data_5B48 # _model_server_result.job_id ZXZwHyy-NFsvvfgdjURVAQ _model_server_result.datetime_utc '2024-10-28 02:43:01' _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 5b48 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 5B48 # _exptl.entry_id 5B48 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 482.386 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(2E)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-(1-oxidanylpropylidene)-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate' _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 90 _cell.angle_gamma 90 _cell.entry_id 5B48 _cell.length_a 75.15 _cell.length_b 145.878 _cell.length_c 170.094 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B48 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_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 _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 4 _struct_asym.id F _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 metalc ? metalc1 B SG CYS 12 B CYS 12 1_555 E FE2 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc2 B SG CYS 15 B CYS 15 1_555 E FE4 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc3 B SG CYS 46 B CYS 46 1_555 E FE3 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc4 B OD1 ASP 90 B ASP 90 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc5 B O VAL 120 B VAL 120 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc6 B SG CYS 197 B CYS 197 1_555 E FE1 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc7 F O3B TDN . B TDN 402 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc8 F O1A TDN . B TDN 402 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? # _chem_comp.formula 'C15 H24 N4 O8 P2 S' _chem_comp.formula_weight 482.386 _chem_comp.id TDN _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(2E)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-(1-oxidanylpropylidene)-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate' _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 CM2 C2' TDN sing 302 n n O2A PA TDN sing 303 n n C2' N3' TDN doub 304 n y C2' N1' TDN sing 305 n y N3' C4' TDN sing 306 n y N1' C6' TDN doub 307 n y PA O1A TDN doub 308 n n PA O3A TDN sing 309 n n PA O7 TDN sing 310 n n C4' N4' TDN sing 311 n n C4' C5' TDN doub 312 n y O3A PB TDN sing 313 n n O2B PB TDN sing 314 n n C6' C5' TDN sing 315 n y C5' C7' TDN sing 316 n n O7 C7 TDN sing 317 n n C7 C6 TDN sing 318 n n CM4 C4 TDN sing 319 n n PB O3B TDN sing 320 n n PB O1B TDN doub 321 n n C6 C5 TDN sing 322 n n C4 C5 TDN doub 323 n n C4 N3 TDN sing 324 n n C5 S1 TDN sing 325 n n N3 C7' TDN sing 326 n n N3 C2 TDN sing 327 n n S1 C2 TDN sing 328 n n C2 C27 TDN doub 329 e n C30 C29 TDN sing 330 n n C27 O28 TDN sing 331 n n C27 C29 TDN sing 332 n n O3B H1 TDN sing 333 n n C7 H4 TDN sing 334 n n C7 H5 TDN sing 335 n n C6 H6 TDN sing 336 n n C6 H7 TDN sing 337 n n CM4 H8 TDN sing 338 n n CM4 H9 TDN sing 339 n n CM4 H10 TDN sing 340 n n O28 H12 TDN sing 341 n n C29 H13 TDN sing 342 n n C29 H14 TDN sing 343 n n C30 H15 TDN sing 344 n n C30 H16 TDN sing 345 n n C30 H17 TDN sing 346 n n C7' H18 TDN sing 347 n n C7' H19 TDN sing 348 n n C6' H20 TDN sing 349 n n CM2 H21 TDN sing 350 n n CM2 H22 TDN sing 351 n n CM2 H23 TDN sing 352 n n N4' H24 TDN sing 353 n n N4' H25 TDN sing 354 n n O2B H26 TDN sing 355 n n O2A H2 TDN sing 356 n n # _atom_sites.entry_id 5B48 _atom_sites.fract_transf_matrix[1][1] 0.013307 _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] 0.006855 _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] 0.005879 _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 3 SF4 B 1 401 628 SF4 SF4 . F 4 TDN B 1 402 1611 TDN TDN . G 5 MG B 1 403 630 MG MG . H 6 HOH A 1 701 32 HOH HOH . H 6 HOH A 2 702 19 HOH HOH . H 6 HOH A 3 703 10 HOH HOH . H 6 HOH A 4 704 27 HOH HOH . H 6 HOH A 5 705 35 HOH HOH . H 6 HOH A 6 706 17 HOH HOH . H 6 HOH A 7 707 14 HOH HOH . H 6 HOH A 8 708 55 HOH HOH . H 6 HOH A 9 709 52 HOH HOH . H 6 HOH A 10 710 16 HOH HOH . H 6 HOH A 11 711 36 HOH HOH . H 6 HOH A 12 712 37 HOH HOH . H 6 HOH A 13 713 21 HOH HOH . H 6 HOH A 14 714 58 HOH HOH . H 6 HOH A 15 715 3 HOH HOH . H 6 HOH A 16 716 7 HOH HOH . H 6 HOH A 17 717 28 HOH HOH . H 6 HOH A 18 718 47 HOH HOH . H 6 HOH A 19 719 25 HOH HOH . H 6 HOH A 20 720 5 HOH HOH . H 6 HOH A 21 721 59 HOH HOH . H 6 HOH A 22 722 6 HOH HOH . H 6 HOH A 23 723 29 HOH HOH . H 6 HOH A 24 724 33 HOH HOH . H 6 HOH A 25 725 2 HOH HOH . I 6 HOH B 1 501 41 HOH HOH . I 6 HOH B 2 502 38 HOH HOH . I 6 HOH B 3 503 40 HOH HOH . I 6 HOH B 4 504 56 HOH HOH . I 6 HOH B 5 505 39 HOH HOH . J 6 HOH C 1 701 11 HOH HOH . J 6 HOH C 2 702 23 HOH HOH . J 6 HOH C 3 703 44 HOH HOH . J 6 HOH C 4 704 57 HOH HOH . J 6 HOH C 5 705 26 HOH HOH . J 6 HOH C 6 706 54 HOH HOH . J 6 HOH C 7 707 18 HOH HOH . J 6 HOH C 8 708 4 HOH HOH . J 6 HOH C 9 709 30 HOH HOH . J 6 HOH C 10 710 48 HOH HOH . J 6 HOH C 11 711 53 HOH HOH . J 6 HOH C 12 712 31 HOH HOH . J 6 HOH C 13 713 45 HOH HOH . J 6 HOH C 14 714 42 HOH HOH . J 6 HOH C 15 715 24 HOH HOH . J 6 HOH C 16 716 34 HOH HOH . J 6 HOH C 17 717 22 HOH HOH . J 6 HOH C 18 718 12 HOH HOH . J 6 HOH C 19 719 9 HOH HOH . J 6 HOH C 20 720 15 HOH HOH . J 6 HOH C 21 721 8 HOH HOH . J 6 HOH C 22 722 13 HOH HOH . J 6 HOH C 23 723 43 HOH HOH . K 6 HOH D 1 401 46 HOH HOH . K 6 HOH D 2 402 1 HOH HOH . K 6 HOH D 3 403 51 HOH HOH . K 6 HOH D 4 404 49 HOH HOH . K 6 HOH D 5 405 50 HOH HOH . K 6 HOH D 6 406 60 HOH HOH . K 6 HOH D 7 407 20 HOH HOH . K 6 HOH D 8 408 61 HOH HOH . # 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 O O2B TDN . . . F 4 12.123 49.725 215.796 1 62.48 ? O2B TDN 402 B 1 HETATM 2 P PB TDN . . . F 4 13.013 48.856 216.586 1 48.56 ? PB TDN 402 B 1 HETATM 3 O O3B TDN . . . F 4 14.379 49.294 216.846 1 48.52 ? O3B TDN 402 B 1 HETATM 4 O O1B TDN . . . F 4 12.422 47.957 217.59 1 59.63 ? O1B TDN 402 B 1 HETATM 5 O O3A TDN . . . F 4 13.229 47.702 215.401 1 47.58 ? O3A TDN 402 B 1 HETATM 6 P PA TDN . . . F 4 14.707 46.989 214.898 1 50.03 ? PA TDN 402 B 1 HETATM 7 O O1A TDN . . . F 4 15.879 47.897 214.931 1 50.4 ? O1A TDN 402 B 1 HETATM 8 O O2A TDN . . . F 4 14.475 46.241 213.607 1 53.29 ? O2A TDN 402 B 1 HETATM 9 O O7 TDN . . . F 4 14.798 45.979 216.246 1 55.42 ? O7 TDN 402 B 1 HETATM 10 C C7 TDN . . . F 4 14.636 44.534 216.25 1 55.82 ? C7 TDN 402 B 1 HETATM 11 C C6 TDN . . . F 4 13.315 44.114 216.852 1 55.54 ? C6 TDN 402 B 1 HETATM 12 C C5 TDN . . . F 4 12.935 42.834 217.104 1 62.89 ? C5 TDN 402 B 1 HETATM 13 C C4 TDN . . . F 4 13.473 41.565 216.947 1 60.24 ? C4 TDN 402 B 1 HETATM 14 C CM4 TDN . . . F 4 14.915 41.346 216.455 1 52.03 ? CM4 TDN 402 B 1 HETATM 15 S S1 TDN . . . F 4 11.471 42.68 217.686 1 68.39 ? S1 TDN 402 B 1 HETATM 16 C C2 TDN . . . F 4 11.44 40.986 217.763 1 66.99 ? C2 TDN 402 B 1 HETATM 17 C C27 TDN . . . F 4 10.305 40.378 218.232 1 65.91 ? C27 TDN 402 B 1 HETATM 18 O O28 TDN . . . F 4 10.203 39.032 218.371 1 67.63 ? O28 TDN 402 B 1 HETATM 19 C C29 TDN . . . F 4 9.13 41.232 218.678 1 63.27 ? C29 TDN 402 B 1 HETATM 20 C C30 TDN . . . F 4 7.83 40.806 218.028 1 61.91 ? C30 TDN 402 B 1 HETATM 21 N N3 TDN . . . F 4 12.639 40.502 217.277 1 58.92 ? N3 TDN 402 B 1 HETATM 22 C C7' TDN . . . F 4 13.044 39.037 217.377 1 57.5 ? C7' TDN 402 B 1 HETATM 23 C C5' TDN . . . F 4 13.3 38.298 216.176 1 57.43 ? C5' TDN 402 B 1 HETATM 24 C C6' TDN . . . F 4 14.619 37.857 215.926 1 58.93 ? C6' TDN 402 B 1 HETATM 25 N N1' TDN . . . F 4 14.93 37.127 214.775 1 60.73 ? N1' TDN 402 B 1 HETATM 26 C C2' TDN . . . F 4 13.94 36.806 213.914 1 63.11 ? C2' TDN 402 B 1 HETATM 27 C CM2 TDN . . . F 4 14.291 36.067 212.785 1 58.64 ? CM2 TDN 402 B 1 HETATM 28 N N3' TDN . . . F 4 12.65 37.19 214.146 1 60.2 ? N3' TDN 402 B 1 HETATM 29 C C4' TDN . . . F 4 12.318 37.911 215.241 1 58.19 ? C4' TDN 402 B 1 HETATM 30 N N4' TDN . . . F 4 11.045 38.252 215.45 1 63.28 ? N4' TDN 402 B 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #