data_3WB4 # _model_server_result.job_id Eopd1SogCAj3SAEdxA_d7A _model_server_result.datetime_utc '2024-12-27 17:37:21' _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 3wb4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":507}' # _entry.id 3WB4 # _exptl.entry_id 3WB4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 245.32 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-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 3WB4 _cell.length_a 102.208 _cell.length_b 102.208 _cell.length_c 169.984 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WB4 _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 4 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 A SG CYS 240 A CYS 217 1_555 A SG CYS 405 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf3 A SG CYS 292 A CYS 269 1_555 A SG CYS 342 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? # _chem_comp.formula 'C14 H19 N3 O' _chem_comp.formula_weight 245.32 _chem_comp.id 0B3 _chem_comp.mon_nstd_flag . _chem_comp.name (6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-5,6-dihydropyrimidin-4(3H)-one _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 O C5 0B3 doub 1 n n C6 C5 0B3 sing 2 n n C6 C2 0B3 sing 3 n n C5 N3 0B3 sing 4 n n C1 C2 0B3 sing 5 n n C2 C7 0B3 sing 6 n n C2 N1 0B3 sing 7 n n C7 C8 0B3 sing 8 n n N3 C4 0B3 sing 9 n n N3 C3 0B3 sing 10 n n C14 C13 0B3 doub 11 n y C14 C9 0B3 sing 12 n y C13 C12 0B3 sing 13 n y N1 C3 0B3 doub 14 n n C8 C9 0B3 sing 15 n n C3 N2 0B3 sing 16 n n C9 C10 0B3 doub 17 n y C12 C11 0B3 doub 18 n y C10 C11 0B3 sing 19 n y C4 H1 0B3 sing 20 n n C4 H2 0B3 sing 21 n n C4 H3 0B3 sing 22 n n N2 H4 0B3 sing 23 n n N2 H5 0B3 sing 24 n n C6 H6 0B3 sing 25 n n C6 H7 0B3 sing 26 n n C1 H8 0B3 sing 27 n n C1 H9 0B3 sing 28 n n C1 H10 0B3 sing 29 n n C7 H11 0B3 sing 30 n n C7 H12 0B3 sing 31 n n C8 H13 0B3 sing 32 n n C8 H14 0B3 sing 33 n n C14 H15 0B3 sing 34 n n C13 H16 0B3 sing 35 n n C12 H17 0B3 sing 36 n n C11 H18 0B3 sing 37 n n C10 H19 0B3 sing 38 n n # _atom_sites.entry_id 3WB4 _atom_sites.fract_transf_matrix[1][1] 0.009784 _atom_sites.fract_transf_matrix[1][2] 0.005649 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011298 _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] 0.005883 _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 GOL A 1 501 501 GOL GOL . C 2 GOL A 1 502 502 GOL GOL . D 2 GOL A 1 503 503 GOL GOL . E 2 GOL A 1 504 504 GOL GOL . F 3 IOD A 1 505 601 IOD IOD . G 3 IOD A 1 506 602 IOD IOD . H 4 0B3 A 1 507 701 0B3 0B3 . I 5 HOH A 1 1001 1001 HOH HOH . I 5 HOH A 2 1002 1002 HOH HOH . I 5 HOH A 3 1003 1003 HOH HOH . I 5 HOH A 4 1004 1004 HOH HOH . I 5 HOH A 5 1005 1005 HOH HOH . I 5 HOH A 6 1006 1006 HOH HOH . I 5 HOH A 7 1007 1007 HOH HOH . I 5 HOH A 8 1008 1008 HOH HOH . I 5 HOH A 9 1009 1009 HOH HOH . I 5 HOH A 10 1010 1010 HOH HOH . I 5 HOH A 11 1011 1011 HOH HOH . I 5 HOH A 12 1012 1012 HOH HOH . I 5 HOH A 13 1013 1013 HOH HOH . I 5 HOH A 14 1014 1014 HOH HOH . I 5 HOH A 15 1015 1015 HOH HOH . I 5 HOH A 16 1016 1016 HOH HOH . I 5 HOH A 17 1017 1017 HOH HOH . I 5 HOH A 18 1018 1018 HOH HOH . I 5 HOH A 19 1019 1019 HOH HOH . I 5 HOH A 20 1020 1020 HOH HOH . I 5 HOH A 21 1021 1021 HOH HOH . I 5 HOH A 22 1022 1022 HOH HOH . I 5 HOH A 23 1023 1023 HOH HOH . I 5 HOH A 24 1024 1024 HOH HOH . I 5 HOH A 25 1025 1025 HOH HOH . I 5 HOH A 26 1026 1026 HOH HOH . I 5 HOH A 27 1027 1027 HOH HOH . I 5 HOH A 28 1028 1028 HOH HOH . I 5 HOH A 29 1029 1029 HOH HOH . I 5 HOH A 30 1030 1030 HOH HOH . I 5 HOH A 31 1031 1031 HOH HOH . I 5 HOH A 32 1032 1032 HOH HOH . I 5 HOH A 33 1033 1033 HOH HOH . I 5 HOH A 34 1034 1034 HOH HOH . I 5 HOH A 35 1035 1035 HOH HOH . I 5 HOH A 36 1036 1036 HOH HOH . I 5 HOH A 37 1037 1037 HOH HOH . I 5 HOH A 38 1038 1038 HOH HOH . I 5 HOH A 39 1039 1039 HOH HOH . I 5 HOH A 40 1040 1040 HOH HOH . I 5 HOH A 41 1041 1041 HOH HOH . I 5 HOH A 42 1042 1042 HOH HOH . I 5 HOH A 43 1043 1043 HOH HOH . I 5 HOH A 44 1044 1044 HOH HOH . I 5 HOH A 45 1045 1045 HOH HOH . I 5 HOH A 46 1046 1046 HOH HOH . I 5 HOH A 47 1047 1047 HOH HOH . I 5 HOH A 48 1048 1048 HOH HOH . I 5 HOH A 49 1049 1049 HOH HOH . I 5 HOH A 50 1050 1050 HOH HOH . I 5 HOH A 51 1051 1051 HOH HOH . I 5 HOH A 52 1052 1052 HOH HOH . I 5 HOH A 53 1053 1053 HOH HOH . I 5 HOH A 54 1054 1054 HOH HOH . I 5 HOH A 55 1055 1055 HOH HOH . I 5 HOH A 56 1056 1056 HOH HOH . I 5 HOH A 57 1057 1057 HOH HOH . I 5 HOH A 58 1058 1058 HOH HOH . I 5 HOH A 59 1059 1059 HOH HOH . I 5 HOH A 60 1060 1060 HOH HOH . I 5 HOH A 61 1061 1061 HOH HOH . I 5 HOH A 62 1062 1062 HOH HOH . I 5 HOH A 63 1063 1063 HOH HOH . I 5 HOH A 64 1064 1064 HOH HOH . I 5 HOH A 65 1065 1065 HOH HOH . I 5 HOH A 66 1066 1066 HOH HOH . I 5 HOH A 67 1067 1067 HOH HOH . I 5 HOH A 68 1068 1068 HOH HOH . I 5 HOH A 69 1069 1069 HOH HOH . I 5 HOH A 70 1070 1070 HOH HOH . I 5 HOH A 71 1071 1071 HOH HOH . I 5 HOH A 72 1072 1072 HOH HOH . I 5 HOH A 73 1073 1073 HOH HOH . I 5 HOH A 74 1074 1074 HOH HOH . I 5 HOH A 75 1075 1075 HOH HOH . I 5 HOH A 76 1076 1076 HOH HOH . I 5 HOH A 77 1077 1077 HOH HOH . I 5 HOH A 78 1078 1078 HOH HOH . I 5 HOH A 79 1079 1079 HOH HOH . I 5 HOH A 80 1080 1080 HOH HOH . I 5 HOH A 81 1081 1081 HOH HOH . I 5 HOH A 82 1082 1083 HOH HOH . I 5 HOH A 83 1083 1084 HOH HOH . I 5 HOH A 84 1084 1085 HOH HOH . I 5 HOH A 85 1085 1086 HOH HOH . I 5 HOH A 86 1086 1087 HOH HOH . I 5 HOH A 87 1087 1088 HOH HOH . I 5 HOH A 88 1088 1089 HOH HOH . I 5 HOH A 89 1089 1090 HOH HOH . I 5 HOH A 90 1090 1091 HOH HOH . I 5 HOH A 91 1091 1092 HOH HOH . I 5 HOH A 92 1092 1093 HOH HOH . I 5 HOH A 93 1093 1094 HOH HOH . I 5 HOH A 94 1094 1095 HOH HOH . I 5 HOH A 95 1095 1096 HOH HOH . I 5 HOH A 96 1096 1097 HOH HOH . I 5 HOH A 97 1097 1098 HOH HOH . I 5 HOH A 98 1098 1099 HOH HOH . I 5 HOH A 99 1099 1100 HOH HOH . I 5 HOH A 100 1100 1101 HOH HOH . I 5 HOH A 101 1101 1102 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 0B3 . . . H 4 16.523 41.982 -10.052 1 40.44 ? O 0B3 507 A 1 HETATM 2 C C5 0B3 . . . H 4 16.315 41.025 -9.331 1 42.05 ? C5 0B3 507 A 1 HETATM 3 N N3 0B3 . . . H 4 15.998 41.17 -8.03 1 39.03 ? N3 0B3 507 A 1 HETATM 4 C C4 0B3 . . . H 4 15.764 42.519 -7.521 1 29.36 ? C4 0B3 507 A 1 HETATM 5 C C3 0B3 . . . H 4 15.889 40.048 -7.263 1 34.79 ? C3 0B3 507 A 1 HETATM 6 N N2 0B3 . . . H 4 15.241 40.116 -6.108 1 31.19 ? N2 0B3 507 A 1 HETATM 7 N N1 0B3 . . . H 4 16.379 38.93 -7.585 1 34.09 ? N1 0B3 507 A 1 HETATM 8 C C6 0B3 . . . H 4 16.421 39.632 -9.888 1 42.02 ? C6 0B3 507 A 1 HETATM 9 C C2 0B3 . . . H 4 17.098 38.762 -8.839 1 38.89 ? C2 0B3 507 A 1 HETATM 10 C C1 0B3 . . . H 4 17.053 37.306 -9.275 1 37.85 ? C1 0B3 507 A 1 HETATM 11 C C7 0B3 . . . H 4 18.564 39.21 -8.709 1 37.93 ? C7 0B3 507 A 1 HETATM 12 C C8 0B3 . . . H 4 19.192 38.744 -7.392 1 42.46 ? C8 0B3 507 A 1 HETATM 13 C C9 0B3 . . . H 4 20.534 39.401 -7.13 1 42.71 ? C9 0B3 507 A 1 HETATM 14 C C14 0B3 . . . H 4 21.623 39.187 -7.969 1 47.2 ? C14 0B3 507 A 1 HETATM 15 C C13 0B3 . . . H 4 22.854 39.806 -7.706 1 48.2 ? C13 0B3 507 A 1 HETATM 16 C C12 0B3 . . . H 4 22.996 40.637 -6.593 1 45.81 ? C12 0B3 507 A 1 HETATM 17 C C11 0B3 . . . H 4 21.919 40.853 -5.743 1 48.57 ? C11 0B3 507 A 1 HETATM 18 C C10 0B3 . . . H 4 20.697 40.228 -6.021 1 48.43 ? C10 0B3 507 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 18 #