data_7QGM # _model_server_result.job_id n4pxlFKXiJ8auo1TIzlG_Q _model_server_result.datetime_utc '2024-10-20 12:43:15' _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 7qgm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":604}' # _entry.id 7QGM # _exptl.entry_id 7QGM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 555.797 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-[(4-chlorophenyl)methoxyimino]-3-methyl-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic 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 7QGM _cell.length_a 54.989 _cell.length_b 98.185 _cell.length_c 234.902 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7QGM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 3_454 -x-1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -54.989 0 -117.451 # _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 # 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 51 A CYS 51 1_555 A SG CYS 57 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 A SG CYS 353 A CYS 353 1_555 A SG CYS 358 A CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 365 A CYS 365 1_555 A SG CYS 387 A CYS 387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 A SG CYS 476 A CYS 476 1_555 A SG CYS 479 A CYS 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 A NE2 HIS 38 A HIS 38 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc2 A OD2 ASP 85 A ASP 85 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc3 A OD2 ASP 85 A ASP 85 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc4 A OD1 ASN 117 A ASN 117 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc5 A O ASN 213 A ASN 213 1_555 D CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.165 ? metalc ? metalc6 A NE2 HIS 220 A HIS 220 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc7 A OD1 ASP 237 A ASP 237 1_555 D CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.176 ? metalc ? metalc8 A OD2 ASP 237 A ASP 237 1_555 D CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc9 A ND1 HIS 243 A HIS 243 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc10 A O GLY 298 A GLY 298 1_555 D CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc11 C ZN ZN . A ZN 602 1_555 E O2 BOI . A BOI 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? # _chem_comp.formula 'C18 H24 Cl N3 O11 P2' _chem_comp.formula_weight 555.797 _chem_comp.id BOI _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-[(4-chlorophenyl)methoxyimino]-3-methyl-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid' _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 CL C11 BOI sing 70 n n C10 C11 BOI doub 71 n y C10 C9 BOI sing 72 n y C11 C12 BOI sing 73 n y C9 C8 BOI doub 74 n y C12 C13 BOI doub 75 n y C8 C13 BOI sing 76 n y C8 C7 BOI sing 77 n n C7 O7 BOI sing 78 n n O7 N1 BOI sing 79 n n N1 C6 BOI doub 80 e n C14 N2 BOI sing 81 n n C6 N2 BOI sing 82 n n C6 C5 BOI sing 83 n n N2 C15 BOI sing 84 n n C5 C4 BOI doub 85 n n C15 O8 BOI doub 86 n n C15 N BOI sing 87 n n C4 N BOI sing 88 n n N C3 BOI sing 89 n n O2 P BOI sing 90 n n O1 P BOI sing 91 n n C3 O6 BOI sing 92 n n C3 C16 BOI sing 93 n n O6 C2 BOI sing 94 n n P O BOI doub 95 n n P C BOI sing 96 n n C16 O9 BOI sing 97 n n C16 C17 BOI sing 98 n n O5 C1 BOI sing 99 n n O5 P1 BOI sing 100 n n O4 P1 BOI sing 101 n n C2 C1 BOI sing 102 n n C2 C17 BOI sing 103 n n C P1 BOI sing 104 n n P1 O3 BOI doub 105 n n C17 O10 BOI sing 106 n n C14 H19 BOI sing 107 n n C14 H17 BOI sing 108 n n C14 H18 BOI sing 109 n n C7 H12 BOI sing 110 n n C7 H11 BOI sing 111 n n C13 H16 BOI sing 112 n n C12 H15 BOI sing 113 n n C10 H14 BOI sing 114 n n C9 H13 BOI sing 115 n n C5 H10 BOI sing 116 n n C4 H9 BOI sing 117 n n C3 H1 BOI sing 118 n n C16 H20 BOI sing 119 n n O9 H21 BOI sing 120 n n C17 H22 BOI sing 121 n n O10 H23 BOI sing 122 n n C2 H BOI sing 123 n n C1 H7 BOI sing 124 n n C1 H8 BOI sing 125 n n O4 H6 BOI sing 126 n n C H4 BOI sing 127 n n C H5 BOI sing 128 n n O2 H3 BOI sing 129 n n O1 H2 BOI sing 130 n n # _atom_sites.entry_id 7QGM _atom_sites.fract_transf_matrix[1][1] 0.018185 _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] 0.010185 _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] 0.004257 _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 B 2 ZN A 1 601 601 ZN ZN . C 2 ZN A 1 602 602 ZN ZN . D 3 CA A 1 603 603 CA CA . E 4 BOI A 1 604 700 BOI CBC . # 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 O8 BOI . . . E 4 -15.587 22.212 -37.404 1 95.89 ? O8 BOI 604 A 1 HETATM 2 C C15 BOI . . . E 4 -14.89 22.297 -36.41 1 97.07 ? C15 BOI 604 A 1 HETATM 3 N N2 BOI . . . E 4 -13.981 23.338 -36.249 1 97.79 ? N2 BOI 604 A 1 HETATM 4 C C14 BOI . . . E 4 -13.95 24.362 -37.298 1 96.92 ? C14 BOI 604 A 1 HETATM 5 C C6 BOI . . . E 4 -13.105 23.456 -35.178 1 98.83 ? C6 BOI 604 A 1 HETATM 6 N N1 BOI . . . E 4 -12.311 24.476 -35.216 1 99.72 ? N1 BOI 604 A 1 HETATM 7 O O7 BOI . . . E 4 -11.451 24.52 -34.092 1 100.81 ? O7 BOI 604 A 1 HETATM 8 C C7 BOI . . . E 4 -10.629 25.689 -34.206 1 100.58 ? C7 BOI 604 A 1 HETATM 9 C C8 BOI . . . E 4 -11.414 26.923 -33.859 1 101.89 ? C8 BOI 604 A 1 HETATM 10 C C13 BOI . . . E 4 -12.135 26.99 -32.674 1 104.34 ? C13 BOI 604 A 1 HETATM 11 C C12 BOI . . . E 4 -12.868 28.113 -32.348 1 105.96 ? C12 BOI 604 A 1 HETATM 12 C C11 BOI . . . E 4 -12.884 29.185 -33.214 1 105.77 ? C11 BOI 604 A 1 HETATM 13 CL CL BOI . . . E 4 -13.825 30.592 -32.823 1 108.4 ? CL BOI 604 A 1 HETATM 14 C C10 BOI . . . E 4 -12.174 29.147 -34.394 1 104.21 ? C10 BOI 604 A 1 HETATM 15 C C9 BOI . . . E 4 -11.444 28.019 -34.71 1 108.21 ? C9 BOI 604 A 1 HETATM 16 C C5 BOI . . . E 4 -13.178 22.451 -34.182 1 98.58 ? C5 BOI 604 A 1 HETATM 17 C C4 BOI . . . E 4 -14.065 21.449 -34.316 1 97.58 ? C4 BOI 604 A 1 HETATM 18 N N BOI . . . E 4 -14.908 21.363 -35.394 1 96.88 ? N BOI 604 A 1 HETATM 19 C C3 BOI . . . E 4 -15.868 20.247 -35.51 1 95.98 ? C3 BOI 604 A 1 HETATM 20 O O6 BOI . . . E 4 -16.508 20.066 -34.257 1 96.15 ? O6 BOI 604 A 1 HETATM 21 C C16 BOI . . . E 4 -15.213 18.908 -35.892 1 96.29 ? C16 BOI 604 A 1 HETATM 22 O O9 BOI . . . E 4 -15.922 18.329 -36.984 1 97.31 ? O9 BOI 604 A 1 HETATM 23 C C17 BOI . . . E 4 -15.359 18.071 -34.616 1 95.19 ? C17 BOI 604 A 1 HETATM 24 O O10 BOI . . . E 4 -15.529 16.685 -34.894 1 94.79 ? O10 BOI 604 A 1 HETATM 25 C C2 BOI . . . E 4 -16.612 18.655 -33.982 1 95.5 ? C2 BOI 604 A 1 HETATM 26 C C1 BOI . . . E 4 -16.753 18.429 -32.498 1 96.18 ? C1 BOI 604 A 1 HETATM 27 O O5 BOI . . . E 4 -18.106 18.743 -32.097 1 96.17 ? O5 BOI 604 A 1 HETATM 28 P P1 BOI . . . E 4 -18.861 17.925 -30.987 1 96.29 ? P1 BOI 604 A 1 HETATM 29 O O3 BOI . . . E 4 -18.769 16.427 -31.178 1 92.77 ? O3 BOI 604 A 1 HETATM 30 O O4 BOI . . . E 4 -20.364 18.316 -31.106 1 97.65 ? O4 BOI 604 A 1 HETATM 31 C C BOI . . . E 4 -18.268 18.63 -29.441 1 95.82 ? C BOI 604 A 1 HETATM 32 P P BOI . . . E 4 -18.249 20.426 -29.332 1 99.97 ? P BOI 604 A 1 HETATM 33 O O BOI . . . E 4 -19.531 21.066 -29.757 1 102.22 ? O BOI 604 A 1 HETATM 34 O O2 BOI . . . E 4 -17.889 20.775 -27.872 1 102.15 ? O2 BOI 604 A 1 HETATM 35 O O1 BOI . . . E 4 -17.055 20.882 -30.2 1 101.89 ? O1 BOI 604 A 1 HETATM 36 H H19 BOI . . . E 4 -12.972 24.429 -37.772 1 117.95 ? H19 BOI 604 A 1 HETATM 37 H H17 BOI . . . E 4 -14.18 25.352 -36.906 1 117.95 ? H17 BOI 604 A 1 HETATM 38 H H18 BOI . . . E 4 -14.672 24.158 -38.087 1 117.95 ? H18 BOI 604 A 1 HETATM 39 H H12 BOI . . . E 4 -10.239 25.764 -35.22 1 122.34 ? H12 BOI 604 A 1 HETATM 40 H H11 BOI . . . E 4 -9.766 25.595 -33.55 1 122.34 ? H11 BOI 604 A 1 HETATM 41 H H16 BOI . . . E 4 -12.131 26.15 -31.98 1 126.85 ? H16 BOI 604 A 1 HETATM 42 H H15 BOI . . . E 4 -13.43 28.157 -31.417 1 128.8 ? H15 BOI 604 A 1 HETATM 43 H H14 BOI . . . E 4 -12.194 30.004 -35.065 1 126.7 ? H14 BOI 604 A 1 HETATM 44 H H13 BOI . . . E 4 -10.884 27.994 -35.644 1 131.5 ? H13 BOI 604 A 1 HETATM 45 H H10 BOI . . . E 4 -12.516 22.5 -33.319 1 119.94 ? H10 BOI 604 A 1 HETATM 46 H H9 BOI . . . E 4 -14.136 20.669 -33.56 1 118.74 ? H9 BOI 604 A 1 HETATM 47 H H1 BOI . . . E 4 -16.665 20.527 -36.198 1 116.82 ? H1 BOI 604 A 1 HETATM 48 H H20 BOI . . . E 4 -14.162 19.025 -36.15 1 117.19 ? H20 BOI 604 A 1 HETATM 49 H H21 BOI . . . E 4 -15.244 17.994 -37.627 1 118.42 ? H21 BOI 604 A 1 HETATM 50 H H22 BOI . . . E 4 -14.483 18.077 -33.969 1 115.87 ? H22 BOI 604 A 1 HETATM 51 H H23 BOI . . . E 4 -14.69 16.206 -34.667 1 115.39 ? H23 BOI 604 A 1 HETATM 52 H H BOI . . . E 4 -17.529 18.333 -34.475 1 116.24 ? H BOI 604 A 1 HETATM 53 H H7 BOI . . . E 4 -16.541 17.395 -32.23 1 117.06 ? H7 BOI 604 A 1 HETATM 54 H H8 BOI . . . E 4 -16.067 19.058 -31.932 1 117.06 ? H8 BOI 604 A 1 HETATM 55 H H6 BOI . . . E 4 -21.064 17.612 -31.081 1 118.83 ? H6 BOI 604 A 1 HETATM 56 H H4 BOI . . . E 4 -18.831 18.245 -28.592 1 116.63 ? H4 BOI 604 A 1 HETATM 57 H H5 BOI . . . E 4 -17.271 18.265 -29.2 1 116.63 ? H5 BOI 604 A 1 HETATM 58 H H3 BOI . . . E 4 -18.158 21.603 -27.394 1 124.22 ? H3 BOI 604 A 1 HETATM 59 H H2 BOI . . . E 4 -16.203 21.232 -29.827 1 123.92 ? H2 BOI 604 A 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 70 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 642 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 59 #