data_5FIT # _model_server_result.job_id '_GfUnuLn4L-8kkXOUJnAkg' _model_server_result.datetime_utc '2025-03-04 14:45:48' _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 5fit # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":200}' # _entry.id 5FIT # _exptl.entry_id 5FIT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.228 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 120 _cell.entry_id 5FIT _cell.length_a 50.64 _cell.length_b 50.64 _cell.length_c 267.52 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FIT _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 44.586667 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A C SER 81 A SER 81 1_555 A N MSE 82 A MSE 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale2 A C MSE 82 A MSE 82 1_555 A N GLN 83 A GLN 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 A C GLU 134 A GLU 134 1_555 A N MSE 135 A MSE 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C MSE 135 A MSE 135 1_555 A N ALA 136 A ALA 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? # _chem_comp.formula 'C11 H17 N5 O9 P2' _chem_comp.formula_weight 425.228 _chem_comp.id AP2 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 PB O1B AP2 doub 13 n n PB O2B AP2 sing 14 n n PB O3B AP2 sing 15 n n PB C3A AP2 sing 16 n n O2B HOB2 AP2 sing 17 n n O3B HOB3 AP2 sing 18 n n C3A PA AP2 sing 19 n n C3A H3A1 AP2 sing 20 n n C3A H3A2 AP2 sing 21 n n PA O1A AP2 doub 22 n n PA O2A AP2 sing 23 n n PA O5' AP2 sing 24 n n O2A HOA2 AP2 sing 25 n n O5' C5' AP2 sing 26 n n C5' C4' AP2 sing 27 n n C5' "H5'1" AP2 sing 28 n n C5' "H5'2" AP2 sing 29 n n C4' O4' AP2 sing 30 n n C4' C3' AP2 sing 31 n n C4' H4' AP2 sing 32 n n O4' C1' AP2 sing 33 n n C3' O3' AP2 sing 34 n n C3' C2' AP2 sing 35 n n C3' H3' AP2 sing 36 n n O3' HO3' AP2 sing 37 n n C2' O2' AP2 sing 38 n n C2' C1' AP2 sing 39 n n C2' H2' AP2 sing 40 n n O2' HO2' AP2 sing 41 n n C1' N9 AP2 sing 42 n n C1' H1' AP2 sing 43 n n N9 C8 AP2 sing 44 n y N9 C4 AP2 sing 45 n y C8 N7 AP2 doub 46 n y C8 H8 AP2 sing 47 n n N7 C5 AP2 sing 48 n y C5 C6 AP2 sing 49 n y C5 C4 AP2 doub 50 n y C6 N6 AP2 sing 51 n n C6 N1 AP2 doub 52 n y N6 HN61 AP2 sing 53 n n N6 HN62 AP2 sing 54 n n N1 C2 AP2 sing 55 n y C2 N3 AP2 doub 56 n y C2 H2 AP2 sing 57 n n N3 C4 AP2 sing 58 n y # _atom_sites.entry_id 5FIT _atom_sites.fract_transf_matrix[1][1] 0.019747 _atom_sites.fract_transf_matrix[1][2] 0.011401 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022802 _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] 0.003738 _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 AP2 A 1 200 200 AP2 AP2 . C 3 HOH A 1 201 1 HOH HOH . C 3 HOH A 2 202 2 HOH HOH . C 3 HOH A 3 203 3 HOH HOH . C 3 HOH A 4 204 4 HOH HOH . C 3 HOH A 5 205 5 HOH HOH . C 3 HOH A 6 206 6 HOH HOH . C 3 HOH A 7 207 7 HOH HOH . C 3 HOH A 8 208 8 HOH HOH . C 3 HOH A 9 209 9 HOH HOH . C 3 HOH A 10 210 10 HOH HOH . C 3 HOH A 11 211 11 HOH HOH . C 3 HOH A 12 212 12 HOH HOH . C 3 HOH A 13 213 13 HOH HOH . C 3 HOH A 14 214 14 HOH HOH . C 3 HOH A 15 215 15 HOH HOH . C 3 HOH A 16 216 16 HOH HOH . C 3 HOH A 17 217 17 HOH HOH . C 3 HOH A 18 218 18 HOH HOH . C 3 HOH A 19 219 19 HOH HOH . C 3 HOH A 20 220 20 HOH HOH . C 3 HOH A 21 221 21 HOH HOH . C 3 HOH A 22 222 22 HOH HOH . C 3 HOH A 23 223 23 HOH HOH . C 3 HOH A 24 224 24 HOH HOH . C 3 HOH A 25 225 25 HOH HOH . C 3 HOH A 26 226 26 HOH HOH . C 3 HOH A 27 227 27 HOH HOH . C 3 HOH A 28 228 28 HOH HOH . C 3 HOH A 29 229 29 HOH HOH . C 3 HOH A 30 230 30 HOH HOH . C 3 HOH A 31 231 31 HOH HOH . C 3 HOH A 32 232 32 HOH HOH . C 3 HOH A 33 233 33 HOH HOH . C 3 HOH A 34 234 34 HOH HOH . C 3 HOH A 35 235 35 HOH HOH . C 3 HOH A 36 236 36 HOH HOH . C 3 HOH A 37 237 37 HOH HOH . C 3 HOH A 38 238 38 HOH HOH . C 3 HOH A 39 239 39 HOH HOH . C 3 HOH A 40 240 40 HOH HOH . C 3 HOH A 41 241 41 HOH HOH . C 3 HOH A 42 242 42 HOH HOH . C 3 HOH A 43 243 43 HOH HOH . C 3 HOH A 44 244 44 HOH HOH . C 3 HOH A 45 245 45 HOH HOH . C 3 HOH A 46 246 46 HOH HOH . C 3 HOH A 47 247 47 HOH HOH . C 3 HOH A 48 248 48 HOH HOH . C 3 HOH A 49 249 49 HOH HOH . C 3 HOH A 50 250 50 HOH HOH . C 3 HOH A 51 251 51 HOH HOH . C 3 HOH A 52 252 52 HOH HOH . C 3 HOH A 53 253 53 HOH HOH . C 3 HOH A 54 254 54 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 C C3A AP2 . . . B 2 8.43 17.374 20.544 1 48.95 ? C3A AP2 200 A 1 HETATM 2 P PA AP2 . . . B 2 9.702 18.117 20.601 1 42.74 ? PA AP2 200 A 1 HETATM 3 O O1A AP2 . . . B 2 10.87 17.224 20.531 1 41.7 ? O1A AP2 200 A 1 HETATM 4 O O2A AP2 . . . B 2 9.94 19.428 19.965 1 40.28 ? O2A AP2 200 A 1 HETATM 5 O O5' AP2 . . . B 2 9.824 18.625 22.114 1 50.73 ? O5' AP2 200 A 1 HETATM 6 C C5' AP2 . . . B 2 8.827 19.48 22.698 1 55.54 ? C5' AP2 200 A 1 HETATM 7 C C4' AP2 . . . B 2 8.956 19.729 24.213 1 53.55 ? C4' AP2 200 A 1 HETATM 8 O O4' AP2 . . . B 2 9.092 21.161 24.345 1 52.88 ? O4' AP2 200 A 1 HETATM 9 C C3' AP2 . . . B 2 7.823 19.062 25.021 1 55.34 ? C3' AP2 200 A 1 HETATM 10 O O3' AP2 . . . B 2 8.383 18.288 26.109 1 40.38 ? O3' AP2 200 A 1 HETATM 11 C C2' AP2 . . . B 2 7.163 20.367 25.532 1 65.93 ? C2' AP2 200 A 1 HETATM 12 O O2' AP2 . . . B 2 6.653 20.237 26.886 1 72.33 ? O2' AP2 200 A 1 HETATM 13 C C1' AP2 . . . B 2 8.328 21.381 25.551 1 62.65 ? C1' AP2 200 A 1 HETATM 14 N N9 AP2 . . . B 2 7.854 22.797 25.547 1 62.95 ? N9 AP2 200 A 1 HETATM 15 C C8 AP2 . . . B 2 7.158 23.466 24.556 1 64.27 ? C8 AP2 200 A 1 HETATM 16 N N7 AP2 . . . B 2 6.889 24.719 24.833 1 65.97 ? N7 AP2 200 A 1 HETATM 17 C C5 AP2 . . . B 2 7.448 24.872 26.104 1 66.09 ? C5 AP2 200 A 1 HETATM 18 C C6 AP2 . . . B 2 7.486 25.984 26.976 1 63.8 ? C6 AP2 200 A 1 HETATM 19 N N6 AP2 . . . B 2 6.905 27.116 26.576 1 59.86 ? N6 AP2 200 A 1 HETATM 20 N N1 AP2 . . . B 2 8.105 25.824 28.165 1 65.68 ? N1 AP2 200 A 1 HETATM 21 C C2 AP2 . . . B 2 8.656 24.673 28.541 1 55.73 ? C2 AP2 200 A 1 HETATM 22 N N3 AP2 . . . B 2 8.657 23.576 27.783 1 52.27 ? N3 AP2 200 A 1 HETATM 23 C C4 AP2 . . . B 2 8.038 23.716 26.571 1 64.04 ? C4 AP2 200 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #