data_6UML # _model_server_result.job_id vixdRr_2uhrOt1zcTNstHQ _model_server_result.datetime_utc '2024-11-22 05:44:06' _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 6uml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 6UML # _exptl.entry_id 6UML _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 273.244 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-Pomalidomide _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 109.694 _cell.angle_gamma 90 _cell.entry_id 6UML _cell.length_a 77.409 _cell.length_b 127.725 _cell.length_c 110.174 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UML _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 5 _struct_asym.id E _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 18 A CYS 18 1_555 A SG CYS 313 A CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 B SG CYS 287 C CYS 323 1_555 D ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc2 B SG CYS 290 C CYS 326 1_555 D ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc3 B SG CYS 355 C CYS 391 1_555 D ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc4 B SG CYS 358 C CYS 394 1_555 D ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc5 C SG CYS 8 E CYS 412 1_555 F ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc6 C SG CYS 11 E CYS 415 1_555 F ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc7 C NE2 HIS 24 E HIS 428 1_555 F ZN ZN . E ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? # _chem_comp.formula 'C13 H11 N3 O4' _chem_comp.formula_weight 273.244 _chem_comp.id Y70 _chem_comp.mon_nstd_flag . _chem_comp.name S-Pomalidomide _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 Y70 sing 374 n y C1 C6 Y70 doub 375 n y C2 C3 Y70 doub 376 n y C3 C4 Y70 sing 377 n y C4 C5 Y70 doub 378 n y C4 C7 Y70 sing 379 n n C5 C6 Y70 sing 380 n y C5 C9 Y70 sing 381 n n C6 N10 Y70 sing 382 n n C7 N8 Y70 sing 383 n n C7 O13 Y70 doub 384 n n N8 C9 Y70 sing 385 n n N8 C12 Y70 sing 386 n n C9 O11 Y70 doub 387 n n C12 C14 Y70 sing 388 n n C12 C15 Y70 sing 389 n n C14 C18 Y70 sing 390 n n C15 N16 Y70 sing 391 n n C15 O19 Y70 doub 392 n n N16 C17 Y70 sing 393 n n C17 C18 Y70 sing 394 n n C17 O20 Y70 doub 395 n n C1 H1 Y70 sing 396 n n C2 H2 Y70 sing 397 n n C3 H3 Y70 sing 398 n n N10 H101 Y70 sing 399 n n N10 H102 Y70 sing 400 n n C12 H12 Y70 sing 401 n n C14 H141 Y70 sing 402 n n C14 H142 Y70 sing 403 n n C18 H181 Y70 sing 404 n n C18 H182 Y70 sing 405 n n N16 H16 Y70 sing 406 n n # _atom_sites.entry_id 6UML _atom_sites.fract_transf_matrix[1][1] 0.012918 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004624 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007829 _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] 0.00964 _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 D 4 ZN C 1 501 2 ZN ZN . E 5 Y70 C 1 502 501 Y70 MOL . F 4 ZN E 1 501 1 ZN ZN . # 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 Y70 . . . E 5 7.487 32.216 -100.025 1 83.82 ? C1 Y70 502 C 1 HETATM 2 C C2 Y70 . . . E 5 7.846 32.831 -98.827 1 83.01 ? C2 Y70 502 C 1 HETATM 3 C C3 Y70 . . . E 5 7.954 32.086 -97.655 1 85.01 ? C3 Y70 502 C 1 HETATM 4 C C4 Y70 . . . E 5 7.698 30.719 -97.687 1 85.93 ? C4 Y70 502 C 1 HETATM 5 C C5 Y70 . . . E 5 7.338 30.111 -98.886 1 86.3 ? C5 Y70 502 C 1 HETATM 6 C C6 Y70 . . . E 5 7.231 30.85 -100.057 1 84.74 ? C6 Y70 502 C 1 HETATM 7 C C7 Y70 . . . E 5 7.712 29.708 -96.727 1 86.87 ? C7 Y70 502 C 1 HETATM 8 N N8 Y70 . . . E 5 7.377 28.557 -97.31 1 87.5 ? N8 Y70 502 C 1 HETATM 9 C C9 Y70 . . . E 5 7.156 28.766 -98.605 1 89.58 ? C9 Y70 502 C 1 HETATM 10 N N10 Y70 . . . E 5 6.887 30.244 -101.193 1 86.55 ? N10 Y70 502 C 1 HETATM 11 O O11 Y70 . . . E 5 6.825 27.915 -99.433 1 92.85 ? O11 Y70 502 C 1 HETATM 12 C C12 Y70 . . . E 5 7.282 27.242 -96.666 1 78.16 ? C12 Y70 502 C 1 HETATM 13 O O13 Y70 . . . E 5 7.986 29.857 -95.535 1 85.75 ? O13 Y70 502 C 1 HETATM 14 C C14 Y70 . . . E 5 5.81 26.922 -96.403 1 74.26 ? C14 Y70 502 C 1 HETATM 15 C C15 Y70 . . . E 5 7.868 26.166 -97.592 1 70.99 ? C15 Y70 502 C 1 HETATM 16 N N16 Y70 . . . E 5 7.361 24.859 -97.56 1 66.79 ? N16 Y70 502 C 1 HETATM 17 C C17 Y70 . . . E 5 6.318 24.501 -96.688 1 68.65 ? C17 Y70 502 C 1 HETATM 18 C C18 Y70 . . . E 5 5.708 25.551 -95.744 1 70.62 ? C18 Y70 502 C 1 HETATM 19 O O19 Y70 . . . E 5 8.783 26.452 -98.367 1 75.56 ? O19 Y70 502 C 1 HETATM 20 O O20 Y70 . . . E 5 5.897 23.344 -96.695 1 71.64 ? O20 Y70 502 C 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 20 #