data_3UDK # _model_server_result.job_id MQozIa5OHKPTK5inxmSS-g _model_server_result.datetime_utc '2024-10-19 22:30:29' _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 3udk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3UDK # _exptl.entry_id 3UDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 316.352 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "tetrahydro-2H-pyran-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate" _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 3UDK _cell.length_a 74.797 _cell.length_b 104.425 _cell.length_c 101.333 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G,H _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 159 A CYS 155 1_555 A SG CYS 363 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 221 A CYS 217 1_555 A SG CYS 386 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 273 A CYS 269 1_555 A SG CYS 323 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc1 A OD2 ASP 135 A ASP 131 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.778 ? metalc ? metalc2 A OD1 ASP 135 A ASP 131 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc3 A ND1 HIS 400 A HIS 396 1_555 G ZN ZN . A ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc4 A ND1 HIS 401 A HIS 397 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc5 A NE2 HIS 402 A HIS 398 1_555 G ZN ZN . A ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? # _chem_comp.formula 'C17 H20 N2 O4' _chem_comp.formula_weight 316.352 _chem_comp.id 095 _chem_comp.mon_nstd_flag . _chem_comp.name "tetrahydro-2H-pyran-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate" _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 N10 C7 095 sing 1 n n N10 C13 095 sing 2 n n C3 C5 095 doub 3 n y C3 C1 095 sing 4 n y C5 C8 095 sing 5 n y C7 C4 095 sing 6 n n C7 C9 095 sing 7 n n C13 C2 095 sing 8 n n C4 C2 095 sing 9 n n C1 C2 095 sing 10 n n C1 C17 095 doub 11 n y C2 C14 095 sing 12 n n C8 C6 095 doub 13 n y C9 O11 095 sing 14 n n C9 O12 095 doub 15 n n O11 C18 095 sing 16 n n C17 C6 095 sing 17 n y C17 N16 095 sing 18 n n C23 C18 095 sing 19 n n C23 C22 095 sing 20 n n C14 N16 095 sing 21 n n C14 O15 095 doub 22 n n C18 C19 095 sing 23 n n O21 C22 095 sing 24 n n O21 C20 095 sing 25 n n C19 C20 095 sing 26 n n C5 H1 095 sing 27 n n C8 H2 095 sing 28 n n C3 H3 095 sing 29 n n C6 H4 095 sing 30 n n C19 H5 095 sing 31 n n C19 H6 095 sing 32 n n C23 H7 095 sing 33 n n C23 H8 095 sing 34 n n C4 H9 095 sing 35 n n C4 H10 095 sing 36 n n C13 H11 095 sing 37 n n C13 H12 095 sing 38 n n C20 H13 095 sing 39 n n C20 H14 095 sing 40 n n C22 H15 095 sing 41 n n C22 H16 095 sing 42 n n C7 H17 095 sing 43 n n C18 H18 095 sing 44 n n N16 H19 095 sing 45 n n N10 H20 095 sing 46 n n # _atom_sites.entry_id 3UDK _atom_sites.fract_transf_matrix[1][1] 0.01337 _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] 0.009576 _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] 0.009868 _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 2 095 A 1 501 399 095 095 . C 3 EDO A 1 502 401 EDO EDO . D 3 EDO A 1 503 403 EDO EDO . E 4 PEG A 1 504 409 PEG PEG . F 5 ZN A 1 505 1 ZN ZN . G 5 ZN A 1 506 2 ZN ZN . H 6 HOH A 1 601 1 HOH HOH . H 6 HOH A 2 602 3 HOH HOH . H 6 HOH A 3 603 4 HOH HOH . H 6 HOH A 4 604 5 HOH HOH . H 6 HOH A 5 605 6 HOH HOH . H 6 HOH A 6 606 7 HOH HOH . H 6 HOH A 7 607 12 HOH HOH . H 6 HOH A 8 608 13 HOH HOH . H 6 HOH A 9 609 16 HOH HOH . H 6 HOH A 10 610 18 HOH HOH . H 6 HOH A 11 611 19 HOH HOH . H 6 HOH A 12 612 21 HOH HOH . H 6 HOH A 13 613 23 HOH HOH . H 6 HOH A 14 614 24 HOH HOH . H 6 HOH A 15 615 26 HOH HOH . H 6 HOH A 16 616 28 HOH HOH . H 6 HOH A 17 617 29 HOH HOH . H 6 HOH A 18 618 30 HOH HOH . H 6 HOH A 19 619 32 HOH HOH . H 6 HOH A 20 620 35 HOH HOH . H 6 HOH A 21 621 1 HOH HOH . H 6 HOH A 22 622 12 HOH HOH . H 6 HOH A 23 623 14 HOH HOH . H 6 HOH A 24 624 15 HOH HOH . H 6 HOH A 25 625 20 HOH HOH . H 6 HOH A 26 626 21 HOH HOH . H 6 HOH A 27 627 1 HOH HOH . H 6 HOH A 28 628 11 HOH HOH . H 6 HOH A 29 629 12 HOH HOH . H 6 HOH A 30 630 22 HOH HOH . H 6 HOH A 31 631 4 HOH HOH . H 6 HOH A 32 632 16 HOH HOH . H 6 HOH A 33 633 18 HOH HOH . H 6 HOH A 34 634 6 HOH HOH . H 6 HOH A 35 635 9 HOH HOH . H 6 HOH A 36 636 18 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 C5 095 . . . B 2 26.876 37.995 40.965 1 22.89 ? C5 095 501 A 1 HETATM 2 C C8 095 . . . B 2 27.478 38.051 42.209 1 21.42 ? C8 095 501 A 1 HETATM 3 C C3 095 . . . B 2 25.536 37.695 40.837 1 22.75 ? C3 095 501 A 1 HETATM 4 C C6 095 . . . B 2 26.763 37.78 43.356 1 19.94 ? C6 095 501 A 1 HETATM 5 C C1 095 . . . B 2 24.825 37.452 41.986 1 21.95 ? C1 095 501 A 1 HETATM 6 C C17 095 . . . B 2 25.434 37.477 43.207 1 23.5 ? C17 095 501 A 1 HETATM 7 C C14 095 . . . B 2 23.286 36.937 43.635 1 22.73 ? C14 095 501 A 1 HETATM 8 C C9 095 . . . B 2 20.322 37.055 42.33 1 27.25 ? C9 095 501 A 1 HETATM 9 C C19 095 . . . B 2 19.872 34.033 44.16 1 38.14 ? C19 095 501 A 1 HETATM 10 C C23 095 . . . B 2 17.989 35.576 43.372 1 36.93 ? C23 095 501 A 1 HETATM 11 C C4 095 . . . B 2 22.43 38.1 41.645 1 21.87 ? C4 095 501 A 1 HETATM 12 C C13 095 . . . B 2 23.097 35.766 41.443 1 20.93 ? C13 095 501 A 1 HETATM 13 C C20 095 . . . B 2 18.755 33.165 44.701 1 39.35 ? C20 095 501 A 1 HETATM 14 C C22 095 . . . B 2 17.113 34.619 44.146 1 37.44 ? C22 095 501 A 1 HETATM 15 C C7 095 . . . B 2 21.249 37.3 41.169 1 22.36 ? C7 095 501 A 1 HETATM 16 C C18 095 . . . B 2 19.45 35.44 43.757 1 36.2 ? C18 095 501 A 1 HETATM 17 C C2 095 . . . B 2 23.408 37.072 42.139 1 21.19 ? C2 095 501 A 1 HETATM 18 N N16 095 . . . B 2 24.516 37.188 44.213 1 22.77 ? N16 095 501 A 1 HETATM 19 N N10 095 . . . B 2 21.842 36.022 40.696 1 21.32 ? N10 095 501 A 1 HETATM 20 O O15 095 . . . B 2 22.245 36.67 44.216 1 24.02 ? O15 095 501 A 1 HETATM 21 O O12 095 . . . B 2 19.765 37.934 42.968 1 26.85 ? O12 095 501 A 1 HETATM 22 O O21 095 . . . B 2 17.591 33.306 43.905 1 39.24 ? O21 095 501 A 1 HETATM 23 O O11 095 . . . B 2 20.214 35.722 42.589 1 32.07 ? O11 095 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 23 #