data_4YDX # _model_server_result.job_id gE3tv_z3tYL2PLpbUIA3yw _model_server_result.datetime_utc '2024-11-23 15:46:05' _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 4ydx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":103}' # _entry.id 4YDX # _exptl.entry_id 4YDX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 250.186 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3,3',3''-phosphanetriyltripropanoic 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 120 _cell.entry_id 4YDX _cell.length_a 54.07 _cell.length_b 54.07 _cell.length_c 55.578 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YDX _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 D _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 metalc ? metalc1 A N CYS 11 A CYS 12 1_555 B PT PT . A PT 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc2 A SG CYS 11 A CYS 12 1_555 B PT PT . A PT 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc3 A SG CYS 14 A CYS 15 1_555 B PT PT . A PT 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? # _chem_comp.formula 'C9 H15 O6 P' _chem_comp.formula_weight 250.186 _chem_comp.id TCE _chem_comp.mon_nstd_flag . _chem_comp.name "3,3',3''-phosphanetriyltripropanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '3-[bis(2-carboxyethyl)phosphanyl]propanoic acid' # 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 O16 C14 TCE doub 275 n n C14 O15 TCE sing 276 n n C14 C5 TCE sing 277 n n O15 HO15 TCE sing 278 n n C2 C5 TCE sing 279 n n C5 H5 TCE sing 280 n n C5 H5A TCE sing 281 n n C2 P TCE sing 282 n n C2 H2 TCE sing 283 n n C2 H2A TCE sing 284 n n C1 P TCE sing 285 n n P C3 TCE sing 286 n n C3 C6 TCE sing 287 n n C3 H3 TCE sing 288 n n C3 H3A TCE sing 289 n n C6 C8 TCE sing 290 n n C6 H6 TCE sing 291 n n C6 H6A TCE sing 292 n n O10 C8 TCE doub 293 n n C8 O9 TCE sing 294 n n O9 HO9 TCE sing 295 n n C4 C1 TCE sing 296 n n C1 H1 TCE sing 297 n n C1 H1A TCE sing 298 n n C11 C4 TCE sing 299 n n C4 H4 TCE sing 300 n n C4 H4A TCE sing 301 n n O13 C11 TCE doub 302 n n O12 C11 TCE sing 303 n n O12 HO12 TCE sing 304 n n # _atom_sites.entry_id 4YDX _atom_sites.fract_transf_matrix[1][1] 0.018495 _atom_sites.fract_transf_matrix[1][2] 0.010678 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021356 _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] 0.017993 _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 PT A 1 101 69 PT PT . C 3 SO4 A 1 102 70 SO4 SO4 . D 4 TCE A 1 103 71 TCE TCE . E 5 HOH A 1 201 115 HOH HOH . E 5 HOH A 2 202 126 HOH HOH . E 5 HOH A 3 203 163 HOH HOH . E 5 HOH A 4 204 117 HOH HOH . E 5 HOH A 5 205 119 HOH HOH . E 5 HOH A 6 206 123 HOH HOH . E 5 HOH A 7 207 136 HOH HOH . E 5 HOH A 8 208 134 HOH HOH . E 5 HOH A 9 209 137 HOH HOH . E 5 HOH A 10 210 135 HOH HOH . E 5 HOH A 11 211 251 HOH HOH . E 5 HOH A 12 212 114 HOH HOH . E 5 HOH A 13 213 231 HOH HOH . E 5 HOH A 14 214 110 HOH HOH . E 5 HOH A 15 215 120 HOH HOH . E 5 HOH A 16 216 116 HOH HOH . E 5 HOH A 17 217 164 HOH HOH . E 5 HOH A 18 218 103 HOH HOH . E 5 HOH A 19 219 256 HOH HOH . E 5 HOH A 20 220 229 HOH HOH . E 5 HOH A 21 221 230 HOH HOH . E 5 HOH A 22 222 124 HOH HOH . E 5 HOH A 23 223 107 HOH HOH . E 5 HOH A 24 224 244 HOH HOH . E 5 HOH A 25 225 139 HOH HOH . E 5 HOH A 26 226 131 HOH HOH . E 5 HOH A 27 227 147 HOH HOH . E 5 HOH A 28 228 253 HOH HOH . E 5 HOH A 29 229 241 HOH HOH . E 5 HOH A 30 230 108 HOH HOH . E 5 HOH A 31 231 152 HOH HOH . E 5 HOH A 32 232 104 HOH HOH . E 5 HOH A 33 233 169 HOH HOH . E 5 HOH A 34 234 132 HOH HOH . E 5 HOH A 35 235 249 HOH HOH . E 5 HOH A 36 236 254 HOH HOH . E 5 HOH A 37 237 240 HOH HOH . E 5 HOH A 38 238 156 HOH HOH . E 5 HOH A 39 239 159 HOH HOH . E 5 HOH A 40 240 257 HOH HOH . E 5 HOH A 41 241 233 HOH HOH . E 5 HOH A 42 242 238 HOH HOH . E 5 HOH A 43 243 153 HOH HOH . E 5 HOH A 44 244 109 HOH HOH . E 5 HOH A 45 245 146 HOH HOH . E 5 HOH A 46 246 234 HOH HOH . E 5 HOH A 47 247 101 HOH HOH . E 5 HOH A 48 248 102 HOH HOH . E 5 HOH A 49 249 106 HOH HOH . E 5 HOH A 50 250 111 HOH HOH . E 5 HOH A 51 251 112 HOH HOH . E 5 HOH A 52 252 113 HOH HOH . E 5 HOH A 53 253 118 HOH HOH . E 5 HOH A 54 254 121 HOH HOH . E 5 HOH A 55 255 122 HOH HOH . E 5 HOH A 56 256 125 HOH HOH . E 5 HOH A 57 257 127 HOH HOH . E 5 HOH A 58 258 128 HOH HOH . E 5 HOH A 59 259 129 HOH HOH . E 5 HOH A 60 260 130 HOH HOH . E 5 HOH A 61 261 133 HOH HOH . E 5 HOH A 62 262 138 HOH HOH . E 5 HOH A 63 263 140 HOH HOH . E 5 HOH A 64 264 141 HOH HOH . E 5 HOH A 65 265 142 HOH HOH . E 5 HOH A 66 266 143 HOH HOH . E 5 HOH A 67 267 144 HOH HOH . E 5 HOH A 68 268 145 HOH HOH . E 5 HOH A 69 269 149 HOH HOH . E 5 HOH A 70 270 150 HOH HOH . E 5 HOH A 71 271 151 HOH HOH . E 5 HOH A 72 272 157 HOH HOH . E 5 HOH A 73 273 158 HOH HOH . E 5 HOH A 74 274 160 HOH HOH . E 5 HOH A 75 275 161 HOH HOH . E 5 HOH A 76 276 162 HOH HOH . E 5 HOH A 77 277 165 HOH HOH . E 5 HOH A 78 278 166 HOH HOH . E 5 HOH A 79 279 167 HOH HOH . E 5 HOH A 80 280 170 HOH HOH . E 5 HOH A 81 281 171 HOH HOH . E 5 HOH A 82 282 232 HOH HOH . E 5 HOH A 83 283 235 HOH HOH . E 5 HOH A 84 284 236 HOH HOH . E 5 HOH A 85 285 237 HOH HOH . E 5 HOH A 86 286 239 HOH HOH . E 5 HOH A 87 287 242 HOH HOH . E 5 HOH A 88 288 245 HOH HOH . E 5 HOH A 89 289 246 HOH HOH . E 5 HOH A 90 290 247 HOH HOH . E 5 HOH A 91 291 248 HOH HOH . E 5 HOH A 92 292 250 HOH HOH . E 5 HOH A 93 293 255 HOH HOH . E 5 HOH A 94 294 258 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 O16 TCE . . . D 4 40.84 30.347 12.298 0.9 39.55 ? O16 TCE 103 A 1 HETATM 2 C C14 TCE . . . D 4 41.155 29.159 12.521 0.9 36.11 ? C14 TCE 103 A 1 HETATM 3 O O15 TCE . . . D 4 41.446 28.755 13.668 0.9 34.65 ? O15 TCE 103 A 1 HETATM 4 C C5 TCE . . . D 4 41.162 28.213 11.339 0.9 33.76 ? C5 TCE 103 A 1 HETATM 5 C C2 TCE . . . D 4 41.235 26.75 11.757 0.9 33.26 ? C2 TCE 103 A 1 HETATM 6 P P TCE . . . D 4 40.869 25.587 10.375 0.9 22.76 ? P TCE 103 A 1 HETATM 7 C C3 TCE . . . D 4 41.807 26.231 8.916 0.9 38.6 ? C3 TCE 103 A 1 HETATM 8 C C6 TCE . . . D 4 43.326 26.228 9.105 0.9 41.26 ? C6 TCE 103 A 1 HETATM 9 C C8 TCE . . . D 4 44.003 26.923 7.935 0.9 44.33 ? C8 TCE 103 A 1 HETATM 10 O O10 TCE . . . D 4 43.67 26.611 6.768 0.9 44.33 ? O10 TCE 103 A 1 HETATM 11 O O9 TCE . . . D 4 44.886 27.781 8.174 0.9 45.82 ? O9 TCE 103 A 1 HETATM 12 C C1 TCE . . . D 4 41.861 24.138 10.949 0.9 30.6 ? C1 TCE 103 A 1 HETATM 13 C C4 TCE . . . D 4 41.844 23.041 9.893 0.9 29.16 ? C4 TCE 103 A 1 HETATM 14 C C11 TCE . . . D 4 42.469 21.746 10.364 0.9 30.07 ? C11 TCE 103 A 1 HETATM 15 O O12 TCE . . . D 4 42.3 21.366 11.542 0.9 28.39 ? O12 TCE 103 A 1 HETATM 16 O O13 TCE . . . D 4 43.133 21.084 9.537 0.9 31.74 ? O13 TCE 103 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 16 #