data_5YHB # _model_server_result.job_id p94YC0XCNfYQMOfRJm521A _model_server_result.datetime_utc '2025-07-08 02:49:01' _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 5yhb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":308}' # _entry.id 5YHB # _exptl.entry_id 5YHB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.492 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Palladium(II) allyl complex' _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 5YHB _cell.length_a 105.92 _cell.length_b 105.92 _cell.length_c 105.92 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YHB _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id I _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 ND1 HIS 141 A HIS 141 1_555 I PD PLL . A PLL 308 24_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc2 A NE2 HIS 183 A HIS 183 1_555 B PD PD . A PD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc3 A NH2 ARG 206 A ARG 209 1_555 E PD PD . A PD 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc4 A NH1 ARG 206 A ARG 209 1_555 G PD PD . A PD 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc5 A SG CYS 208 A CYS 211 1_555 E PD PD . A PD 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc6 A SG CYS 208 A CYS 211 1_555 F PD PD . A PD 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc7 A SG CYS 208 A CYS 211 1_555 G PD PD . A PD 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc8 A OE1 GLU 216 A GLU 219 1_555 C PD PD . A PD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc9 A NE2 HIS 220 A HIS 223 1_555 C PD PD . A PD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc10 A ND1 HIS 220 A HIS 223 1_555 D PD PD . A PD 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc11 A ND1 HIS 235 A HIS 238 1_555 H PD PD . A PD 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc12 A NE2 HIS 235 A HIS 238 1_555 I PD PLL . A PLL 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc13 B PD PD . A PD 301 1_555 J O HOH . A HOH 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc14 D PD PD . A PD 303 1_555 J O HOH . A HOH 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc15 G PD PD . A PD 306 1_555 J O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? # _chem_comp.formula 'C3 H5 Pd' _chem_comp.formula_weight 147.492 _chem_comp.id PLL _chem_comp.mon_nstd_flag . _chem_comp.name 'Palladium(II) allyl complex' _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 C20 C21 PLL sing 266 n n C21 C19 PLL sing 267 n n PD C19 PLL sing 268 n n PD C20 PLL sing 269 n n PD C21 PLL sing 270 n n C20 H20 PLL sing 271 n n C20 H20A PLL sing 272 n n C21 H21 PLL sing 273 n n C19 H19 PLL sing 274 n n C19 H19A PLL sing 275 n n # _atom_sites.entry_id 5YHB _atom_sites.fract_transf_matrix[1][1] 0.009441 _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] 0.009441 _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] 0.009441 _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 PD A 1 301 1 PD PD . C 2 PD A 1 302 2 PD PD . D 2 PD A 1 303 3 PD PD . E 2 PD A 1 304 4 PD PD . F 2 PD A 1 305 5 PD PD . G 2 PD A 1 306 6 PD PD . H 2 PD A 1 307 7 PD PD . I 3 PLL A 1 308 1 PLL PLL . J 4 HOH A 1 401 387 HOH HOH . J 4 HOH A 2 402 256 HOH HOH . J 4 HOH A 3 403 265 HOH HOH . J 4 HOH A 4 404 385 HOH HOH . J 4 HOH A 5 405 258 HOH HOH . J 4 HOH A 6 406 255 HOH HOH . J 4 HOH A 7 407 333 HOH HOH . J 4 HOH A 8 408 320 HOH HOH . J 4 HOH A 9 409 257 HOH HOH . J 4 HOH A 10 410 274 HOH HOH . J 4 HOH A 11 411 321 HOH HOH . J 4 HOH A 12 412 386 HOH HOH . J 4 HOH A 13 413 374 HOH HOH . J 4 HOH A 14 414 259 HOH HOH . J 4 HOH A 15 415 379 HOH HOH . J 4 HOH A 16 416 315 HOH HOH . J 4 HOH A 17 417 325 HOH HOH . J 4 HOH A 18 418 263 HOH HOH . J 4 HOH A 19 419 388 HOH HOH . J 4 HOH A 20 420 389 HOH HOH . J 4 HOH A 21 421 319 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 C20 PLL . . . I 3 60.926 25.768 13.482 1 42.29 ? C20 PLL 308 A 1 HETATM 2 C C21 PLL . . . I 3 60.672 27.034 14.25 1 38.11 ? C21 PLL 308 A 1 HETATM 3 PD PD PLL . . . I 3 61.092 27.332 12.358 1 35.26 ? PD PLL 308 A 1 HETATM 4 C C19 PLL . . . I 3 61.662 28.117 14.006 1 36.88 ? C19 PLL 308 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 4 #