data_1DB4 # _model_server_result.job_id i_tDfVMJTR75wgvbr4p0Eg _model_server_result.datetime_utc '2024-11-18 11:30:45' _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 1db4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":200}' # _entry.id 1DB4 # _exptl.entry_id 1DB4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 416.407 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[3-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-PROPYL-]-PHOSPHONIC 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 1DB4 _cell.length_a 77.012 _cell.length_b 77.012 _cell.length_c 91.62 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DB4 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 3 _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 disulf ? disulf1 A SG CYS 26 A CYS 26 1_555 A SG CYS 117 A CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 A SG CYS 28 A CYS 28 1_555 A SG CYS 44 A CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 43 A CYS 43 1_555 A SG CYS 97 A CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 A SG CYS 49 A CYS 49 1_555 A SG CYS 124 A CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf5 A SG CYS 50 A CYS 50 1_555 A SG CYS 90 A CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf6 A SG CYS 59 A CYS 59 1_555 A SG CYS 83 A CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf7 A SG CYS 77 A CYS 77 1_555 A SG CYS 88 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A O PHE 23 A PHE 23 1_555 C CA CA . A CA 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc2 A O GLY 25 A GLY 25 1_555 C CA CA . A CA 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc3 A O HIS 27 A HIS 27 1_555 B CA CA . A CA 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc4 A O GLY 29 A GLY 29 1_555 B CA CA . A CA 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc5 A O GLY 31 A GLY 31 1_555 B CA CA . A CA 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc6 A OD1 ASP 48 A ASP 48 1_555 B CA CA . A CA 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc7 A OD2 ASP 48 A ASP 48 1_555 B CA CA . A CA 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc8 A O TYR 112 A TYR 112 1_555 C CA CA . A CA 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc9 A OD1 ASN 114 A ASN 114 1_555 C CA CA . A CA 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc10 B CA CA . A CA 198 1_555 D O12 8IN . A 8IN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc11 B CA CA . A CA 198 1_555 D O29 8IN . A 8IN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc12 C CA CA . A CA 199 1_555 E O HOH . A HOH 229 12_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc13 C CA CA . A CA 199 1_555 E O HOH . A HOH 260 12_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? # _chem_comp.formula 'C21 H25 N2 O5 P' _chem_comp.formula_weight 416.407 _chem_comp.id 8IN _chem_comp.mon_nstd_flag . _chem_comp.name '[3-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-PROPYL-]-PHOSPHONIC 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 C1 C2 8IN doub 1 n y C1 C6 8IN sing 2 n y C1 H1 8IN sing 3 n n C2 C3 8IN sing 4 n y C2 H2 8IN sing 5 n n C3 C4 8IN doub 6 n y C3 N7 8IN sing 7 n y C4 C5 8IN sing 8 n y C4 C9 8IN sing 9 n y C5 C6 8IN doub 10 n y C5 H5 8IN sing 11 n n C6 O22 8IN sing 12 n n N7 C8 8IN sing 13 n y N7 C15 8IN sing 14 n n C8 C9 8IN doub 15 n y C8 C14 8IN sing 16 n n C9 C10 8IN sing 17 n n C10 C11 8IN sing 18 n n C10 H101 8IN sing 19 n n C10 H102 8IN sing 20 n n C11 O12 8IN doub 21 n n C11 N13 8IN sing 22 n n N13 H131 8IN sing 23 n n N13 H132 8IN sing 24 n n C14 H141 8IN sing 25 n n C14 H142 8IN sing 26 n n C14 H143 8IN sing 27 n n C15 C16 8IN sing 28 n n C15 H151 8IN sing 29 n n C15 H152 8IN sing 30 n n C16 C17 8IN doub 31 n y C16 C21 8IN sing 32 n y C17 C18 8IN sing 33 n y C17 H17 8IN sing 34 n n C18 C19 8IN doub 35 n y C18 H18 8IN sing 36 n n C19 C20 8IN sing 37 n y C19 H19 8IN sing 38 n n C20 C21 8IN doub 39 n y C20 H20 8IN sing 40 n n C21 H21 8IN sing 41 n n O22 C23 8IN sing 42 n n C23 C24 8IN sing 43 n n C23 H231 8IN sing 44 n n C23 H232 8IN sing 45 n n C24 C25 8IN sing 46 n n C24 H241 8IN sing 47 n n C24 H242 8IN sing 48 n n C25 P26 8IN sing 49 n n C25 H251 8IN sing 50 n n C25 H252 8IN sing 51 n n P26 O27 8IN doub 52 n n P26 O28 8IN sing 53 n n P26 O29 8IN sing 54 n n O28 H28 8IN sing 55 n n O29 H29 8IN sing 56 n n # _atom_sites.entry_id 1DB4 _atom_sites.fract_transf_matrix[1][1] 0.012985 _atom_sites.fract_transf_matrix[1][2] 0.007497 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014994 _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] 0.010915 _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 CA A 1 198 198 CA CA . C 2 CA A 1 199 199 CA CA . D 3 8IN A 1 200 150 8IN 8IN . E 4 HOH A 1 201 201 HOH HOH . E 4 HOH A 2 202 202 HOH HOH . E 4 HOH A 3 203 203 HOH HOH . E 4 HOH A 4 204 204 HOH HOH . E 4 HOH A 5 205 205 HOH HOH . E 4 HOH A 6 206 206 HOH HOH . E 4 HOH A 7 207 207 HOH HOH . E 4 HOH A 8 208 208 HOH HOH . E 4 HOH A 9 209 209 HOH HOH . E 4 HOH A 10 210 210 HOH HOH . E 4 HOH A 11 211 211 HOH HOH . E 4 HOH A 12 212 212 HOH HOH . E 4 HOH A 13 213 213 HOH HOH . E 4 HOH A 14 214 214 HOH HOH . E 4 HOH A 15 215 215 HOH HOH . E 4 HOH A 16 216 216 HOH HOH . E 4 HOH A 17 217 217 HOH HOH . E 4 HOH A 18 218 218 HOH HOH . E 4 HOH A 19 219 219 HOH HOH . E 4 HOH A 20 220 220 HOH HOH . E 4 HOH A 21 221 221 HOH HOH . E 4 HOH A 22 222 222 HOH HOH . E 4 HOH A 23 223 223 HOH HOH . E 4 HOH A 24 224 224 HOH HOH . E 4 HOH A 25 225 225 HOH HOH . E 4 HOH A 26 226 226 HOH HOH . E 4 HOH A 27 227 227 HOH HOH . E 4 HOH A 28 228 228 HOH HOH . E 4 HOH A 29 229 229 HOH HOH . E 4 HOH A 30 230 230 HOH HOH . E 4 HOH A 31 231 231 HOH HOH . E 4 HOH A 32 232 232 HOH HOH . E 4 HOH A 33 233 233 HOH HOH . E 4 HOH A 34 234 234 HOH HOH . E 4 HOH A 35 235 235 HOH HOH . E 4 HOH A 36 236 236 HOH HOH . E 4 HOH A 37 237 237 HOH HOH . E 4 HOH A 38 238 238 HOH HOH . E 4 HOH A 39 239 239 HOH HOH . E 4 HOH A 40 240 240 HOH HOH . E 4 HOH A 41 241 241 HOH HOH . E 4 HOH A 42 242 242 HOH HOH . E 4 HOH A 43 243 243 HOH HOH . E 4 HOH A 44 244 244 HOH HOH . E 4 HOH A 45 245 245 HOH HOH . E 4 HOH A 46 246 246 HOH HOH . E 4 HOH A 47 247 247 HOH HOH . E 4 HOH A 48 248 248 HOH HOH . E 4 HOH A 49 249 249 HOH HOH . E 4 HOH A 50 250 250 HOH HOH . E 4 HOH A 51 251 226 HOH HOH . E 4 HOH A 52 252 227 HOH HOH . E 4 HOH A 53 253 228 HOH HOH . E 4 HOH A 54 254 229 HOH HOH . E 4 HOH A 55 255 230 HOH HOH . E 4 HOH A 56 256 231 HOH HOH . E 4 HOH A 57 257 232 HOH HOH . E 4 HOH A 58 258 233 HOH HOH . E 4 HOH A 59 259 234 HOH HOH . E 4 HOH A 60 260 235 HOH HOH . E 4 HOH A 61 261 236 HOH HOH . E 4 HOH A 62 262 337 HOH HOH . E 4 HOH A 63 263 338 HOH HOH . E 4 HOH A 64 264 339 HOH HOH . E 4 HOH A 65 265 340 HOH HOH . E 4 HOH A 66 266 341 HOH HOH . E 4 HOH A 67 267 342 HOH HOH . E 4 HOH A 68 268 343 HOH HOH . E 4 HOH A 69 269 344 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 C1 8IN . . . D 3 60.228 28.66 48.411 1 19.73 ? C1 8IN 200 A 1 HETATM 2 C C2 8IN . . . D 3 60.172 30.037 48.664 1 17.81 ? C2 8IN 200 A 1 HETATM 3 C C3 8IN . . . D 3 59.607 30.948 47.693 1 17.98 ? C3 8IN 200 A 1 HETATM 4 C C4 8IN . . . D 3 59.123 30.419 46.482 1 17.58 ? C4 8IN 200 A 1 HETATM 5 C C5 8IN . . . D 3 59.216 29.031 46.292 1 17.64 ? C5 8IN 200 A 1 HETATM 6 C C6 8IN . . . D 3 59.753 28.15 47.224 1 18.37 ? C6 8IN 200 A 1 HETATM 7 N N7 8IN . . . D 3 59.414 32.343 47.633 1 17.35 ? N7 8IN 200 A 1 HETATM 8 C C8 8IN . . . D 3 58.793 32.642 46.369 1 18.17 ? C8 8IN 200 A 1 HETATM 9 C C9 8IN . . . D 3 58.601 31.456 45.625 1 16.04 ? C9 8IN 200 A 1 HETATM 10 C C10 8IN . . . D 3 57.965 31.254 44.173 1 17.85 ? C10 8IN 200 A 1 HETATM 11 C C11 8IN . . . D 3 56.961 30.108 44.114 1 19.9 ? C11 8IN 200 A 1 HETATM 12 O O12 8IN . . . D 3 56.073 30.004 44.928 1 21.43 ? O12 8IN 200 A 1 HETATM 13 N N13 8IN . . . D 3 57.133 29.234 43.14 1 17.74 ? N13 8IN 200 A 1 HETATM 14 C C14 8IN . . . D 3 58.356 34.048 45.797 1 14.82 ? C14 8IN 200 A 1 HETATM 15 C C15 8IN . . . D 3 59.83 33.301 48.746 1 19.84 ? C15 8IN 200 A 1 HETATM 16 C C16 8IN . . . D 3 61.374 33.356 48.895 1 23.63 ? C16 8IN 200 A 1 HETATM 17 C C17 8IN . . . D 3 61.926 33.501 50.187 1 26.01 ? C17 8IN 200 A 1 HETATM 18 C C18 8IN . . . D 3 63.319 33.531 50.299 1 26 ? C18 8IN 200 A 1 HETATM 19 C C19 8IN . . . D 3 64.136 33.411 49.118 1 26.3 ? C19 8IN 200 A 1 HETATM 20 C C20 8IN . . . D 3 63.623 33.269 47.84 1 24.35 ? C20 8IN 200 A 1 HETATM 21 C C21 8IN . . . D 3 62.238 33.242 47.733 1 23.91 ? C21 8IN 200 A 1 HETATM 22 O O22 8IN . . . D 3 59.895 26.764 47.115 1 22 ? O22 8IN 200 A 1 HETATM 23 C C23 8IN . . . D 3 59.326 25.849 46.194 1 21.72 ? C23 8IN 200 A 1 HETATM 24 C C24 8IN . . . D 3 57.857 25.494 46.567 1 20.59 ? C24 8IN 200 A 1 HETATM 25 C C25 8IN . . . D 3 57.031 25.129 45.316 1 20.38 ? C25 8IN 200 A 1 HETATM 26 P P26 8IN . . . D 3 55.385 24.741 45.896 1 22.71 ? P26 8IN 200 A 1 HETATM 27 O O27 8IN . . . D 3 55.398 23.923 47.015 1 18.84 ? O27 8IN 200 A 1 HETATM 28 O O28 8IN . . . D 3 54.774 24.125 44.799 1 17.56 ? O28 8IN 200 A 1 HETATM 29 O O29 8IN . . . D 3 54.83 26.12 46.186 1 17.17 ? O29 8IN 200 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #