data_7MII # _model_server_result.job_id m1B0dEfVNqO3BD9V5zdvWA _model_server_result.datetime_utc '2025-02-17 01:51:56' _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 7mii # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":603}' # _entry.id 7MII # _exptl.entry_id 7MII _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 484.141 _entity.id 3 _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 7MII _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MII _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 ? 3 F N N ? 3 K N N ? 3 N N N ? 3 S 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 F O2A UTP . A UTP 602 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc2 F O2B UTP . A UTP 602 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc3 F O3B UTP . A UTP 602 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc4 F O1G UTP . A UTP 602 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc5 F O2G UTP . A UTP 602 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc6 H MG MG . A MG 604 1_555 K O2G UTP . B UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc7 H MG MG . A MG 604 1_555 K O1A UTP . B UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc8 H MG MG . A MG 604 1_555 K O3G UTP . B UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc9 H MG MG . A MG 604 1_555 K O1B UTP . B UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc10 H MG MG . A MG 604 1_555 K O3B UTP . B UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc11 N O1A UTP . C UTP 602 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc12 N O1B UTP . C UTP 602 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc13 N O3B UTP . C UTP 602 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc14 N O2G UTP . C UTP 602 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc15 N O3G UTP . C UTP 602 1_555 Q MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc16 P MG MG . C MG 604 1_555 S O2A UTP . E UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc17 P MG MG . C MG 604 1_555 S O2B UTP . E UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc18 P MG MG . C MG 604 1_555 S O3B UTP . E UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc19 P MG MG . C MG 604 1_555 S O1G UTP . E UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc20 P MG MG . C MG 604 1_555 S O2G UTP . E UTP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? # _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 356 n n PA O2A UTP sing 357 n n PA O3A UTP sing 358 n n PA O5' UTP sing 359 n n O2A H2A UTP sing 360 n n O3A PB UTP sing 361 n n O5' C5' UTP sing 362 n n PB O1B UTP sing 363 n n PB O2B UTP doub 364 n n PB O3B UTP sing 365 n n O1B H1B UTP sing 366 n n O3B PG UTP sing 367 n n PG O1G UTP sing 368 n n PG O2G UTP doub 369 n n PG O3G UTP sing 370 n n O1G H1G UTP sing 371 n n O3G H3G UTP sing 372 n n C5' C4' UTP sing 373 n n C5' "H5'1" UTP sing 374 n n C5' "H5'2" UTP sing 375 n n C4' O4' UTP sing 376 n n C4' C3' UTP sing 377 n n C4' H4' UTP sing 378 n n O4' C1' UTP sing 379 n n C1' C2' UTP sing 380 n n C1' N1 UTP sing 381 n n C1' H1' UTP sing 382 n n C2' O2' UTP sing 383 n n C2' C3' UTP sing 384 n n C2' H2' UTP sing 385 n n O2' HA UTP sing 386 n n C3' O3' UTP sing 387 n n C3' H3' UTP sing 388 n n O3' HB UTP sing 389 n n N1 C6 UTP sing 390 n y N1 C2 UTP sing 391 n y C6 C5 UTP doub 392 n y C6 H6 UTP sing 393 n n C2 O2 UTP doub 394 n n C2 N3 UTP sing 395 n y N3 C4 UTP sing 396 n y N3 H3 UTP sing 397 n n C4 O4 UTP doub 398 n n C4 C5 UTP sing 399 n y C5 H5 UTP sing 400 n n # _atom_sites.entry_id 7MII _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 ZFY A 1 601 1 ZFY LIG . F 3 UTP A 1 602 602 UTP UTP . G 4 GLN A 1 603 611 GLN GLN . H 5 MG A 1 604 1 MG MG . I 5 MG B 1 601 1 MG MG . J 2 ZFY B 1 602 1 ZFY LIG . K 3 UTP B 1 603 602 UTP UTP . L 4 GLN B 1 604 611 GLN GLN . M 2 ZFY C 1 601 1 ZFY LIG . N 3 UTP C 1 602 602 UTP UTP . O 4 GLN C 1 603 611 GLN GLN . P 5 MG C 1 604 1 MG MG . Q 5 MG E 1 601 1 MG MG . R 2 ZFY E 1 602 1 ZFY LIG . S 3 UTP E 1 603 602 UTP UTP . T 4 GLN E 1 604 611 GLN GLN . # 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 . . . K 3 141.59 170.155 156.384 1 26.88 ? PA UTP 603 B 1 HETATM 2 O O1A UTP . . . K 3 140.391 170.981 155.964 1 26.88 ? O1A UTP 603 B 1 HETATM 3 O O2A UTP . . . K 3 141.56 169.18 157.531 1 26.88 ? O2A UTP 603 B 1 HETATM 4 O O3A UTP . . . K 3 142.137 169.332 155.019 1 26.88 ? O3A UTP 603 B 1 HETATM 5 O O5' UTP . . . K 3 142.945 171.18 156.592 1 26.88 ? O5' UTP 603 B 1 HETATM 6 P PB UTP . . . K 3 141.851 169.324 153.367 1 26.88 ? PB UTP 603 B 1 HETATM 7 O O1B UTP . . . K 3 141.043 170.569 153.075 1 26.88 ? O1B UTP 603 B 1 HETATM 8 O O2B UTP . . . K 3 143.124 168.929 152.66 1 26.88 ? O2B UTP 603 B 1 HETATM 9 O O3B UTP . . . K 3 140.78 168.038 153.373 1 26.88 ? O3B UTP 603 B 1 HETATM 10 P PG UTP . . . K 3 139.121 168.029 153.781 1 26.88 ? PG UTP 603 B 1 HETATM 11 O O1G UTP . . . K 3 138.6 166.615 153.58 1 26.88 ? O1G UTP 603 B 1 HETATM 12 O O2G UTP . . . K 3 138.489 169.11 152.898 1 26.88 ? O2G UTP 603 B 1 HETATM 13 O O3G UTP . . . K 3 139.042 168.534 155.225 1 26.88 ? O3G UTP 603 B 1 HETATM 14 C C5' UTP . . . K 3 143.218 172.168 155.613 1 26.88 ? C5' UTP 603 B 1 HETATM 15 C C4' UTP . . . K 3 144.256 173.158 156.17 1 26.88 ? C4' UTP 603 B 1 HETATM 16 O O4' UTP . . . K 3 143.639 173.844 157.254 1 26.88 ? O4' UTP 603 B 1 HETATM 17 C C1' UTP . . . K 3 144.371 173.662 158.428 1 26.88 ? C1' UTP 603 B 1 HETATM 18 C C2' UTP . . . K 3 145.175 172.359 158.244 1 26.88 ? C2' UTP 603 B 1 HETATM 19 O O2' UTP . . . K 3 146.237 172.18 159.177 1 26.88 ? O2' UTP 603 B 1 HETATM 20 C C3' UTP . . . K 3 145.528 172.514 156.763 1 26.88 ? C3' UTP 603 B 1 HETATM 21 O O3' UTP . . . K 3 146.694 173.294 156.517 1 26.88 ? O3' UTP 603 B 1 HETATM 22 N N1 UTP . . . K 3 143.457 173.733 159.556 1 26.88 ? N1 UTP 603 B 1 HETATM 23 C C6 UTP . . . K 3 142.387 172.87 159.628 1 26.88 ? C6 UTP 603 B 1 HETATM 24 C C2 UTP . . . K 3 143.671 174.68 160.526 1 26.88 ? C2 UTP 603 B 1 HETATM 25 O O2 UTP . . . K 3 144.53 175.55 160.537 1 26.88 ? O2 UTP 603 B 1 HETATM 26 N N3 UTP . . . K 3 142.808 174.609 161.564 1 26.88 ? N3 UTP 603 B 1 HETATM 27 C C4 UTP . . . K 3 141.794 173.752 161.786 1 26.88 ? C4 UTP 603 B 1 HETATM 28 O O4 UTP . . . K 3 141.185 173.733 162.844 1 26.88 ? O4 UTP 603 B 1 HETATM 29 C C5 UTP . . . K 3 141.557 172.847 160.684 1 26.88 ? C5 UTP 603 B 1 HETATM 30 H "H5'1" UTP . . . K 3 143.613 171.692 154.715 1 0 ? "H5'1" UTP 603 B 1 HETATM 31 H "H5'2" UTP . . . K 3 142.3 172.703 155.369 1 0 ? "H5'2" UTP 603 B 1 HETATM 32 H H4' UTP . . . K 3 144.534 173.872 155.395 1 0 ? H4' UTP 603 B 1 HETATM 33 H H1' UTP . . . K 3 145.079 174.486 158.514 1 0 ? H1' UTP 603 B 1 HETATM 34 H H2' UTP . . . K 3 144.488 171.518 158.344 1 0 ? H2' UTP 603 B 1 HETATM 35 H HA UTP . . . K 3 146.238 171.273 159.492 1 0 ? HA UTP 603 B 1 HETATM 36 H H3' UTP . . . K 3 145.663 171.525 156.325 1 0 ? H3' UTP 603 B 1 HETATM 37 H HB UTP . . . K 3 147.463 172.84 156.872 1 0 ? HB UTP 603 B 1 HETATM 38 H H6 UTP . . . K 3 142.209 172.189 158.809 1 0 ? H6 UTP 603 B 1 HETATM 39 H H3 UTP . . . K 3 142.945 175.305 162.283 1 0 ? H3 UTP 603 B 1 HETATM 40 H H5 UTP . . . K 3 140.723 172.162 160.709 1 0 ? H5 UTP 603 B 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 40 #