data_8RQA # _model_server_result.job_id TjZq-XYUr3rXZrSR25mukw _model_server_result.datetime_utc '2024-12-01 21:22:08' _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 8rqa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8RQA # _exptl.entry_id 8RQA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 259.261 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-Lenalidomide _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 8RQA _cell.length_a 51.989 _cell.length_b 95.717 _cell.length_c 148.252 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RQA _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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 metalc ? metalc1 A SG CYS 226 A CYS 323 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc2 A SG CYS 229 A CYS 326 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc3 A SG CYS 294 A CYS 391 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc4 A SG CYS 297 A CYS 394 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? # _chem_comp.formula 'C13 H13 N3 O3' _chem_comp.formula_weight 259.261 _chem_comp.id LVY _chem_comp.mon_nstd_flag . _chem_comp.name S-Lenalidomide _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 LVY sing 194 n n C1 C6 LVY sing 195 n n C1 N10 LVY sing 196 n n C2 C3 LVY sing 197 n n C3 C4 LVY sing 198 n n C4 N5 LVY sing 199 n n C4 O19 LVY doub 200 n n N5 C6 LVY sing 201 n n C6 O18 LVY doub 202 n n C7 C8 LVY sing 203 n y C7 C11 LVY sing 204 n n C7 C15 LVY doub 205 n y C8 C9 LVY sing 206 n n C8 C14 LVY doub 207 n y C9 N10 LVY sing 208 n n N10 C11 LVY sing 209 n n C11 O16 LVY doub 210 n n C12 C13 LVY doub 211 n y C12 C15 LVY sing 212 n y C13 C14 LVY sing 213 n y C14 N17 LVY sing 214 n n C1 H1 LVY sing 215 n n C2 H21C LVY sing 216 n n C2 H22C LVY sing 217 n n C3 H31C LVY sing 218 n n C3 H32C LVY sing 219 n n N5 H5 LVY sing 220 n n C15 H15 LVY sing 221 n n C9 H91 LVY sing 222 n n C9 H92 LVY sing 223 n n C12 H12 LVY sing 224 n n C13 H13 LVY sing 225 n n N17 H171 LVY sing 226 n n N17 H172 LVY sing 227 n n # _atom_sites.entry_id 8RQA _atom_sites.fract_transf_matrix[1][1] 0.019235 _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] 0.010447 _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] 0.006745 _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 LVY A 1 501 501 LVY LVY . C 3 ZN A 1 502 1 ZN ZN . D 4 HOH A 1 601 3 HOH HOH . D 4 HOH A 2 602 1 HOH HOH . D 4 HOH A 3 603 10 HOH HOH . D 4 HOH A 4 604 8 HOH HOH . D 4 HOH A 5 605 7 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 LVY . . . B 2 -3.208 -26.892 29.183 1 51.33 ? C1 LVY 501 A 1 HETATM 2 C C2 LVY . . . B 2 -2.824 -28.098 28.333 1 59.9 ? C2 LVY 501 A 1 HETATM 3 C C3 LVY . . . B 2 -3.737 -28.191 27.115 1 54.16 ? C3 LVY 501 A 1 HETATM 4 C C4 LVY . . . B 2 -5.187 -28.153 27.471 1 53.87 ? C4 LVY 501 A 1 HETATM 5 N N5 LVY . . . B 2 -5.497 -27.662 28.721 1 53.03 ? N5 LVY 501 A 1 HETATM 6 C C6 LVY . . . B 2 -4.699 -26.856 29.497 1 54.18 ? C6 LVY 501 A 1 HETATM 7 C C7 LVY . . . B 2 -0.722 -26.346 31.861 1 67.01 ? C7 LVY 501 A 1 HETATM 8 C C8 LVY . . . B 2 -1.535 -27.267 32.493 1 66.35 ? C8 LVY 501 A 1 HETATM 9 C C9 LVY . . . B 2 -2.682 -27.624 31.599 1 61.59 ? C9 LVY 501 A 1 HETATM 10 N N10 LVY . . . B 2 -2.404 -26.834 30.4 1 60.02 ? N10 LVY 501 A 1 HETATM 11 C C11 LVY . . . B 2 -1.295 -26.053 30.534 1 61.71 ? C11 LVY 501 A 1 HETATM 12 C C12 LVY . . . B 2 0.725 -26.284 33.727 1 69.55 ? C12 LVY 501 A 1 HETATM 13 C C13 LVY . . . B 2 -0.088 -27.215 34.373 1 64.94 ? C13 LVY 501 A 1 HETATM 14 C C14 LVY . . . B 2 -1.237 -27.728 33.775 1 66.17 ? C14 LVY 501 A 1 HETATM 15 C C15 LVY . . . B 2 0.421 -25.833 32.457 1 69.59 ? C15 LVY 501 A 1 HETATM 16 O O16 LVY . . . B 2 -0.879 -25.264 29.69 1 62.83 ? O16 LVY 501 A 1 HETATM 17 N N17 LVY . . . B 2 -2.033 -28.64 34.409 1 69.16 ? N17 LVY 501 A 1 HETATM 18 O O18 LVY . . . B 2 -5.182 -26.147 30.353 1 61.72 ? O18 LVY 501 A 1 HETATM 19 O O19 LVY . . . B 2 -6.064 -28.532 26.718 1 51.88 ? O19 LVY 501 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #