data_3WB5 # _model_server_result.job_id 0hH5UzFBHHErHAQ2vIh7sA _model_server_result.datetime_utc '2024-10-19 16:43:41' _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 3wb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":507}' # _entry.id 3WB5 # _exptl.entry_id 3WB5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 257.331 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-5,6-dihydropyrimidin-4(3H)-one _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 120 _cell.entry_id 3WB5 _cell.length_a 101.926 _cell.length_b 101.926 _cell.length_c 168.936 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WB5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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,E,F,G,H,I _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 H _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 178 A CYS 155 1_555 A SG CYS 382 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 240 A CYS 217 1_555 A SG CYS 405 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _chem_comp.formula 'C15 H19 N3 O' _chem_comp.formula_weight 257.331 _chem_comp.id 0B4 _chem_comp.mon_nstd_flag . _chem_comp.name (6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-5,6-dihydropyrimidin-4(3H)-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3WB5 _atom_sites.fract_transf_matrix[1][1] 0.009811 _atom_sites.fract_transf_matrix[1][2] 0.005664 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011329 _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] 0.005919 _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 IOD A 1 501 501 IOD IOD . C 2 IOD A 1 502 502 IOD IOD . D 2 IOD A 1 503 503 IOD IOD . E 3 GOL A 1 504 601 GOL GOL . F 3 GOL A 1 505 602 GOL GOL . G 4 DMS A 1 506 603 DMS DMS . H 5 0B4 A 1 507 701 0B4 0B4 . I 6 HOH A 1 1001 1001 HOH HOH . I 6 HOH A 2 1002 1002 HOH HOH . I 6 HOH A 3 1003 1003 HOH HOH . I 6 HOH A 4 1004 1004 HOH HOH . I 6 HOH A 5 1005 1005 HOH HOH . I 6 HOH A 6 1006 1006 HOH HOH . I 6 HOH A 7 1007 1007 HOH HOH . I 6 HOH A 8 1008 1008 HOH HOH . I 6 HOH A 9 1009 1009 HOH HOH . I 6 HOH A 10 1010 1010 HOH HOH . I 6 HOH A 11 1011 1011 HOH HOH . I 6 HOH A 12 1012 1012 HOH HOH . I 6 HOH A 13 1013 1013 HOH HOH . I 6 HOH A 14 1014 1014 HOH HOH . I 6 HOH A 15 1015 1015 HOH HOH . I 6 HOH A 16 1016 1016 HOH HOH . I 6 HOH A 17 1017 1017 HOH HOH . I 6 HOH A 18 1018 1018 HOH HOH . I 6 HOH A 19 1019 1019 HOH HOH . I 6 HOH A 20 1020 1020 HOH HOH . I 6 HOH A 21 1021 1021 HOH HOH . I 6 HOH A 22 1022 1022 HOH HOH . I 6 HOH A 23 1023 1023 HOH HOH . I 6 HOH A 24 1024 1024 HOH HOH . I 6 HOH A 25 1025 1025 HOH HOH . I 6 HOH A 26 1026 1026 HOH HOH . I 6 HOH A 27 1027 1027 HOH HOH . I 6 HOH A 28 1028 1028 HOH HOH . I 6 HOH A 29 1029 1029 HOH HOH . I 6 HOH A 30 1030 1030 HOH HOH . I 6 HOH A 31 1031 1031 HOH HOH . I 6 HOH A 32 1032 1032 HOH HOH . I 6 HOH A 33 1033 1033 HOH HOH . I 6 HOH A 34 1034 1034 HOH HOH . I 6 HOH A 35 1035 1035 HOH HOH . I 6 HOH A 36 1036 1036 HOH HOH . I 6 HOH A 37 1037 1037 HOH HOH . I 6 HOH A 38 1038 1038 HOH HOH . I 6 HOH A 39 1039 1039 HOH HOH . I 6 HOH A 40 1040 1040 HOH HOH . I 6 HOH A 41 1041 1041 HOH HOH . I 6 HOH A 42 1042 1042 HOH HOH . I 6 HOH A 43 1043 1043 HOH HOH . I 6 HOH A 44 1044 1044 HOH HOH . I 6 HOH A 45 1045 1045 HOH HOH . I 6 HOH A 46 1046 1046 HOH HOH . I 6 HOH A 47 1047 1047 HOH HOH . I 6 HOH A 48 1048 1048 HOH HOH . I 6 HOH A 49 1049 1049 HOH HOH . I 6 HOH A 50 1050 1050 HOH HOH . I 6 HOH A 51 1051 1051 HOH HOH . I 6 HOH A 52 1052 1052 HOH HOH . I 6 HOH A 53 1053 1053 HOH HOH . I 6 HOH A 54 1054 1054 HOH HOH . I 6 HOH A 55 1055 1055 HOH HOH . I 6 HOH A 56 1056 1056 HOH HOH . I 6 HOH A 57 1057 1057 HOH HOH . I 6 HOH A 58 1058 1058 HOH HOH . I 6 HOH A 59 1059 1059 HOH HOH . I 6 HOH A 60 1060 1060 HOH HOH . I 6 HOH A 61 1061 1061 HOH HOH . I 6 HOH A 62 1062 1062 HOH HOH . I 6 HOH A 63 1063 1063 HOH HOH . I 6 HOH A 64 1064 1064 HOH HOH . I 6 HOH A 65 1065 1065 HOH HOH . I 6 HOH A 66 1066 1066 HOH HOH . I 6 HOH A 67 1067 1067 HOH HOH . I 6 HOH A 68 1068 1068 HOH HOH . I 6 HOH A 69 1069 1069 HOH HOH . I 6 HOH A 70 1070 1070 HOH HOH . I 6 HOH A 71 1071 1071 HOH HOH . I 6 HOH A 72 1072 1072 HOH HOH . I 6 HOH A 73 1073 1073 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 O O 0B4 . . . H 5 18.176 40.749 -9.55 1 30.42 ? O 0B4 507 A 1 HETATM 2 C C5 0B4 . . . H 5 17.768 39.864 -8.819 1 29.86 ? C5 0B4 507 A 1 HETATM 3 N N3 0B4 . . . H 5 17.259 40.119 -7.605 1 31.96 ? N3 0B4 507 A 1 HETATM 4 C C4 0B4 . . . H 5 16.956 41.483 -7.187 1 20.34 ? C4 0B4 507 A 1 HETATM 5 C C3 0B4 . . . H 5 17.054 39.092 -6.774 1 30.92 ? C3 0B4 507 A 1 HETATM 6 N N2 0B4 . . . H 5 16.208 39.232 -5.755 1 32.8 ? N2 0B4 507 A 1 HETATM 7 N N1 0B4 . . . H 5 17.681 38.002 -6.9 1 27.47 ? N1 0B4 507 A 1 HETATM 8 C C6 0B4 . . . H 5 17.864 38.437 -9.29 1 22.34 ? C6 0B4 507 A 1 HETATM 9 C C2 0B4 . . . H 5 18.33 37.579 -8.131 1 23.85 ? C2 0B4 507 A 1 HETATM 10 C C1 0B4 . . . H 5 18.007 36.122 -8.425 1 17.22 ? C1 0B4 507 A 1 HETATM 11 C C7 0B4 . . . H 5 19.846 37.722 -8.023 1 25.82 ? C7 0B4 507 A 1 HETATM 12 C C9 0B4 . . . H 5 20.42 37 -6.808 1 27.63 ? C9 0B4 507 A 1 HETATM 13 C C8 0B4 . . . H 5 20.238 38.512 -6.778 1 28.57 ? C8 0B4 507 A 1 HETATM 14 C C10 0B4 . . . H 5 21.496 39.228 -7.072 1 31.81 ? C10 0B4 507 A 1 HETATM 15 C C15 0B4 . . . H 5 21.533 40.613 -6.974 1 31.96 ? C15 0B4 507 A 1 HETATM 16 C C14 0B4 . . . H 5 22.71 41.297 -7.25 1 31.82 ? C14 0B4 507 A 1 HETATM 17 C C13 0B4 . . . H 5 23.847 40.595 -7.625 1 32.62 ? C13 0B4 507 A 1 HETATM 18 C C12 0B4 . . . H 5 23.808 39.21 -7.724 1 33.18 ? C12 0B4 507 A 1 HETATM 19 C C11 0B4 . . . H 5 22.632 38.524 -7.452 1 33.55 ? C11 0B4 507 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #