data_7MIG # _model_server_result.job_id bfN3-NvxrFQJR2ytEVI93w _model_server_result.datetime_utc '2024-11-15 08:57:30' _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 7mig # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":604}' # _entry.id 7MIG # _exptl.entry_id 7MIG _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 484.141 _entity.id 5 _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 7MIG _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MIG _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 ? 5 H N N ? 5 J N N ? 5 P N N ? 5 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 disulf ? disulf1 A SG CYS 218 C CYS 218 1_555 A SG CYS 243 C CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 B SG CYS 218 A CYS 218 1_555 B SG CYS 243 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 C SG CYS 218 B CYS 218 1_555 C SG CYS 243 B CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 D SG CYS 218 E CYS 218 1_555 D SG CYS 243 E CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc1 G MG MG . C MG 603 1_555 H O1B UTP . C UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc2 G MG MG . C MG 603 1_555 H O1A UTP . C UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc3 G MG MG . C MG 603 1_555 H O3G UTP . C UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc4 I MG MG . A MG 601 1_555 J O2A UTP . A UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc5 I MG MG . A MG 601 1_555 J O2B UTP . A UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc6 I MG MG . A MG 601 1_555 J O3G UTP . A UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc7 O MG MG . B MG 603 1_555 P O2A UTP . B UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc8 O MG MG . B MG 603 1_555 P O2B UTP . B UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc9 O MG MG . B MG 603 1_555 P O3G UTP . B UTP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc10 Q MG MG . E MG 601 1_555 R O1B UTP . E UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc11 Q MG MG . E MG 601 1_555 R O1A UTP . E UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc12 Q MG MG . E MG 601 1_555 R O3G UTP . E UTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? # _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 7MIG _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 C 1 601 1 ZFY LIG . F 3 GLN C 1 602 611 GLN GLN . G 4 MG C 1 603 1 MG MG . H 5 UTP C 1 604 602 UTP UTP . I 4 MG A 1 601 1 MG MG . J 5 UTP A 1 602 602 UTP UTP . K 2 ZFY A 1 603 1 ZFY LIG . L 3 GLN A 1 604 611 GLN GLN . M 2 ZFY B 1 601 1 ZFY LIG . N 3 GLN B 1 602 611 GLN GLN . O 4 MG B 1 603 1 MG MG . P 5 UTP B 1 604 602 UTP UTP . Q 4 MG E 1 601 1 MG MG . R 5 UTP E 1 602 602 UTP UTP . S 2 ZFY E 1 603 1 ZFY LIG . T 3 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 . . . P 5 173.985 170.371 159.316 1 33.22 ? PA UTP 604 B 1 HETATM 2 O O1A UTP . . . P 5 173.442 169.763 158.048 1 33.22 ? O1A UTP 604 B 1 HETATM 3 O O2A UTP . . . P 5 175.399 170.89 159.463 1 33.22 ? O2A UTP 604 B 1 HETATM 4 O O3A UTP . . . P 5 173.626 169.363 160.609 1 33.22 ? O3A UTP 604 B 1 HETATM 5 O O5' UTP . . . P 5 172.922 171.556 159.948 1 33.22 ? O5' UTP 604 B 1 HETATM 6 P PB UTP . . . P 5 173.956 169.308 162.249 1 33.22 ? PB UTP 604 B 1 HETATM 7 O O1B UTP . . . P 5 172.691 168.985 163.005 1 33.22 ? O1B UTP 604 B 1 HETATM 8 O O2B UTP . . . P 5 174.835 170.507 162.55 1 33.22 ? O2B UTP 604 B 1 HETATM 9 O O3B UTP . . . P 5 174.93 167.945 162.21 1 33.22 ? O3B UTP 604 B 1 HETATM 10 P PG UTP . . . P 5 176.529 167.678 161.662 1 33.22 ? PG UTP 604 B 1 HETATM 11 O O1G UTP . . . P 5 177.356 167.385 162.911 1 33.22 ? O1G UTP 604 B 1 HETATM 12 O O2G UTP . . . P 5 176.443 166.493 160.695 1 33.22 ? O2G UTP 604 B 1 HETATM 13 O O3G UTP . . . P 5 176.966 168.987 160.983 1 33.22 ? O3G UTP 604 B 1 HETATM 14 C C5' UTP . . . P 5 172.946 172.845 159.376 1 33.22 ? C5' UTP 604 B 1 HETATM 15 C C4' UTP . . . P 5 171.532 173.195 158.906 1 33.22 ? C4' UTP 604 B 1 HETATM 16 O O4' UTP . . . P 5 171.652 174.217 157.921 1 33.22 ? O4' UTP 604 B 1 HETATM 17 C C1' UTP . . . P 5 170.856 173.939 156.815 1 33.22 ? C1' UTP 604 B 1 HETATM 18 C C2' UTP . . . P 5 169.927 172.744 157.172 1 33.22 ? C2' UTP 604 B 1 HETATM 19 O O2' UTP . . . P 5 168.665 173.158 157.718 1 33.22 ? O2' UTP 604 B 1 HETATM 20 C C3' UTP . . . P 5 170.74 172.044 158.258 1 33.22 ? C3' UTP 604 B 1 HETATM 21 O O3' UTP . . . P 5 169.935 171.3 159.172 1 33.22 ? O3' UTP 604 B 1 HETATM 22 N N1 UTP . . . P 5 171.675 173.92 155.603 1 33.22 ? N1 UTP 604 B 1 HETATM 23 C C6 UTP . . . P 5 171.457 174.817 154.577 1 33.22 ? C6 UTP 604 B 1 HETATM 24 C C2 UTP . . . P 5 172.688 172.992 155.502 1 33.22 ? C2 UTP 604 B 1 HETATM 25 O O2 UTP . . . P 5 173 172.108 156.272 1 33.22 ? O2 UTP 604 B 1 HETATM 26 N N3 UTP . . . P 5 173.418 173.061 154.376 1 33.22 ? N3 UTP 604 B 1 HETATM 27 C C4 UTP . . . P 5 173.252 173.831 153.293 1 33.22 ? C4 UTP 604 B 1 HETATM 28 O O4 UTP . . . P 5 173.884 173.613 152.272 1 33.22 ? O4 UTP 604 B 1 HETATM 29 C C5 UTP . . . P 5 172.199 174.805 153.452 1 33.22 ? C5 UTP 604 B 1 HETATM 30 H "H5'1" UTP . . . P 5 173.276 173.571 160.119 1 0 ? "H5'1" UTP 604 B 1 HETATM 31 H "H5'2" UTP . . . P 5 173.628 172.856 158.526 1 0 ? "H5'2" UTP 604 B 1 HETATM 32 H H4' UTP . . . P 5 170.964 173.583 159.751 1 0 ? H4' UTP 604 B 1 HETATM 33 H H1' UTP . . . P 5 170.196 174.8 156.707 1 0 ? H1' UTP 604 B 1 HETATM 34 H H2' UTP . . . P 5 169.784 172.091 156.311 1 0 ? H2' UTP 604 B 1 HETATM 35 H HA UTP . . . P 5 168.072 173.404 157.004 1 0 ? HA UTP 604 B 1 HETATM 36 H H3' UTP . . . P 5 171.444 171.363 157.781 1 0 ? H3' UTP 604 B 1 HETATM 37 H HB UTP . . . P 5 170.498 170.884 159.829 1 0 ? HB UTP 604 B 1 HETATM 38 H H6 UTP . . . P 5 170.67 175.549 154.679 1 0 ? H6 UTP 604 B 1 HETATM 39 H H3 UTP . . . P 5 174.212 172.438 154.341 1 0 ? H3 UTP 604 B 1 HETATM 40 H H5 UTP . . . P 5 172.006 175.524 152.67 1 0 ? H5 UTP 604 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 414 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 40 #