data_7MGZ # _model_server_result.job_id ZK7ETLjx_EtfnZm4S7eIJg _model_server_result.datetime_utc '2024-10-18 16:26:44' _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 7mgz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 7MGZ # _exptl.entry_id 7MGZ _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 ? # _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,U,V,W,X _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 J N N ? 2 P N N ? 2 U 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 OD2 ASP 70 F ASP 70 1_555 G MG MG . F MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc2 A OE2 GLU 146 F GLU 146 1_555 G MG MG . F MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc3 E O2A UTP . F UTP 601 1_555 O MG MG . P MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc4 E O2B UTP . F UTP 601 1_555 O MG MG . P MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc5 G MG MG . F MG 603 1_555 H O1G ANP . F ANP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc6 G MG MG . F MG 603 1_555 H O2B ANP . F ANP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc7 I MG MG . F MG 605 1_555 P O1B UTP . P UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc8 I MG MG . F MG 605 1_555 P O1A UTP . P UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc9 B OD2 ASP 70 O ASP 70 1_555 L MG MG . O MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc10 B OE2 GLU 146 O GLU 146 1_555 L MG MG . O MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc11 J O2A UTP . O UTP 601 1_555 T MG MG . Q MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc12 J O2B UTP . O UTP 601 1_555 T MG MG . Q MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc13 L MG MG . O MG 603 1_555 M O1G ANP . O ANP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc14 L MG MG . O MG 603 1_555 M O2B ANP . O ANP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc15 N MG MG . O MG 605 1_555 U O1B UTP . Q UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc16 N MG MG . O MG 605 1_555 U O1A UTP . Q UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc17 C OD2 ASP 70 P ASP 70 1_555 R MG MG . P MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc18 C OE2 GLU 146 P GLU 146 1_555 R MG MG . P MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc19 R MG MG . P MG 604 1_555 S O1G ANP . P ANP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc20 R MG MG . P MG 604 1_555 S O2B ANP . P ANP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc21 D OD2 ASP 70 Q ASP 70 1_555 W MG MG . Q MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc22 D OE2 GLU 146 Q GLU 146 1_555 W MG MG . Q MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc23 W MG MG . Q MG 604 1_555 X O1G ANP . Q ANP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc24 W MG MG . Q MG 604 1_555 X O2B ANP . Q ANP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? # _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 406 n n PA O2A UTP sing 407 n n PA O3A UTP sing 408 n n PA O5' UTP sing 409 n n O2A H2A UTP sing 410 n n O3A PB UTP sing 411 n n O5' C5' UTP sing 412 n n PB O1B UTP sing 413 n n PB O2B UTP doub 414 n n PB O3B UTP sing 415 n n O1B H1B UTP sing 416 n n O3B PG UTP sing 417 n n PG O1G UTP sing 418 n n PG O2G UTP doub 419 n n PG O3G UTP sing 420 n n O1G H1G UTP sing 421 n n O3G H3G UTP sing 422 n n C5' C4' UTP sing 423 n n C5' "H5'1" UTP sing 424 n n C5' "H5'2" UTP sing 425 n n C4' O4' UTP sing 426 n n C4' C3' UTP sing 427 n n C4' H4' UTP sing 428 n n O4' C1' UTP sing 429 n n C1' C2' UTP sing 430 n n C1' N1 UTP sing 431 n n C1' H1' UTP sing 432 n n C2' O2' UTP sing 433 n n C2' C3' UTP sing 434 n n C2' H2' UTP sing 435 n n O2' HA UTP sing 436 n n C3' O3' UTP sing 437 n n C3' H3' UTP sing 438 n n O3' HB UTP sing 439 n n N1 C6 UTP sing 440 n y N1 C2 UTP sing 441 n y C6 C5 UTP doub 442 n y C6 H6 UTP sing 443 n n C2 O2 UTP doub 444 n n C2 N3 UTP sing 445 n y N3 C4 UTP sing 446 n y N3 H3 UTP sing 447 n n C4 O4 UTP doub 448 n n C4 C5 UTP sing 449 n y C5 H5 UTP sing 450 n n # _atom_sites.entry_id 7MGZ _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 F 1 601 602 UTP UTP . F 3 GLN F 1 602 611 GLN GLN . G 4 MG F 1 603 2 MG MG . H 5 ANP F 1 604 1 ANP ANP . I 4 MG F 1 605 3 MG MG . J 2 UTP O 1 601 602 UTP UTP . K 3 GLN O 1 602 611 GLN GLN . L 4 MG O 1 603 2 MG MG . M 5 ANP O 1 604 1 ANP ANP . N 4 MG O 1 605 3 MG MG . O 4 MG P 1 601 3 MG MG . P 2 UTP P 1 602 602 UTP UTP . Q 3 GLN P 1 603 611 GLN GLN . R 4 MG P 1 604 2 MG MG . S 5 ANP P 1 605 1 ANP ANP . T 4 MG Q 1 601 3 MG MG . U 2 UTP Q 1 602 602 UTP UTP . V 3 GLN Q 1 603 611 GLN GLN . W 4 MG Q 1 604 2 MG MG . X 5 ANP Q 1 605 1 ANP ANP . # 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 . . . E 2 141.339 144.558 158.971 1 33.26 ? PA UTP 601 F 1 HETATM 2 O O1A UTP . . . E 2 140.542 145.041 157.835 1 33.26 ? O1A UTP 601 F 1 HETATM 3 O O2A UTP . . . E 2 140.571 143.495 159.742 1 33.26 ? O2A UTP 601 F 1 HETATM 4 O O3A UTP . . . E 2 141.704 145.831 159.971 1 33.26 ? O3A UTP 601 F 1 HETATM 5 O O5' UTP . . . E 2 142.703 143.957 158.482 1 33.26 ? O5' UTP 601 F 1 HETATM 6 P PB UTP . . . E 2 141.5 145.866 161.646 1 33.26 ? PB UTP 601 F 1 HETATM 7 O O1B UTP . . . E 2 142.799 146.092 162.248 1 33.26 ? O1B UTP 601 F 1 HETATM 8 O O2B UTP . . . E 2 140.936 144.563 162.084 1 33.26 ? O2B UTP 601 F 1 HETATM 9 O O3B UTP . . . E 2 140.354 147.057 162.034 1 33.26 ? O3B UTP 601 F 1 HETATM 10 P PG UTP . . . E 2 138.792 146.883 161.542 1 33.26 ? PG UTP 601 F 1 HETATM 11 O O1G UTP . . . E 2 137.912 147.038 162.846 1 33.26 ? O1G UTP 601 F 1 HETATM 12 O O2G UTP . . . E 2 138.374 147.984 160.533 1 33.26 ? O2G UTP 601 F 1 HETATM 13 O O3G UTP . . . E 2 138.704 145.538 160.844 1 33.26 ? O3G UTP 601 F 1 HETATM 14 C C5' UTP . . . E 2 143.43 143.138 159.384 1 33.26 ? C5' UTP 601 F 1 HETATM 15 C C4' UTP . . . E 2 144.305 142.294 158.666 1 33.26 ? C4' UTP 601 F 1 HETATM 16 O O4' UTP . . . E 2 143.507 141.158 158.008 1 33.26 ? O4' UTP 601 F 1 HETATM 17 C C1' UTP . . . E 2 144.137 140.911 156.83 1 33.26 ? C1' UTP 601 F 1 HETATM 18 C C2' UTP . . . E 2 145.306 141.992 156.668 1 33.26 ? C2' UTP 601 F 1 HETATM 19 O O2' UTP . . . E 2 146.562 141.369 157.109 1 33.26 ? O2' UTP 601 F 1 HETATM 20 C C3' UTP . . . E 2 144.95 143.019 157.461 1 33.26 ? C3' UTP 601 F 1 HETATM 21 O O3' UTP . . . E 2 146.082 143.837 157.881 1 33.26 ? O3' UTP 601 F 1 HETATM 22 N N1 UTP . . . E 2 143.21 140.944 155.705 1 33.26 ? N1 UTP 601 F 1 HETATM 23 C C6 UTP . . . E 2 143.224 139.93 154.833 1 33.26 ? C6 UTP 601 F 1 HETATM 24 C C2 UTP . . . E 2 142.342 141.967 155.516 1 33.26 ? C2 UTP 601 F 1 HETATM 25 O O2 UTP . . . E 2 142.307 142.832 156.224 1 33.26 ? O2 UTP 601 F 1 HETATM 26 N N3 UTP . . . E 2 141.5 141.967 154.459 1 33.26 ? N3 UTP 601 F 1 HETATM 27 C C4 UTP . . . E 2 141.514 140.955 153.594 1 33.26 ? C4 UTP 601 F 1 HETATM 28 O O4 UTP . . . E 2 140.75 140.959 152.64 1 33.26 ? O4 UTP 601 F 1 HETATM 29 C C5 UTP . . . E 2 142.38 139.929 153.776 1 33.26 ? C5 UTP 601 F 1 HETATM 30 H "H5'1" UTP . . . E 2 142.734 142.531 159.964 1 0 ? "H5'1" UTP 601 F 1 HETATM 31 H "H5'2" UTP . . . E 2 144.009 143.77 160.059 1 0 ? "H5'2" UTP 601 F 1 HETATM 32 H H4' UTP . . . E 2 145.075 141.892 159.326 1 0 ? H4' UTP 601 F 1 HETATM 33 H H1' UTP . . . E 2 144.586 139.92 156.881 1 0 ? H1' UTP 601 F 1 HETATM 34 H H2' UTP . . . E 2 145.384 142.317 155.63 1 0 ? H2' UTP 601 F 1 HETATM 35 H HA UTP . . . E 2 146.785 140.643 156.521 1 0 ? HA UTP 601 F 1 HETATM 36 H H3' UTP . . . E 2 144.207 143.637 156.958 1 0 ? H3' UTP 601 F 1 HETATM 37 H HB UTP . . . E 2 145.771 144.552 158.443 1 0 ? HB UTP 601 F 1 HETATM 38 H H6 UTP . . . E 2 143.913 139.112 154.974 1 0 ? H6 UTP 601 F 1 HETATM 39 H H3 UTP . . . E 2 140.857 142.732 154.327 1 0 ? H3 UTP 601 F 1 HETATM 40 H H5 UTP . . . E 2 142.395 139.106 153.076 1 0 ? H5 UTP 601 F 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 40 #