data_5KM8 # _model_server_result.job_id qnFkxTc6lYWwLm2H96CLAg _model_server_result.datetime_utc '2024-11-18 09:34:57' _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 5km8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5KM8 # _exptl.entry_id 5KM8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 279.187 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid' _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 5KM8 _cell.length_a 37.99 _cell.length_b 73.852 _cell.length_c 77.464 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KM8 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 _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 E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C8 H14 N3 O6 P' _chem_comp.formula_weight 279.187 _chem_comp.id L8P _chem_comp.mon_nstd_flag . _chem_comp.name '({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Cidofovir # 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 P C4' L8P sing 204 n n P OP1 L8P sing 205 n n P OP2 L8P doub 206 n n N1 C2 L8P sing 207 n n N1 C6 L8P sing 208 n n N1 C1' L8P sing 209 n n C2 O2 L8P doub 210 n n C2 N3 L8P sing 211 n n N3 C4 L8P doub 212 n n C4 N4 L8P sing 213 n n C4 C5 L8P sing 214 n n N4 HN4 L8P sing 215 n n N4 HN4A L8P sing 216 n n C5 C6 L8P doub 217 n n C5 H5 L8P sing 218 n n C6 H6 L8P sing 219 n n C1' C2' L8P sing 220 n n C1' H1' L8P sing 221 n n C1' "H1'A" L8P sing 222 n n C2' C3' L8P sing 223 n n C2' O4' L8P sing 224 n n C2' H2' L8P sing 225 n n C3' O3' L8P sing 226 n n C3' H3' L8P sing 227 n n C3' "H3'A" L8P sing 228 n n C4' O4' L8P sing 229 n n C4' H4' L8P sing 230 n n C4' "H4'A" L8P sing 231 n n P O6 L8P sing 232 n n O3' H12 L8P sing 233 n n OP1 H13 L8P sing 234 n n O6 H14 L8P sing 235 n n # _atom_sites.entry_id 5KM8 _atom_sites.fract_transf_matrix[1][1] 0.026323 _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] 0.013541 _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] 0.012909 _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 C 2 CL A 1 201 1 CL CL . D 3 DMS A 1 202 1 DMS DMS . E 4 L8P B 1 201 1 L8P CID . F 5 EDO B 1 202 1 EDO EDO . G 5 EDO B 1 203 1 EDO EDO . H 6 GOL B 1 204 1 GOL GOL . I 7 HOH A 1 301 4 HOH HOH . I 7 HOH A 2 302 41 HOH HOH . I 7 HOH A 3 303 5 HOH HOH . I 7 HOH A 4 304 13 HOH HOH . I 7 HOH A 5 305 11 HOH HOH . I 7 HOH A 6 306 59 HOH HOH . I 7 HOH A 7 307 3 HOH HOH . I 7 HOH A 8 308 18 HOH HOH . I 7 HOH A 9 309 98 HOH HOH . I 7 HOH A 10 310 12 HOH HOH . I 7 HOH A 11 311 88 HOH HOH . I 7 HOH A 12 312 14 HOH HOH . I 7 HOH A 13 313 58 HOH HOH . I 7 HOH A 14 314 56 HOH HOH . I 7 HOH A 15 315 82 HOH HOH . I 7 HOH A 16 316 34 HOH HOH . I 7 HOH A 17 317 77 HOH HOH . I 7 HOH A 18 318 67 HOH HOH . I 7 HOH A 19 319 103 HOH HOH . I 7 HOH A 20 320 1 HOH HOH . I 7 HOH A 21 321 17 HOH HOH . I 7 HOH A 22 322 54 HOH HOH . I 7 HOH A 23 323 70 HOH HOH . I 7 HOH A 24 324 5 HOH HOH . I 7 HOH A 25 325 63 HOH HOH . I 7 HOH A 26 326 72 HOH HOH . I 7 HOH A 27 327 35 HOH HOH . I 7 HOH A 28 328 38 HOH HOH . I 7 HOH A 29 329 1 HOH HOH . I 7 HOH A 30 330 65 HOH HOH . I 7 HOH A 31 331 31 HOH HOH . I 7 HOH A 32 332 89 HOH HOH . I 7 HOH A 33 333 71 HOH HOH . I 7 HOH A 34 334 109 HOH HOH . I 7 HOH A 35 335 96 HOH HOH . I 7 HOH A 36 336 81 HOH HOH . I 7 HOH A 37 337 91 HOH HOH . I 7 HOH A 38 338 97 HOH HOH . I 7 HOH A 39 339 75 HOH HOH . I 7 HOH A 40 340 107 HOH HOH . I 7 HOH A 41 341 8 HOH HOH . I 7 HOH A 42 342 6 HOH HOH . I 7 HOH A 43 343 68 HOH HOH . I 7 HOH A 44 344 76 HOH HOH . I 7 HOH A 45 345 3 HOH HOH . I 7 HOH A 46 346 87 HOH HOH . I 7 HOH A 47 347 79 HOH HOH . I 7 HOH A 48 348 84 HOH HOH . I 7 HOH A 49 349 39 HOH HOH . I 7 HOH A 50 350 30 HOH HOH . I 7 HOH A 51 351 22 HOH HOH . I 7 HOH A 52 352 112 HOH HOH . I 7 HOH A 53 353 28 HOH HOH . I 7 HOH A 54 354 37 HOH HOH . J 7 HOH B 1 301 21 HOH HOH . J 7 HOH B 2 302 73 HOH HOH . J 7 HOH B 3 303 20 HOH HOH . J 7 HOH B 4 304 64 HOH HOH . J 7 HOH B 5 305 2 HOH HOH . J 7 HOH B 6 306 9 HOH HOH . J 7 HOH B 7 307 6 HOH HOH . J 7 HOH B 8 308 10 HOH HOH . J 7 HOH B 9 309 16 HOH HOH . J 7 HOH B 10 310 50 HOH HOH . J 7 HOH B 11 311 101 HOH HOH . J 7 HOH B 12 312 15 HOH HOH . J 7 HOH B 13 313 36 HOH HOH . J 7 HOH B 14 314 66 HOH HOH . J 7 HOH B 15 315 2 HOH HOH . J 7 HOH B 16 316 33 HOH HOH . J 7 HOH B 17 317 114 HOH HOH . J 7 HOH B 18 318 94 HOH HOH . J 7 HOH B 19 319 8 HOH HOH . J 7 HOH B 20 320 86 HOH HOH . J 7 HOH B 21 321 61 HOH HOH . J 7 HOH B 22 322 19 HOH HOH . J 7 HOH B 23 323 7 HOH HOH . J 7 HOH B 24 324 93 HOH HOH . J 7 HOH B 25 325 32 HOH HOH . J 7 HOH B 26 326 1 HOH HOH . J 7 HOH B 27 327 92 HOH HOH . J 7 HOH B 28 328 25 HOH HOH . J 7 HOH B 29 329 40 HOH HOH . J 7 HOH B 30 330 85 HOH HOH . J 7 HOH B 31 331 74 HOH HOH . J 7 HOH B 32 332 4 HOH HOH . J 7 HOH B 33 333 23 HOH HOH . J 7 HOH B 34 334 26 HOH HOH . J 7 HOH B 35 335 90 HOH HOH . J 7 HOH B 36 336 95 HOH HOH . J 7 HOH B 37 337 55 HOH HOH . J 7 HOH B 38 338 46 HOH HOH . J 7 HOH B 39 339 104 HOH HOH . J 7 HOH B 40 340 29 HOH HOH . J 7 HOH B 41 341 102 HOH HOH . J 7 HOH B 42 342 47 HOH HOH . J 7 HOH B 43 343 62 HOH HOH . J 7 HOH B 44 344 52 HOH HOH . J 7 HOH B 45 345 60 HOH HOH . J 7 HOH B 46 346 78 HOH HOH . J 7 HOH B 47 347 108 HOH HOH . J 7 HOH B 48 348 44 HOH HOH . J 7 HOH B 49 349 48 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 P P L8P . . . E 4 -11.573 1.1 -0.277 1 28.03 ? P L8P 201 B 1 HETATM 2 N N1 L8P . . . E 4 -16.308 -1.297 3.282 1 41.4 ? N1 L8P 201 B 1 HETATM 3 C C2 L8P . . . E 4 -16.223 -2.706 3.157 1 40.87 ? C2 L8P 201 B 1 HETATM 4 O O2 L8P . . . E 4 -15.147 -3.242 2.817 1 44.44 ? O2 L8P 201 B 1 HETATM 5 N N3 L8P . . . E 4 -17.306 -3.486 3.407 1 44.86 ? N3 L8P 201 B 1 HETATM 6 C C4 L8P . . . E 4 -18.482 -2.929 3.779 1 42.96 ? C4 L8P 201 B 1 HETATM 7 N N4 L8P . . . E 4 -19.664 -3.79 4.05 1 47.79 ? N4 L8P 201 B 1 HETATM 8 C C5 L8P . . . E 4 -18.586 -1.548 3.91 1 44.6 ? C5 L8P 201 B 1 HETATM 9 C C6 L8P . . . E 4 -17.473 -0.745 3.659 1 44.4 ? C6 L8P 201 B 1 HETATM 10 C C1' L8P . . . E 4 -15.137 -0.443 3.017 1 37.77 ? C1' L8P 201 B 1 HETATM 11 C C2' L8P . . . E 4 -14.915 -0.189 1.52 1 30.64 ? C2' L8P 201 B 1 HETATM 12 C C3' L8P . . . E 4 -16.036 0.692 0.97 1 32.57 ? C3' L8P 201 B 1 HETATM 13 O O3' L8P . . . E 4 -16.226 1.83 1.821 1 32.32 ? O3' L8P 201 B 1 HETATM 14 C C4' L8P . . . E 4 -13.353 0.802 -0.004 1 28.39 ? C4' L8P 201 B 1 HETATM 15 O O4' L8P . . . E 4 -13.661 0.481 1.358 1 30.12 ? O4' L8P 201 B 1 HETATM 16 O OP1 L8P . . . E 4 -11.103 2.206 0.648 1 29.11 ? OP1 L8P 201 B 1 HETATM 17 O OP2 L8P . . . E 4 -11.496 1.469 -1.742 1 24.9 ? OP2 L8P 201 B 1 HETATM 18 O O6 L8P . . . E 4 -10.951 -0.234 0.103 1 30.17 ? O6 L8P 201 B 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 386 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 18 #