data_5DEX # _model_server_result.job_id i_YlTS6YF6edL2mX55gSzg _model_server_result.datetime_utc '2025-07-12 21:23:06' _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 5dex # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 5DEX # _exptl.entry_id 5DEX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 275.26 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-[(2R)-2-amino-2-carboxyethyl]-1-phenyl-1H-pyrazole-3-carboxylic 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 5DEX _cell.length_a 54.629 _cell.length_b 87.302 _cell.length_c 122.572 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DEX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 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,F _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 disulf ? disulf1 A SG CYS 28 A CYS 28 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 44 A CYS 44 1_555 A SG CYS 63 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 B SG CYS 29 B CYS 32 1_555 B SG CYS 55 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf4 B SG CYS 36 B CYS 39 1_555 B SG CYS 56 B CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 B SG CYS 226 B CYS 229 1_555 B SG CYS 281 B CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? # _chem_comp.formula 'C13 H13 N3 O4' _chem_comp.formula_weight 275.26 _chem_comp.id 5E0 _chem_comp.mon_nstd_flag . _chem_comp.name '5-[(2R)-2-amino-2-carboxyethyl]-1-phenyl-1H-pyrazole-3-carboxylic 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 C13 C12 5E0 doub 1 n y C13 C14 5E0 sing 2 n y C12 C11 5E0 sing 3 n y C14 C09 5E0 doub 4 n y C11 C10 5E0 doub 5 n y C09 C10 5E0 sing 6 n y C09 N08 5E0 sing 7 n n C03 C04 5E0 sing 8 n n C03 C02 5E0 sing 9 n n N01 C02 5E0 sing 10 n n N08 C04 5E0 sing 11 n y N08 N07 5E0 sing 12 n y C04 C05 5E0 doub 13 n y C02 C18 5E0 sing 14 n n O19 C18 5E0 doub 15 n n N07 C06 5E0 doub 16 n y C18 O20 5E0 sing 17 n n C05 C06 5E0 sing 18 n y C06 C15 5E0 sing 19 n n C15 O16 5E0 doub 20 n n C15 O17 5E0 sing 21 n n C10 H1 5E0 sing 22 n n C13 H2 5E0 sing 23 n n C14 H3 5E0 sing 24 n n N01 H4 5E0 sing 25 n n N01 H5 5E0 sing 26 n n C02 H7 5E0 sing 27 n n C03 H8 5E0 sing 28 n n C03 H9 5E0 sing 29 n n C05 H10 5E0 sing 30 n n C11 H11 5E0 sing 31 n n C12 H12 5E0 sing 32 n n O17 H13 5E0 sing 33 n n O20 H14 5E0 sing 34 n n # _atom_sites.entry_id 5DEX _atom_sites.fract_transf_matrix[1][1] 0.018305 _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] 0.011454 _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] 0.008158 _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 C 3 GLY A 1 1001 1001 GLY GLY . D 4 5E0 B 1 301 286 5E0 FR1 . E 5 HOH A 1 1101 1033 HOH HOH . E 5 HOH A 2 1102 1044 HOH HOH . E 5 HOH A 3 1103 1021 HOH HOH . E 5 HOH A 4 1104 1030 HOH HOH . E 5 HOH A 5 1105 1048 HOH HOH . E 5 HOH A 6 1106 1005 HOH HOH . E 5 HOH A 7 1107 1077 HOH HOH . E 5 HOH A 8 1108 1019 HOH HOH . E 5 HOH A 9 1109 1058 HOH HOH . E 5 HOH A 10 1110 1009 HOH HOH . E 5 HOH A 11 1111 1014 HOH HOH . E 5 HOH A 12 1112 1059 HOH HOH . E 5 HOH A 13 1113 1051 HOH HOH . E 5 HOH A 14 1114 1022 HOH HOH . E 5 HOH A 15 1115 1070 HOH HOH . E 5 HOH A 16 1116 1026 HOH HOH . E 5 HOH A 17 1117 1069 HOH HOH . E 5 HOH A 18 1118 1066 HOH HOH . E 5 HOH A 19 1119 1041 HOH HOH . E 5 HOH A 20 1120 1008 HOH HOH . E 5 HOH A 21 1121 1052 HOH HOH . E 5 HOH A 22 1122 1007 HOH HOH . E 5 HOH A 23 1123 1025 HOH HOH . E 5 HOH A 24 1124 1062 HOH HOH . E 5 HOH A 25 1125 1013 HOH HOH . E 5 HOH A 26 1126 1078 HOH HOH . E 5 HOH A 27 1127 1031 HOH HOH . E 5 HOH A 28 1128 1045 HOH HOH . E 5 HOH A 29 1129 1064 HOH HOH . E 5 HOH A 30 1130 1065 HOH HOH . E 5 HOH A 31 1131 1040 HOH HOH . E 5 HOH A 32 1132 1003 HOH HOH . E 5 HOH A 33 1133 1063 HOH HOH . E 5 HOH A 34 1134 1015 HOH HOH . E 5 HOH A 35 1135 1037 HOH HOH . E 5 HOH A 36 1136 1024 HOH HOH . E 5 HOH A 37 1137 1043 HOH HOH . E 5 HOH A 38 1138 1028 HOH HOH . E 5 HOH A 39 1139 1057 HOH HOH . E 5 HOH A 40 1140 1054 HOH HOH . E 5 HOH A 41 1141 1035 HOH HOH . E 5 HOH A 42 1142 1067 HOH HOH . E 5 HOH A 43 1143 1016 HOH HOH . E 5 HOH A 44 1144 1036 HOH HOH . E 5 HOH A 45 1145 1049 HOH HOH . E 5 HOH A 46 1146 1020 HOH HOH . E 5 HOH A 47 1147 1012 HOH HOH . E 5 HOH A 48 1148 1068 HOH HOH . E 5 HOH A 49 1149 1010 HOH HOH . E 5 HOH A 50 1150 1038 HOH HOH . E 5 HOH A 51 1151 1053 HOH HOH . E 5 HOH A 52 1152 1017 HOH HOH . E 5 HOH A 53 1153 1074 HOH HOH . E 5 HOH A 54 1154 1004 HOH HOH . E 5 HOH A 55 1155 1046 HOH HOH . E 5 HOH A 56 1156 1027 HOH HOH . E 5 HOH A 57 1157 1042 HOH HOH . E 5 HOH A 58 1158 1071 HOH HOH . E 5 HOH A 59 1159 1023 HOH HOH . E 5 HOH A 60 1160 1029 HOH HOH . E 5 HOH A 61 1161 1055 HOH HOH . E 5 HOH A 62 1162 1061 HOH HOH . E 5 HOH A 63 1163 1018 HOH HOH . E 5 HOH A 64 1164 1047 HOH HOH . E 5 HOH A 65 1165 1056 HOH HOH . E 5 HOH A 66 1166 1075 HOH HOH . E 5 HOH A 67 1167 1079 HOH HOH . E 5 HOH A 68 1168 1050 HOH HOH . E 5 HOH A 69 1169 1039 HOH HOH . E 5 HOH A 70 1170 1060 HOH HOH . E 5 HOH A 71 1171 1073 HOH HOH . E 5 HOH A 72 1172 1032 HOH HOH . E 5 HOH A 73 1173 1076 HOH HOH . E 5 HOH A 74 1174 1080 HOH HOH . E 5 HOH A 75 1175 1011 HOH HOH . E 5 HOH A 76 1176 1072 HOH HOH . E 5 HOH A 77 1177 1034 HOH HOH . F 5 HOH B 1 401 328 HOH HOH . F 5 HOH B 2 402 351 HOH HOH . F 5 HOH B 3 403 341 HOH HOH . F 5 HOH B 4 404 342 HOH HOH . F 5 HOH B 5 405 309 HOH HOH . F 5 HOH B 6 406 354 HOH HOH . F 5 HOH B 7 407 324 HOH HOH . F 5 HOH B 8 408 303 HOH HOH . F 5 HOH B 9 409 315 HOH HOH . F 5 HOH B 10 410 291 HOH HOH . F 5 HOH B 11 411 329 HOH HOH . F 5 HOH B 12 412 304 HOH HOH . F 5 HOH B 13 413 311 HOH HOH . F 5 HOH B 14 414 322 HOH HOH . F 5 HOH B 15 415 298 HOH HOH . F 5 HOH B 16 416 332 HOH HOH . F 5 HOH B 17 417 335 HOH HOH . F 5 HOH B 18 418 350 HOH HOH . F 5 HOH B 19 419 313 HOH HOH . F 5 HOH B 20 420 299 HOH HOH . F 5 HOH B 21 421 302 HOH HOH . F 5 HOH B 22 422 326 HOH HOH . F 5 HOH B 23 423 346 HOH HOH . F 5 HOH B 24 424 297 HOH HOH . F 5 HOH B 25 425 314 HOH HOH . F 5 HOH B 26 426 292 HOH HOH . F 5 HOH B 27 427 288 HOH HOH . F 5 HOH B 28 428 349 HOH HOH . F 5 HOH B 29 429 290 HOH HOH . F 5 HOH B 30 430 343 HOH HOH . F 5 HOH B 31 431 308 HOH HOH . F 5 HOH B 32 432 295 HOH HOH . F 5 HOH B 33 433 340 HOH HOH . F 5 HOH B 34 434 301 HOH HOH . F 5 HOH B 35 435 330 HOH HOH . F 5 HOH B 36 436 333 HOH HOH . F 5 HOH B 37 437 310 HOH HOH . F 5 HOH B 38 438 336 HOH HOH . F 5 HOH B 39 439 318 HOH HOH . F 5 HOH B 40 440 334 HOH HOH . F 5 HOH B 41 441 331 HOH HOH . F 5 HOH B 42 442 344 HOH HOH . F 5 HOH B 43 443 307 HOH HOH . F 5 HOH B 44 444 319 HOH HOH . F 5 HOH B 45 445 289 HOH HOH . F 5 HOH B 46 446 305 HOH HOH . F 5 HOH B 47 447 293 HOH HOH . F 5 HOH B 48 448 355 HOH HOH . F 5 HOH B 49 449 348 HOH HOH . F 5 HOH B 50 450 287 HOH HOH . F 5 HOH B 51 451 347 HOH HOH . F 5 HOH B 52 452 320 HOH HOH . F 5 HOH B 53 453 312 HOH HOH . F 5 HOH B 54 454 321 HOH HOH . F 5 HOH B 55 455 353 HOH HOH . F 5 HOH B 56 456 325 HOH HOH . F 5 HOH B 57 457 1006 HOH HOH . F 5 HOH B 58 458 316 HOH HOH . F 5 HOH B 59 459 339 HOH HOH . F 5 HOH B 60 460 300 HOH HOH . F 5 HOH B 61 461 338 HOH HOH . F 5 HOH B 62 462 345 HOH HOH . F 5 HOH B 63 463 352 HOH HOH . F 5 HOH B 64 464 327 HOH HOH . F 5 HOH B 65 465 337 HOH HOH . F 5 HOH B 66 466 296 HOH HOH . F 5 HOH B 67 467 317 HOH HOH . F 5 HOH B 68 468 294 HOH HOH . F 5 HOH B 69 469 306 HOH HOH . F 5 HOH B 70 470 356 HOH HOH . F 5 HOH B 71 471 1002 HOH HOH . F 5 HOH B 72 472 323 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 C10 5E0 . . . D 4 -17.366 20.734 -13.023 1 15.09 ? C10 5E0 301 B 1 HETATM 2 C C13 5E0 . . . D 4 -18.048 19.172 -15.51 1 15.19 ? C13 5E0 301 B 1 HETATM 3 C C14 5E0 . . . D 4 -19.05 19.294 -14.428 1 13.94 ? C14 5E0 301 B 1 HETATM 4 C C15 5E0 . . . D 4 -20.526 21.692 -8.932 1 17.74 ? C15 5E0 301 B 1 HETATM 5 N N01 5E0 . . . D 4 -20.968 15.953 -12.11 1 19.39 ? N01 5E0 301 B 1 HETATM 6 C C02 5E0 . . . D 4 -20.569 16.722 -10.99 1 17.02 ? C02 5E0 301 B 1 HETATM 7 C C03 5E0 . . . D 4 -19.759 17.91 -11.429 1 15.76 ? C03 5E0 301 B 1 HETATM 8 C C04 5E0 . . . D 4 -20.59 19.062 -11.625 1 15.74 ? C04 5E0 301 B 1 HETATM 9 C C05 5E0 . . . D 4 -21.126 19.642 -10.287 1 15.01 ? C05 5E0 301 B 1 HETATM 10 C C06 5E0 . . . D 4 -20.266 20.669 -10.047 1 14.82 ? C06 5E0 301 B 1 HETATM 11 N N07 5E0 . . . D 4 -19.873 21.205 -11.33 1 16.82 ? N07 5E0 301 B 1 HETATM 12 N N08 5E0 . . . D 4 -19.671 20.172 -12.111 1 17.17 ? N08 5E0 301 B 1 HETATM 13 C C09 5E0 . . . D 4 -18.697 20.07 -13.192 1 14.97 ? C09 5E0 301 B 1 HETATM 14 C C11 5E0 . . . D 4 -16.357 20.603 -14.126 1 13.92 ? C11 5E0 301 B 1 HETATM 15 C C12 5E0 . . . D 4 -16.68 19.802 -15.343 1 14.05 ? C12 5E0 301 B 1 HETATM 16 O O16 5E0 . . . D 4 -19.801 22.722 -8.847 1 19.47 -1 O16 5E0 301 B 1 HETATM 17 O O17 5E0 . . . D 4 -21.475 21.507 -8.117 1 24.55 ? O17 5E0 301 B 1 HETATM 18 C C18 5E0 . . . D 4 -19.541 15.947 -10.17 1 20.18 ? C18 5E0 301 B 1 HETATM 19 O O19 5E0 . . . D 4 -19.238 14.749 -10.424 1 23.14 ? O19 5E0 301 B 1 HETATM 20 O O20 5E0 . . . D 4 -18.985 16.574 -9.24 1 21.07 -1 O20 5E0 301 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 20 #