data_3ESD # _model_server_result.job_id hi8dpWmrxq4I6RovHZGhqA _model_server_result.datetime_utc '2025-08-30 23:50:56' _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 3esd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":215}' # _entry.id 3ESD # _exptl.entry_id 3ESD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 654.871 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description bromo(4-{3-[(R)-ethoxy(4-nitrophenoxy)phosphoryl]propyl}-2,6-bis[(methylsulfanyl-kappaS)methyl]phenyl-kappaC~1~)palladium(2+) _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 3ESD _cell.length_a 72.36 _cell.length_b 72.36 _cell.length_c 110.77 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ESD _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 _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 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 disulf ? disulf1 A SG CYS 31 A CYS 31 1_555 A SG CYS 109 A CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 171 A CYS 171 1_555 A SG CYS 178 A CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? covale ? covale1 A OG SER 120 A SER 120 1_555 B P1 SXC . A SXC 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.572 ? # _chem_comp.formula 'C21 H27 Br N O5 P Pd S2 2' _chem_comp.formula_weight 654.871 _chem_comp.id SXC _chem_comp.mon_nstd_flag . _chem_comp.name bromo(4-{3-[(R)-ethoxy(4-nitrophenoxy)phosphoryl]propyl}-2,6-bis[(methylsulfanyl-kappaS)methyl]phenyl-kappaC~1~)palladium(2+) _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ethyl 4-nitrophenyl P-[3-(4-(bromopallado)-1,3-bis[(methylthio)methyl]-phenyl)propyl]phosphonate' # 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 BR1 PD1 SXC sing 290 n n PD1 C1 SXC sing 291 n n PD1 S2 SXC sing 292 n n S1 C7 SXC sing 293 n n S1 PD1 SXC sing 294 n n S2 C12 SXC sing 295 n n S2 C10 SXC sing 296 n n O3 P1 SXC sing 297 n n P1 O1 SXC sing 298 n n O1 C16 SXC sing 299 n n O2 P1 SXC doub 300 n n C1 C6 SXC doub 301 n y C2 C1 SXC sing 302 n y C2 C3 SXC doub 303 n y C3 C4 SXC sing 304 n y C3 H3 SXC sing 305 n n C4 C5 SXC doub 306 n y C4 C13 SXC sing 307 n n C5 H5 SXC sing 308 n n C6 C10 SXC sing 309 n n C6 C5 SXC sing 310 n y C7 C2 SXC sing 311 n n C7 H17 SXC sing 312 n n C7 H27 SXC sing 313 n n C9 S1 SXC sing 314 n n C9 H19 SXC sing 315 n n C9 H29 SXC sing 316 n n C9 H39 SXC sing 317 n n C10 H110 SXC sing 318 n n C10 H210 SXC sing 319 n n C12 H112 SXC sing 320 n n C12 H212 SXC sing 321 n n C12 H312 SXC sing 322 n n C13 C14 SXC sing 323 n n C13 H113 SXC sing 324 n n C13 H213 SXC sing 325 n n C14 C15 SXC sing 326 n n C14 H114 SXC sing 327 n n C14 H214 SXC sing 328 n n C15 P1 SXC sing 329 n n C15 H115 SXC sing 330 n n C15 H215 SXC sing 331 n n C16 C17 SXC sing 332 n n C16 H116 SXC sing 333 n n C16 H216 SXC sing 334 n n C17 H117 SXC sing 335 n n C17 H217 SXC sing 336 n n C17 H317 SXC sing 337 n n O3 C161 SXC sing 338 n n C19 C161 SXC doub 339 n y C161 C20 SXC sing 340 n y C171 C18 SXC doub 341 n y C18 C19 SXC sing 342 n y C20 C21 SXC doub 343 n y C171 C21 SXC sing 344 n y C171 N1 SXC sing 345 n n N1 O4 SXC sing 346 n n N1 O5 SXC doub 347 n n C18 H24 SXC sing 348 n n C19 H25 SXC sing 349 n n C20 H26 SXC sing 350 n n C21 H271 SXC sing 351 n n # _atom_sites.entry_id 3ESD _atom_sites.fract_transf_matrix[1][1] 0.01382 _atom_sites.fract_transf_matrix[1][2] 0.007979 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015958 _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] 0.009028 _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 SXC A 1 215 1 SXC SXC . C 3 HOH A 1 216 1 HOH HOH . C 3 HOH A 2 217 2 HOH HOH . C 3 HOH A 3 218 3 HOH HOH . C 3 HOH A 4 219 4 HOH HOH . C 3 HOH A 5 220 5 HOH HOH . C 3 HOH A 6 221 6 HOH HOH . C 3 HOH A 7 222 7 HOH HOH . C 3 HOH A 8 223 8 HOH HOH . C 3 HOH A 9 224 9 HOH HOH . C 3 HOH A 10 225 10 HOH HOH . C 3 HOH A 11 226 11 HOH HOH . C 3 HOH A 12 227 12 HOH HOH . C 3 HOH A 13 228 13 HOH HOH . C 3 HOH A 14 229 14 HOH HOH . C 3 HOH A 15 230 15 HOH HOH . C 3 HOH A 16 231 16 HOH HOH . C 3 HOH A 17 232 17 HOH HOH . C 3 HOH A 18 233 18 HOH HOH . C 3 HOH A 19 234 19 HOH HOH . C 3 HOH A 20 235 20 HOH HOH . C 3 HOH A 21 236 21 HOH HOH . C 3 HOH A 22 237 22 HOH HOH . C 3 HOH A 23 238 23 HOH HOH . C 3 HOH A 24 239 24 HOH HOH . C 3 HOH A 25 240 25 HOH HOH . C 3 HOH A 26 241 26 HOH HOH . C 3 HOH A 27 242 27 HOH HOH . C 3 HOH A 28 243 28 HOH HOH . C 3 HOH A 29 244 29 HOH HOH . C 3 HOH A 30 245 30 HOH HOH . C 3 HOH A 31 246 31 HOH HOH . C 3 HOH A 32 247 32 HOH HOH . C 3 HOH A 33 248 33 HOH HOH . C 3 HOH A 34 249 34 HOH HOH . C 3 HOH A 35 250 35 HOH HOH . C 3 HOH A 36 251 36 HOH HOH . C 3 HOH A 37 252 37 HOH HOH . C 3 HOH A 38 253 38 HOH HOH . C 3 HOH A 39 254 39 HOH HOH . C 3 HOH A 40 255 40 HOH HOH . C 3 HOH A 41 256 41 HOH HOH . C 3 HOH A 42 257 42 HOH HOH . C 3 HOH A 43 258 43 HOH HOH . C 3 HOH A 44 259 44 HOH HOH . C 3 HOH A 45 260 45 HOH HOH . C 3 HOH A 46 261 46 HOH HOH . C 3 HOH A 47 262 47 HOH HOH . C 3 HOH A 48 263 48 HOH HOH . C 3 HOH A 49 264 49 HOH HOH . C 3 HOH A 50 265 50 HOH HOH . C 3 HOH A 51 266 51 HOH HOH . C 3 HOH A 52 267 52 HOH HOH . C 3 HOH A 53 268 53 HOH HOH . C 3 HOH A 54 269 54 HOH HOH . C 3 HOH A 55 270 55 HOH HOH . C 3 HOH A 56 271 56 HOH HOH . C 3 HOH A 57 272 57 HOH HOH . C 3 HOH A 58 273 58 HOH HOH . C 3 HOH A 59 274 59 HOH HOH . C 3 HOH A 60 275 60 HOH HOH . C 3 HOH A 61 276 61 HOH HOH . C 3 HOH A 62 277 62 HOH HOH . C 3 HOH A 63 278 63 HOH HOH . C 3 HOH A 64 279 64 HOH HOH . C 3 HOH A 65 280 65 HOH HOH . C 3 HOH A 66 281 66 HOH HOH . C 3 HOH A 67 282 67 HOH HOH . C 3 HOH A 68 283 68 HOH HOH . C 3 HOH A 69 284 69 HOH HOH . C 3 HOH A 70 285 70 HOH HOH . C 3 HOH A 71 286 71 HOH HOH . C 3 HOH A 72 287 72 HOH HOH . C 3 HOH A 73 288 73 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 BR BR1 SXC . . . B 2 39.226 21.496 4.847 1 62.65 ? BR1 SXC 215 A 1 HETATM 2 PD PD1 SXC . . . B 2 38.921 19.486 6.236 1 21.18 ? PD1 SXC 215 A 1 HETATM 3 S S1 SXC . . . B 2 39.356 17.998 4.514 1 22.99 ? S1 SXC 215 A 1 HETATM 4 S S2 SXC . . . B 2 38.478 20.578 8.176 1 21.9 ? S2 SXC 215 A 1 HETATM 5 P P1 SXC . . . B 2 41.386 11.959 11.705 1 12.87 ? P1 SXC 215 A 1 HETATM 6 O O1 SXC . . . B 2 41.677 12.854 12.829 1 15.87 ? O1 SXC 215 A 1 HETATM 7 O O2 SXC . . . B 2 42.218 11.743 10.531 1 16.57 ? O2 SXC 215 A 1 HETATM 8 C C1 SXC . . . B 2 38.716 17.77 7.336 1 8.75 ? C1 SXC 215 A 1 HETATM 9 C C2 SXC . . . B 2 38.566 16.564 6.669 1 15.22 ? C2 SXC 215 A 1 HETATM 10 C C3 SXC . . . B 2 38.439 15.431 7.486 1 12.36 ? C3 SXC 215 A 1 HETATM 11 C C4 SXC . . . B 2 38.556 15.509 8.839 1 10.67 ? C4 SXC 215 A 1 HETATM 12 C C5 SXC . . . B 2 38.677 16.717 9.536 1 13.75 ? C5 SXC 215 A 1 HETATM 13 C C6 SXC . . . B 2 38.669 17.871 8.689 1 13.32 ? C6 SXC 215 A 1 HETATM 14 C C7 SXC . . . B 2 38.579 16.482 5.175 1 16.41 ? C7 SXC 215 A 1 HETATM 15 C C9 SXC . . . B 2 38.155 18.447 3.23 1 42.62 ? C9 SXC 215 A 1 HETATM 16 C C10 SXC . . . B 2 38.788 19.213 9.381 1 14.7 ? C10 SXC 215 A 1 HETATM 17 C C12 SXC . . . B 2 39.939 21.622 8.457 1 20.18 ? C12 SXC 215 A 1 HETATM 18 C C13 SXC . . . B 2 38.487 14.234 9.665 1 11.75 ? C13 SXC 215 A 1 HETATM 19 C C14 SXC . . . B 2 39.919 13.703 10.039 1 15.65 ? C14 SXC 215 A 1 HETATM 20 C C15 SXC . . . B 2 39.748 12.604 11.099 1 10.51 ? C15 SXC 215 A 1 HETATM 21 C C16 SXC . . . B 2 42.55 12.918 13.93 1 18.77 ? C16 SXC 215 A 1 HETATM 22 C C17 SXC . . . B 2 43.069 14.354 14.308 1 14.57 ? C17 SXC 215 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 22 #