . N 2 183.626 163.938 152.253 1 33.26 ? C4 UTP 602 B 1 HETATM 28 O O4 UTP . . . N 2 184.107 162.824 152.477 1 33.26 ? O4 UTP 602 B 1 HETATM 29 C C5 UTP . . . N 2 184.088 165.179 152.79 1 33.26 ? C5 UTP 602 B 1 HETATM 30 H H4' UTP . . . N 2 181.259 170.263 151.769 1 0 ? H4' UTP 602 B 1 HETATM 31 H H1' UTP . . . N 2 181.363 167.498 150.323 1 0 ? H1' UTP 602 B 1 HETATM 32 H H2' UTP . . . N 2 179.975 167.077 152.514 1 0 ? H2' UTP 602 B 1 HETATM 33 H H3' UTP . . . N 2 181.684 168.189 153.774 1 0 ? H3' UTP 602 B 1 HETATM 34 H H6 UTP . . . N 2 183.747 167.12 152.827 1 0 ? H6 UTP 602 B 1 HETATM 35 H H3 UTP . . . N 2 182.12 163.289 151.235 1 0 ? H3 UTP 602 B 1 HETATM 36 H H5 UTP . . . N 2 184.851 165.197 153.335 1 0 ? H5 UTP 602 B 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #