data_5C3H # _model_server_result.job_id vWPf_HPO_sfsDzeYPD2IUQ _model_server_result.datetime_utc '2024-12-21 13:02:17' _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 5c3h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5C3H # _exptl.entry_id 5C3H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 212.312 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[2-oxo-2-(piperidin-1-yl)ethyl]piperazin-1-ium _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 5C3H _cell.length_a 71.562 _cell.length_b 71.562 _cell.length_c 105.726 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C3H _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 3 _struct_asym.id C _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 56 A CYS 300 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc2 A SG CYS 59 A CYS 303 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc3 A NE2 HIS 76 A HIS 320 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc4 A SG CYS 83 A CYS 327 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? # _chem_comp.formula 'C11 H22 N3 O 1' _chem_comp.formula_weight 212.312 _chem_comp.id 4XE _chem_comp.mon_nstd_flag . _chem_comp.name 4-[2-oxo-2-(piperidin-1-yl)ethyl]piperazin-1-ium _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 C13 C12 4XE sing 1 n n C13 C14 4XE sing 2 n n C12 C11 4XE sing 3 n n C14 C15 4XE sing 4 n n C11 N10 4XE sing 5 n n C15 N10 4XE sing 6 n n N10 C2 4XE sing 7 n n C2 O1 4XE doub 8 n n C2 C3 4XE sing 9 n n C3 N4 4XE sing 10 n n N4 C9 4XE sing 11 n n N4 C5 4XE sing 12 n n C9 C8 4XE sing 13 n n C5 C6 4XE sing 14 n n C8 N7 4XE sing 15 n n C6 N7 4XE sing 16 n n C3 H16 4XE sing 17 n n C3 H17 4XE sing 18 n n C5 H19 4XE sing 19 n n C5 H18 4XE sing 20 n n C6 H20 4XE sing 21 n n C6 H21 4XE sing 22 n n C8 H25 4XE sing 23 n n C8 H24 4XE sing 24 n n C11 H29 4XE sing 25 n n C11 H28 4XE sing 26 n n C12 H31 4XE sing 27 n n C12 H30 4XE sing 28 n n C13 H32 4XE sing 29 n n C13 H33 4XE sing 30 n n C14 H35 4XE sing 31 n n C14 H34 4XE sing 32 n n C15 H37 4XE sing 33 n n C15 H36 4XE sing 34 n n N7 H23 4XE sing 35 n n N7 H22 4XE sing 36 n n C9 H26 4XE sing 37 n n C9 H27 4XE sing 38 n n # _atom_sites.entry_id 5C3H _atom_sites.fract_transf_matrix[1][1] 0.013974 _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] 0.013974 _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] 0.009458 _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 ZN A 1 401 1 ZN ZN . C 3 4XE A 1 402 1 4XE L01 . D 4 HOH A 1 501 27 HOH HOH . D 4 HOH A 2 502 17 HOH HOH . D 4 HOH A 3 503 26 HOH HOH . D 4 HOH A 4 504 30 HOH HOH . D 4 HOH A 5 505 2 HOH HOH . D 4 HOH A 6 506 13 HOH HOH . D 4 HOH A 7 507 23 HOH HOH . D 4 HOH A 8 508 28 HOH HOH . D 4 HOH A 9 509 21 HOH HOH . D 4 HOH A 10 510 16 HOH HOH . D 4 HOH A 11 511 58 HOH HOH . D 4 HOH A 12 512 51 HOH HOH . D 4 HOH A 13 513 65 HOH HOH . D 4 HOH A 14 514 20 HOH HOH . D 4 HOH A 15 515 32 HOH HOH . D 4 HOH A 16 516 57 HOH HOH . D 4 HOH A 17 517 18 HOH HOH . D 4 HOH A 18 518 24 HOH HOH . D 4 HOH A 19 519 10 HOH HOH . D 4 HOH A 20 520 25 HOH HOH . D 4 HOH A 21 521 35 HOH HOH . D 4 HOH A 22 522 56 HOH HOH . D 4 HOH A 23 523 43 HOH HOH . D 4 HOH A 24 524 37 HOH HOH . D 4 HOH A 25 525 1 HOH HOH . D 4 HOH A 26 526 12 HOH HOH . D 4 HOH A 27 527 22 HOH HOH . D 4 HOH A 28 528 42 HOH HOH . D 4 HOH A 29 529 19 HOH HOH . D 4 HOH A 30 530 4 HOH HOH . D 4 HOH A 31 531 15 HOH HOH . D 4 HOH A 32 532 46 HOH HOH . D 4 HOH A 33 533 8 HOH HOH . D 4 HOH A 34 534 61 HOH HOH . D 4 HOH A 35 535 14 HOH HOH . D 4 HOH A 36 536 31 HOH HOH . D 4 HOH A 37 537 5 HOH HOH . D 4 HOH A 38 538 47 HOH HOH . D 4 HOH A 39 539 7 HOH HOH . D 4 HOH A 40 540 3 HOH HOH . D 4 HOH A 41 541 45 HOH HOH . D 4 HOH A 42 542 48 HOH HOH . D 4 HOH A 43 543 59 HOH HOH . D 4 HOH A 44 544 11 HOH HOH . D 4 HOH A 45 545 41 HOH HOH . D 4 HOH A 46 546 9 HOH HOH . D 4 HOH A 47 547 6 HOH HOH . D 4 HOH A 48 548 1 HOH HOH . D 4 HOH A 49 549 40 HOH HOH . D 4 HOH A 50 550 39 HOH HOH . D 4 HOH A 51 551 34 HOH HOH . D 4 HOH A 52 552 52 HOH HOH . D 4 HOH A 53 553 63 HOH HOH . D 4 HOH A 54 554 50 HOH HOH . D 4 HOH A 55 555 60 HOH HOH . D 4 HOH A 56 556 54 HOH HOH . D 4 HOH A 57 557 36 HOH HOH . D 4 HOH A 58 558 44 HOH HOH . D 4 HOH A 59 559 49 HOH HOH . D 4 HOH A 60 560 53 HOH HOH . D 4 HOH A 61 561 62 HOH HOH . D 4 HOH A 62 562 55 HOH HOH . D 4 HOH A 63 563 64 HOH HOH . D 4 HOH A 64 564 38 HOH HOH . D 4 HOH A 65 565 33 HOH HOH . D 4 HOH A 66 566 2 HOH HOH . D 4 HOH A 67 567 29 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 C2 4XE . . . C 3 -15.287 -18.979 -4.941 1 99.47 ? C2 4XE 402 A 1 HETATM 2 C C3 4XE . . . C 3 -16.563 -18.959 -4.109 1 98.98 ? C3 4XE 402 A 1 HETATM 3 N N4 4XE . . . C 3 -16.429 -19.282 -2.68 1 98.11 ? N4 4XE 402 A 1 HETATM 4 C C5 4XE . . . C 3 -15.751 -18.23 -1.911 1 98.24 ? C5 4XE 402 A 1 HETATM 5 C C6 4XE . . . C 3 -15.8 -18.542 -0.425 1 97.48 ? C6 4XE 402 A 1 HETATM 6 C C8 4XE . . . C 3 -15.874 -20.943 -0.948 1 93.56 ? C8 4XE 402 A 1 HETATM 7 C C11 4XE . . . C 3 -14.192 -19.008 -7.083 1 101.83 ? C11 4XE 402 A 1 HETATM 8 C C12 4XE . . . C 3 -14.466 -19.576 -8.467 1 101.78 ? C12 4XE 402 A 1 HETATM 9 C C13 4XE . . . C 3 -15.578 -18.809 -9.166 1 102.09 ? C13 4XE 402 A 1 HETATM 10 C C14 4XE . . . C 3 -16.821 -18.764 -8.302 1 101.36 ? C14 4XE 402 A 1 HETATM 11 C C15 4XE . . . C 3 -16.502 -18.19 -6.932 1 102.38 ? C15 4XE 402 A 1 HETATM 12 O O1 4XE . . . C 3 -14.18 -19.019 -4.414 1 97.38 ? O1 4XE 402 A 1 HETATM 13 N N7 4XE . . . C 3 -15.199 -19.878 -0.161 1 96.02 1 N7 4XE 402 A 1 HETATM 14 C C9 4XE . . . C 3 -15.837 -20.604 -2.425 1 95.36 ? C9 4XE 402 A 1 HETATM 15 N N10 4XE . . . C 3 -15.422 -18.947 -6.287 1 102.36 ? N10 4XE 402 A 1 HETATM 16 H H16 4XE . . . C 3 -17.195 -19.593 -4.507 1 98.95 ? H16 4XE 402 A 1 HETATM 17 H H17 4XE . . . C 3 -16.962 -18.066 -4.184 1 99.16 ? H17 4XE 402 A 1 HETATM 18 H H19 4XE . . . C 3 -14.823 -18.162 -2.199 1 98.08 ? H19 4XE 402 A 1 HETATM 19 H H18 4XE . . . C 3 -16.187 -17.37 -2.079 1 98.16 ? H18 4XE 402 A 1 HETATM 20 H H20 4XE . . . C 3 -16.727 -18.536 -0.117 1 97.22 ? H20 4XE 402 A 1 HETATM 21 H H21 4XE . . . C 3 -15.306 -17.859 0.072 1 97.68 ? H21 4XE 402 A 1 HETATM 22 H H25 4XE . . . C 3 -15.423 -21.796 -0.794 1 93.19 ? H25 4XE 402 A 1 HETATM 23 H H24 4XE . . . C 3 -16.801 -21.027 -0.652 1 93.38 ? H24 4XE 402 A 1 HETATM 24 H H29 4XE . . . C 3 -13.816 -18.11 -7.167 1 102.05 ? H29 4XE 402 A 1 HETATM 25 H H28 4XE . . . C 3 -13.536 -19.572 -6.625 1 101.39 ? H28 4XE 402 A 1 HETATM 26 H H31 4XE . . . C 3 -13.651 -19.53 -9.004 1 101.89 ? H31 4XE 402 A 1 HETATM 27 H H30 4XE . . . C 3 -14.721 -20.508 -8.387 1 101.79 ? H30 4XE 402 A 1 HETATM 28 H H32 4XE . . . C 3 -15.788 -19.244 -10.017 1 102.44 ? H32 4XE 402 A 1 HETATM 29 H H33 4XE . . . C 3 -15.279 -17.898 -9.355 1 102.18 ? H33 4XE 402 A 1 HETATM 30 H H35 4XE . . . C 3 -17.501 -18.212 -8.738 1 101.07 ? H35 4XE 402 A 1 HETATM 31 H H34 4XE . . . C 3 -17.182 -19.668 -8.202 1 101.19 ? H34 4XE 402 A 1 HETATM 32 H H37 4XE . . . C 3 -16.23 -17.254 -7.024 1 102.48 ? H37 4XE 402 A 1 HETATM 33 H H36 4XE . . . C 3 -17.298 -18.221 -6.374 1 102.3 ? H36 4XE 402 A 1 HETATM 34 H H23 4XE . . . C 3 -14.319 -19.858 -0.384 1 96.19 ? H23 4XE 402 A 1 HETATM 35 H H22 4XE . . . C 3 -15.266 -20.069 0.726 1 96.38 ? H22 4XE 402 A 1 HETATM 36 H H26 4XE . . . C 3 -16.33 -21.278 -2.922 1 95.36 ? H26 4XE 402 A 1 HETATM 37 H H27 4XE . . . C 3 -14.916 -20.613 -2.735 1 95.36 ? H27 4XE 402 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 37 #