data_8SIJ # _model_server_result.job_id zfElHjoxY9ObzKjWqllQBQ _model_server_result.datetime_utc '2025-01-13 11:41:44' _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 8sij # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 8SIJ # _exptl.entry_id 8SIJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 350.262 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen 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 8SIJ _cell.length_a 98.589 _cell.length_b 98.589 _cell.length_c 278.515 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SIJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 'C12 H19 N2 O8 P' _chem_comp.formula_weight 350.262 _chem_comp.id K9E _chem_comp.mon_nstd_flag . _chem_comp.name '[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen 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 C2A C2 K9E sing 173 n n N1 C2 K9E doub 174 n y N1 C6 K9E sing 175 n y C2 C3 K9E sing 176 n y C6 C5 K9E doub 177 n y C3 O3 K9E sing 178 n n C3 C4 K9E doub 179 n y C5 C4 K9E sing 180 n y C5 C5A K9E sing 181 n n C4 C4A K9E sing 182 n n O4P C5A K9E sing 183 n n O4P P K9E sing 184 n n O3P P K9E doub 185 n n P O1P K9E sing 186 n n P O2P K9E sing 187 n n C4A N K9E doub 188 n n N C K9E sing 189 n n O1 C1 K9E sing 190 n n O2 C21 K9E sing 191 n n C1 C K9E sing 192 n n C C21 K9E sing 193 n n C C31 K9E sing 194 n n O31 C31 K9E sing 195 n n O1P H1 K9E sing 196 n n O2P H2 K9E sing 197 n n C5A H3 K9E sing 198 n n C5A H4 K9E sing 199 n n C6 H5 K9E sing 200 n n C4A H6 K9E sing 201 n n O3 H8 K9E sing 202 n n C2A H9 K9E sing 203 n n C2A H10 K9E sing 204 n n C2A H11 K9E sing 205 n n O31 H12 K9E sing 206 n n C31 H13 K9E sing 207 n n C31 H14 K9E sing 208 n n C21 H17 K9E sing 209 n n C21 H18 K9E sing 210 n n O2 H19 K9E sing 211 n n C1 H20 K9E sing 212 n n C1 H21 K9E sing 213 n n O1 H22 K9E sing 214 n n # _atom_sites.entry_id 8SIJ _atom_sites.fract_transf_matrix[1][1] 0.010143 _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] 0.010143 _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] 0.00359 _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 PLP A 1 501 501 PLP PLP . D 3 CL A 1 502 1 CL CL . E 4 K9E B 1 501 501 K9E LIG . F 3 CL B 1 502 2 CL CL . G 5 HOH A 1 601 4 HOH HOH . G 5 HOH A 2 602 1 HOH HOH . G 5 HOH A 3 603 14 HOH HOH . G 5 HOH A 4 604 29 HOH HOH . G 5 HOH A 5 605 48 HOH HOH . G 5 HOH A 6 606 42 HOH HOH . G 5 HOH A 7 607 5 HOH HOH . G 5 HOH A 8 608 11 HOH HOH . G 5 HOH A 9 609 3 HOH HOH . G 5 HOH A 10 610 36 HOH HOH . G 5 HOH A 11 611 99 HOH HOH . G 5 HOH A 12 612 54 HOH HOH . G 5 HOH A 13 613 97 HOH HOH . G 5 HOH A 14 614 104 HOH HOH . G 5 HOH A 15 615 98 HOH HOH . G 5 HOH A 16 616 17 HOH HOH . G 5 HOH A 17 617 66 HOH HOH . G 5 HOH A 18 618 70 HOH HOH . G 5 HOH A 19 619 31 HOH HOH . G 5 HOH A 20 620 72 HOH HOH . G 5 HOH A 21 621 74 HOH HOH . G 5 HOH A 22 622 16 HOH HOH . G 5 HOH A 23 623 71 HOH HOH . G 5 HOH A 24 624 73 HOH HOH . G 5 HOH A 25 625 75 HOH HOH . G 5 HOH A 26 626 108 HOH HOH . G 5 HOH A 27 627 85 HOH HOH . G 5 HOH A 28 628 22 HOH HOH . G 5 HOH A 29 629 84 HOH HOH . H 5 HOH B 1 601 12 HOH HOH . H 5 HOH B 2 602 6 HOH HOH . H 5 HOH B 3 603 76 HOH HOH . H 5 HOH B 4 604 2 HOH HOH . H 5 HOH B 5 605 78 HOH HOH . H 5 HOH B 6 606 32 HOH HOH . H 5 HOH B 7 607 10 HOH HOH . H 5 HOH B 8 608 106 HOH HOH . H 5 HOH B 9 609 39 HOH HOH . H 5 HOH B 10 610 7 HOH HOH . H 5 HOH B 11 611 20 HOH HOH . H 5 HOH B 12 612 15 HOH HOH . H 5 HOH B 13 613 8 HOH HOH . H 5 HOH B 14 614 13 HOH HOH . H 5 HOH B 15 615 23 HOH HOH . H 5 HOH B 16 616 96 HOH HOH . H 5 HOH B 17 617 59 HOH HOH . H 5 HOH B 18 618 77 HOH HOH . H 5 HOH B 19 619 69 HOH HOH . H 5 HOH B 20 620 82 HOH HOH . H 5 HOH B 21 621 86 HOH HOH . H 5 HOH B 22 622 89 HOH HOH . H 5 HOH B 23 623 80 HOH HOH . H 5 HOH B 24 624 81 HOH HOH . H 5 HOH B 25 625 88 HOH HOH . H 5 HOH B 26 626 79 HOH HOH . H 5 HOH B 27 627 94 HOH HOH . H 5 HOH B 28 628 102 HOH HOH . H 5 HOH B 29 629 100 HOH HOH . H 5 HOH B 30 630 33 HOH HOH . H 5 HOH B 31 631 91 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 O3P K9E . . . E 4 16.176 47.877 -14.013 1 71.55 -1 O3P K9E 501 B 1 HETATM 2 P P K9E . . . E 4 16.498 47.84 -12.528 1 69.97 ? P K9E 501 B 1 HETATM 3 O O1P K9E . . . E 4 16.592 46.367 -12.069 1 69.14 -1 O1P K9E 501 B 1 HETATM 4 O O2P K9E . . . E 4 17.852 48.537 -12.287 1 70.03 ? O2P K9E 501 B 1 HETATM 5 O O4P K9E . . . E 4 15.266 48.676 -11.703 1 71.63 ? O4P K9E 501 B 1 HETATM 6 C C5A K9E . . . E 4 14.4 49.522 -12.479 1 73.38 ? C5A K9E 501 B 1 HETATM 7 C C5 K9E . . . E 4 13.018 49.354 -11.864 1 74.21 ? C5 K9E 501 B 1 HETATM 8 C C6 K9E . . . E 4 12.132 48.436 -12.399 1 74.59 ? C6 K9E 501 B 1 HETATM 9 N N1 K9E . . . E 4 10.937 48.29 -11.845 1 74.67 ? N1 K9E 501 B 1 HETATM 10 C C4 K9E . . . E 4 12.657 50.114 -10.783 1 73.76 ? C4 K9E 501 B 1 HETATM 11 C C4A K9E . . . E 4 13.655 51.104 -10.171 1 72.26 ? C4A K9E 501 B 1 HETATM 12 C C3 K9E . . . E 4 11.398 49.918 -10.212 1 73.69 ? C3 K9E 501 B 1 HETATM 13 O O3 K9E . . . E 4 10.945 50.644 -9.079 1 72.48 ? O3 K9E 501 B 1 HETATM 14 C C2 K9E . . . E 4 10.566 48.985 -10.803 1 74 ? C2 K9E 501 B 1 HETATM 15 C C2A K9E . . . E 4 9.139 48.766 -10.204 1 73.55 ? C2A K9E 501 B 1 HETATM 16 O O31 K9E . . . E 4 16.675 53.159 -9.222 1 69.55 ? O31 K9E 501 B 1 HETATM 17 C C31 K9E . . . E 4 15.559 52.205 -9.227 1 70.91 ? C31 K9E 501 B 1 HETATM 18 C C K9E . . . E 4 14.246 52.961 -9.065 1 72.41 ? C K9E 501 B 1 HETATM 19 N N K9E . . . E 4 13.158 52.102 -9.671 1 72.73 ? N K9E 501 B 1 HETATM 20 C C21 K9E . . . E 4 14.286 54.401 -9.756 1 72.53 ? C21 K9E 501 B 1 HETATM 21 O O2 K9E . . . E 4 13.548 55.281 -8.951 1 72.99 ? O2 K9E 501 B 1 HETATM 22 C C1 K9E . . . E 4 13.865 53.114 -7.507 1 70.12 ? C1 K9E 501 B 1 HETATM 23 O O1 K9E . . . E 4 12.468 52.956 -7.411 1 70.38 ? O1 K9E 501 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 23 #