data_5IRX # _model_server_result.job_id hz4s5PHO39CSk8Nq4r_Nmg _model_server_result.datetime_utc '2025-03-13 18:04:49' _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 5irx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":102}' # _entry.id 5IRX # _exptl.entry_id 5IRX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 341.295 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate' _entity.pdbx_number_of_molecules 4 _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 5IRX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IRX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 R N N ? 6 V N N ? 6 X N N ? 6 Y N 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 E SG CYS 2 E CYS 2 1_555 E SG CYS 16 E CYS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 E SG CYS 9 E CYS 9 1_555 E SG CYS 23 E CYS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 E SG CYS 15 E CYS 15 1_555 E SG CYS 31 E CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 E SG CYS 44 E CYS 44 1_555 E SG CYS 58 E CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 E SG CYS 51 E CYS 51 1_555 E SG CYS 63 E CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 E SG CYS 57 E CYS 57 1_555 E SG CYS 71 E CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 F SG CYS 2 F CYS 2 1_555 F SG CYS 16 F CYS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 F SG CYS 9 F CYS 9 1_555 F SG CYS 23 F CYS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf9 F SG CYS 15 F CYS 15 1_555 F SG CYS 31 F CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 F SG CYS 44 F CYS 44 1_555 F SG CYS 58 F CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 F SG CYS 51 F CYS 51 1_555 F SG CYS 63 F CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 F SG CYS 57 F CYS 57 1_555 F SG CYS 71 F CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _chem_comp.formula 'C12 H24 N O8 P' _chem_comp.formula_weight 341.295 _chem_comp.id 6O9 _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate' _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 C17 C16 6O9 sing 160 n n C16 C15 6O9 sing 161 n n C15 C14 6O9 sing 162 n n C14 C13 6O9 sing 163 n n O18 C13 6O9 doub 164 n n C13 O12 6O9 sing 165 n n O12 C11 6O9 sing 166 n n C11 C10 6O9 sing 167 n n O19 C10 6O9 sing 168 n n O19 C20 6O9 sing 169 n n C21 C20 6O9 sing 170 n n C10 C09 6O9 sing 171 n n C20 O22 6O9 doub 172 n n C09 O08 6O9 sing 173 n n O08 P05 6O9 sing 174 n n P05 O07 6O9 doub 175 n n P05 O04 6O9 sing 176 n n P05 O06 6O9 sing 177 n n O04 C03 6O9 sing 178 n n C03 C02 6O9 sing 179 n n C02 N01 6O9 sing 180 n n N01 H012 6O9 sing 181 n n N01 H011 6O9 sing 182 n n C02 H022 6O9 sing 183 n n C02 H021 6O9 sing 184 n n C03 H032 6O9 sing 185 n n C03 H031 6O9 sing 186 n n O06 H2 6O9 sing 187 n n C09 H092 6O9 sing 188 n n C09 H091 6O9 sing 189 n n C10 H101 6O9 sing 190 n n C11 H111 6O9 sing 191 n n C11 H112 6O9 sing 192 n n C14 H141 6O9 sing 193 n n C14 H142 6O9 sing 194 n n C15 H152 6O9 sing 195 n n C15 H151 6O9 sing 196 n n C16 H161 6O9 sing 197 n n C16 H162 6O9 sing 198 n n C17 H173 6O9 sing 199 n n C17 H172 6O9 sing 200 n n C17 H3 6O9 sing 201 n n C21 H213 6O9 sing 202 n n C21 H212 6O9 sing 203 n n C21 H4 6O9 sing 204 n n # _atom_sites.entry_id 5IRX _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 3 6O8 A 1 801 19 6O8 LPA . H 4 6OE A 1 802 27 6OE LPC . I 4 6OE A 1 803 31 6OE LPC . J 5 6EU A 1 804 4 6EU 6EU . K 3 6O8 B 1 801 20 6O8 LPA . L 4 6OE B 1 802 30 6OE LPC . M 5 6EU B 1 803 2 6EU 6EU . N 3 6O8 C 1 801 18 6O8 LPA . O 4 6OE C 1 802 33 6OE LPC . P 5 6EU C 1 803 3 6EU 6EU . Q 3 6O8 D 1 801 21 6O8 LPA . R 6 6O9 D 1 802 24 6O9 LPB . S 4 6OE D 1 803 28 6OE LPC . T 4 6OE D 1 804 32 6OE LPC . U 5 6EU D 1 805 1 6EU 6EU . V 6 6O9 E 1 101 25 6O9 LPB . W 4 6OE E 1 102 29 6OE LPC . X 6 6O9 F 1 101 22 6O9 LPB . Y 6 6O9 F 1 102 23 6O9 LPB . Z 4 6OE F 1 103 26 6OE LPC . # 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 N N01 6O9 . . . Y 6 86.68 101.642 156.533 1 20 ? N01 6O9 102 F 1 HETATM 2 C C02 6O9 . . . Y 6 85.544 100.752 156.504 1 20 ? C02 6O9 102 F 1 HETATM 3 C C03 6O9 . . . Y 6 85.565 99.989 155.189 1 20 ? C03 6O9 102 F 1 HETATM 4 O O04 6O9 . . . Y 6 84.37 100.233 154.509 1 20 ? O04 6O9 102 F 1 HETATM 5 P P05 6O9 . . . Y 6 84.121 101.749 153.917 1 20 ? P05 6O9 102 F 1 HETATM 6 O O06 6O9 . . . Y 6 85.119 102.692 154.541 1 20 ? O06 6O9 102 F 1 HETATM 7 O O07 6O9 . . . Y 6 82.719 102.203 154.241 1 20 ? O07 6O9 102 F 1 HETATM 8 O O08 6O9 . . . Y 6 84.345 101.725 152.287 1 20 ? O08 6O9 102 F 1 HETATM 9 C C09 6O9 . . . Y 6 84.927 102.84 151.679 1 20 ? C09 6O9 102 F 1 HETATM 10 C C10 6O9 . . . Y 6 86.22 102.409 150.998 1 20 ? C10 6O9 102 F 1 HETATM 11 C C11 6O9 . . . Y 6 86.692 103.425 149.963 1 20 ? C11 6O9 102 F 1 HETATM 12 O O12 6O9 . . . Y 6 87.363 102.748 148.944 1 20 ? O12 6O9 102 F 1 HETATM 13 C C13 6O9 . . . Y 6 87.499 103.479 147.762 1 20 ? C13 6O9 102 F 1 HETATM 14 C C14 6O9 . . . Y 6 88.127 102.813 146.547 1 20 ? C14 6O9 102 F 1 HETATM 15 C C15 6O9 . . . Y 6 87.921 103.574 145.245 1 20 ? C15 6O9 102 F 1 HETATM 16 C C16 6O9 . . . Y 6 88.925 103.142 144.185 1 20 ? C16 6O9 102 F 1 HETATM 17 C C17 6O9 . . . Y 6 88.617 103.661 142.786 1 20 ? C17 6O9 102 F 1 HETATM 18 O O18 6O9 . . . Y 6 87.132 104.601 147.705 1 20 ? O18 6O9 102 F 1 HETATM 19 O O19 6O9 . . . Y 6 85.992 101.192 150.347 1 20 ? O19 6O9 102 F 1 HETATM 20 C C20 6O9 . . . Y 6 86.307 100.049 151.096 1 20 ? C20 6O9 102 F 1 HETATM 21 C C21 6O9 . . . Y 6 86.653 98.736 150.39 1 20 ? C21 6O9 102 F 1 HETATM 22 O O22 6O9 . . . Y 6 86.301 100.095 152.278 1 20 ? O22 6O9 102 F 1 HETATM 23 H H012 6O9 . . . Y 6 86.738 102.059 155.753 1 20 ? H012 6O9 102 F 1 HETATM 24 H H011 6O9 . . . Y 6 87.417 101.165 156.671 1 20 ? H011 6O9 102 F 1 HETATM 25 H H022 6O9 . . . Y 6 84.73 101.27 156.574 1 20 ? H022 6O9 102 F 1 HETATM 26 H H021 6O9 . . . Y 6 85.603 100.128 157.241 1 20 ? H021 6O9 102 F 1 HETATM 27 H H032 6O9 . . . Y 6 86.309 100.302 154.656 1 20 ? H032 6O9 102 F 1 HETATM 28 H H031 6O9 . . . Y 6 85.662 99.042 155.363 1 20 ? H031 6O9 102 F 1 HETATM 29 H H092 6O9 . . . Y 6 84.32 103.201 151.017 1 20 ? H092 6O9 102 F 1 HETATM 30 H H091 6O9 . . . Y 6 85.122 103.514 152.346 1 20 ? H091 6O9 102 F 1 HETATM 31 H H101 6O9 . . . Y 6 86.907 102.295 151.667 1 20 ? H101 6O9 102 F 1 HETATM 32 H H111 6O9 . . . Y 6 85.928 103.889 149.598 1 20 ? H111 6O9 102 F 1 HETATM 33 H H112 6O9 . . . Y 6 87.289 104.061 150.376 1 20 ? H112 6O9 102 F 1 HETATM 34 H H141 6O9 . . . Y 6 87.74 101.934 146.452 1 20 ? H141 6O9 102 F 1 HETATM 35 H H142 6O9 . . . Y 6 89.076 102.722 146.701 1 20 ? H142 6O9 102 F 1 HETATM 36 H H152 6O9 . . . Y 6 87.03 103.402 144.92 1 20 ? H152 6O9 102 F 1 HETATM 37 H H151 6O9 . . . Y 6 88.023 104.52 145.412 1 20 ? H151 6O9 102 F 1 HETATM 38 H H161 6O9 . . . Y 6 88.941 102.176 144.161 1 20 ? H161 6O9 102 F 1 HETATM 39 H H162 6O9 . . . Y 6 89.797 103.464 144.443 1 20 ? H162 6O9 102 F 1 HETATM 40 H H173 6O9 . . . Y 6 88.02 103.047 142.338 1 20 ? H173 6O9 102 F 1 HETATM 41 H H172 6O9 . . . Y 6 88.202 104.53 142.851 1 20 ? H172 6O9 102 F 1 HETATM 42 H H213 6O9 . . . Y 6 85.839 98.304 150.09 1 20 ? H213 6O9 102 F 1 HETATM 43 H H212 6O9 . . . Y 6 87.117 98.15 151.007 1 20 ? H212 6O9 102 F 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #