data_4AB8 # _model_server_result.job_id nnfWYQpiY4XHSVvdmKWBMQ _model_server_result.datetime_utc '2024-11-05 11:04:40' _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 4ab8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1253}' # _entry.id 4AB8 # _exptl.entry_id 4AB8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 179.216 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,4-dihydro-2H-1,5-benzodioxepin-6-ylmethanamine _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 4AB8 _cell.length_a 54.323 _cell.length_b 54.323 _cell.length_c 105.32 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AB8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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,J _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 I _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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _chem_comp.formula 'C10 H13 N O2' _chem_comp.formula_weight 179.216 _chem_comp.id VXU _chem_comp.mon_nstd_flag . _chem_comp.name 3,4-dihydro-2H-1,5-benzodioxepin-6-ylmethanamine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CC00413 # 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 C2 C3 VXU sing 389 n y C2 C1 VXU doub 390 n y C3 C4 VXU doub 391 n y C1 C11 VXU sing 392 n y C4 C5 VXU sing 393 n y C4 C12 VXU sing 394 n n C11 C5 VXU doub 395 n y C11 O10 VXU sing 396 n n C5 O6 VXU sing 397 n n C8 C9 VXU sing 398 n n C8 C7 VXU sing 399 n n C9 O10 VXU sing 400 n n C7 O6 VXU sing 401 n n C12 N13 VXU sing 402 n n C2 H2 VXU sing 403 n n C3 H3 VXU sing 404 n n C1 H1 VXU sing 405 n n C12 H121 VXU sing 406 n n C12 H122 VXU sing 407 n n C8 H81C VXU sing 408 n n C8 H82C VXU sing 409 n n C9 H91C VXU sing 410 n n C9 H92C VXU sing 411 n n C7 H71C VXU sing 412 n n C7 H72C VXU sing 413 n n N13 H131 VXU sing 414 n n N13 H132 VXU sing 415 n n # _atom_sites.entry_id 4AB8 _atom_sites.fract_transf_matrix[1][1] 0.018408 _atom_sites.fract_transf_matrix[1][2] 0.010628 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021256 _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] 0.009495 _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 SO4 A 1 1246 1246 SO4 SO4 . C 3 CA A 1 1247 1247 CA CA . D 4 EDO A 1 1248 1248 EDO EDO . E 4 EDO A 1 1249 1249 EDO EDO . F 4 EDO A 1 1250 1250 EDO EDO . G 4 EDO A 1 1251 1251 EDO EDO . H 4 EDO A 1 1252 1252 EDO EDO . I 5 VXU A 1 1253 1253 VXU VXU . J 6 HOH A 1 2001 2001 HOH HOH . J 6 HOH A 2 2002 2002 HOH HOH . J 6 HOH A 3 2003 2003 HOH HOH . J 6 HOH A 4 2004 2004 HOH HOH . J 6 HOH A 5 2005 2005 HOH HOH . J 6 HOH A 6 2006 2006 HOH HOH . J 6 HOH A 7 2007 2007 HOH HOH . J 6 HOH A 8 2008 2008 HOH HOH . J 6 HOH A 9 2009 2009 HOH HOH . J 6 HOH A 10 2010 2010 HOH HOH . J 6 HOH A 11 2011 2011 HOH HOH . J 6 HOH A 12 2012 2012 HOH HOH . J 6 HOH A 13 2013 2013 HOH HOH . J 6 HOH A 14 2014 2014 HOH HOH . J 6 HOH A 15 2015 2015 HOH HOH . J 6 HOH A 16 2016 2016 HOH HOH . J 6 HOH A 17 2017 2017 HOH HOH . J 6 HOH A 18 2018 2018 HOH HOH . J 6 HOH A 19 2019 2019 HOH HOH . J 6 HOH A 20 2020 2020 HOH HOH . J 6 HOH A 21 2021 2021 HOH HOH . J 6 HOH A 22 2022 2022 HOH HOH . J 6 HOH A 23 2023 2023 HOH HOH . J 6 HOH A 24 2024 2024 HOH HOH . J 6 HOH A 25 2025 2025 HOH HOH . J 6 HOH A 26 2026 2026 HOH HOH . J 6 HOH A 27 2027 2027 HOH HOH . J 6 HOH A 28 2028 2028 HOH HOH . J 6 HOH A 29 2029 2029 HOH HOH . J 6 HOH A 30 2030 2030 HOH HOH . J 6 HOH A 31 2031 2031 HOH HOH . J 6 HOH A 32 2032 2032 HOH HOH . J 6 HOH A 33 2033 2033 HOH HOH . J 6 HOH A 34 2034 2034 HOH HOH . J 6 HOH A 35 2035 2035 HOH HOH . J 6 HOH A 36 2036 2036 HOH HOH . J 6 HOH A 37 2037 2037 HOH HOH . J 6 HOH A 38 2038 2038 HOH HOH . J 6 HOH A 39 2039 2039 HOH HOH . J 6 HOH A 40 2040 2040 HOH HOH . J 6 HOH A 41 2041 2041 HOH HOH . J 6 HOH A 42 2042 2042 HOH HOH . J 6 HOH A 43 2043 2043 HOH HOH . J 6 HOH A 44 2044 2044 HOH HOH . J 6 HOH A 45 2045 2045 HOH HOH . J 6 HOH A 46 2046 2046 HOH HOH . J 6 HOH A 47 2047 2047 HOH HOH . J 6 HOH A 48 2048 2048 HOH HOH . J 6 HOH A 49 2049 2049 HOH HOH . J 6 HOH A 50 2050 2050 HOH HOH . J 6 HOH A 51 2051 2051 HOH HOH . J 6 HOH A 52 2052 2052 HOH HOH . J 6 HOH A 53 2053 2053 HOH HOH . J 6 HOH A 54 2054 2054 HOH HOH . J 6 HOH A 55 2055 2055 HOH HOH . J 6 HOH A 56 2056 2056 HOH HOH . J 6 HOH A 57 2057 2057 HOH HOH . J 6 HOH A 58 2058 2058 HOH HOH . J 6 HOH A 59 2059 2059 HOH HOH . J 6 HOH A 60 2060 2060 HOH HOH . J 6 HOH A 61 2061 2061 HOH HOH . J 6 HOH A 62 2062 2062 HOH HOH . J 6 HOH A 63 2063 2063 HOH HOH . J 6 HOH A 64 2064 2064 HOH HOH . J 6 HOH A 65 2065 2065 HOH HOH . J 6 HOH A 66 2066 2066 HOH HOH . J 6 HOH A 67 2067 2067 HOH HOH . J 6 HOH A 68 2068 2068 HOH HOH . J 6 HOH A 69 2069 2069 HOH HOH . J 6 HOH A 70 2070 2070 HOH HOH . J 6 HOH A 71 2071 2071 HOH HOH . J 6 HOH A 72 2072 2072 HOH HOH . J 6 HOH A 73 2073 2073 HOH HOH . J 6 HOH A 74 2074 2074 HOH HOH . J 6 HOH A 75 2075 2075 HOH HOH . J 6 HOH A 76 2076 2076 HOH HOH . J 6 HOH A 77 2077 2077 HOH HOH . J 6 HOH A 78 2078 2078 HOH HOH . J 6 HOH A 79 2079 2079 HOH HOH . J 6 HOH A 80 2080 2080 HOH HOH . J 6 HOH A 81 2081 2081 HOH HOH . J 6 HOH A 82 2082 2082 HOH HOH . J 6 HOH A 83 2083 2083 HOH HOH . J 6 HOH A 84 2084 2084 HOH HOH . J 6 HOH A 85 2085 2085 HOH HOH . J 6 HOH A 86 2086 2086 HOH HOH . J 6 HOH A 87 2087 2087 HOH HOH . J 6 HOH A 88 2088 2088 HOH HOH . J 6 HOH A 89 2089 2089 HOH HOH . J 6 HOH A 90 2090 2090 HOH HOH . J 6 HOH A 91 2091 2091 HOH HOH . J 6 HOH A 92 2092 2092 HOH HOH . J 6 HOH A 93 2093 2093 HOH HOH . J 6 HOH A 94 2094 2094 HOH HOH . J 6 HOH A 95 2095 2095 HOH HOH . J 6 HOH A 96 2096 2096 HOH HOH . J 6 HOH A 97 2097 2097 HOH HOH . J 6 HOH A 98 2098 2098 HOH HOH . J 6 HOH A 99 2099 2099 HOH HOH . J 6 HOH A 100 2100 2100 HOH HOH . J 6 HOH A 101 2101 2101 HOH HOH . J 6 HOH A 102 2102 2102 HOH HOH . J 6 HOH A 103 2103 2103 HOH HOH . J 6 HOH A 104 2104 2104 HOH HOH . J 6 HOH A 105 2105 2105 HOH HOH . J 6 HOH A 106 2106 2106 HOH HOH . J 6 HOH A 107 2107 2107 HOH HOH . J 6 HOH A 108 2108 2108 HOH HOH . J 6 HOH A 109 2109 2109 HOH HOH . J 6 HOH A 110 2110 2110 HOH HOH . J 6 HOH A 111 2111 2111 HOH HOH . J 6 HOH A 112 2112 2112 HOH HOH . J 6 HOH A 113 2113 2113 HOH HOH . J 6 HOH A 114 2114 2114 HOH HOH . J 6 HOH A 115 2115 2115 HOH HOH . J 6 HOH A 116 2116 2116 HOH HOH . J 6 HOH A 117 2117 2117 HOH HOH . J 6 HOH A 118 2118 2118 HOH HOH . J 6 HOH A 119 2119 2119 HOH HOH . J 6 HOH A 120 2120 2120 HOH HOH . J 6 HOH A 121 2121 2121 HOH HOH . J 6 HOH A 122 2122 2122 HOH HOH . J 6 HOH A 123 2123 2123 HOH HOH . J 6 HOH A 124 2124 2124 HOH HOH . J 6 HOH A 125 2125 2125 HOH HOH . J 6 HOH A 126 2126 2126 HOH HOH . J 6 HOH A 127 2127 2127 HOH HOH . J 6 HOH A 128 2128 2128 HOH HOH . J 6 HOH A 129 2129 2129 HOH HOH . J 6 HOH A 130 2130 2130 HOH HOH . J 6 HOH A 131 2131 2131 HOH HOH . J 6 HOH A 132 2132 2132 HOH HOH . J 6 HOH A 133 2133 2133 HOH HOH . J 6 HOH A 134 2134 2134 HOH HOH . J 6 HOH A 135 2135 2135 HOH HOH . J 6 HOH A 136 2136 2136 HOH HOH . J 6 HOH A 137 2137 2137 HOH HOH . J 6 HOH A 138 2138 2138 HOH HOH . J 6 HOH A 139 2139 2139 HOH HOH . J 6 HOH A 140 2140 2140 HOH HOH . J 6 HOH A 141 2141 2141 HOH HOH . J 6 HOH A 142 2142 2142 HOH HOH . J 6 HOH A 143 2143 2143 HOH HOH . J 6 HOH A 144 2144 2144 HOH HOH . J 6 HOH A 145 2145 2145 HOH HOH . J 6 HOH A 146 2146 2146 HOH HOH . J 6 HOH A 147 2147 2147 HOH HOH . J 6 HOH A 148 2148 2148 HOH HOH . J 6 HOH A 149 2149 2149 HOH HOH . J 6 HOH A 150 2150 2150 HOH HOH . J 6 HOH A 151 2151 2151 HOH HOH . J 6 HOH A 152 2152 2152 HOH HOH . J 6 HOH A 153 2153 2153 HOH HOH . J 6 HOH A 154 2154 2154 HOH HOH . J 6 HOH A 155 2155 2155 HOH HOH . J 6 HOH A 156 2156 2156 HOH HOH . J 6 HOH A 157 2157 2157 HOH HOH . J 6 HOH A 158 2158 2158 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 VXU . A . I 5 -21.654 1.878 14.022 0.3 16.34 ? C2 VXU 1253 A 1 HETATM 2 C C2 VXU . B . I 5 -21.574 2.054 13.971 0.6 16.41 ? C2 VXU 1253 A 1 HETATM 3 C C3 VXU . A . I 5 -20.948 1.488 15.137 0.3 17.33 ? C3 VXU 1253 A 1 HETATM 4 C C3 VXU . B . I 5 -20.794 1.694 15.051 0.6 18.05 ? C3 VXU 1253 A 1 HETATM 5 C C1 VXU . A . I 5 -22.557 2.899 14.143 0.3 17.5 ? C1 VXU 1253 A 1 HETATM 6 C C1 VXU . B . I 5 -22.484 3.067 14.126 0.6 19.25 ? C1 VXU 1253 A 1 HETATM 7 C C4 VXU . A . I 5 -21.16 2.108 16.34 0.3 17.2 ? C4 VXU 1253 A 1 HETATM 8 C C4 VXU . B . I 5 -20.938 2.305 16.267 0.6 17.7 ? C4 VXU 1253 A 1 HETATM 9 C C11 VXU . A . I 5 -22.753 3.543 15.346 0.3 17.95 ? C11 VXU 1253 A 1 HETATM 10 C C11 VXU . B . I 5 -22.625 3.734 15.33 0.6 18.63 ? C11 VXU 1253 A 1 HETATM 11 C C5 VXU . A . I 5 -22.056 3.134 16.458 0.3 17.38 ? C5 VXU 1253 A 1 HETATM 12 C C5 VXU . B . I 5 -21.86 3.331 16.414 0.6 17.79 ? C5 VXU 1253 A 1 HETATM 13 C C8 VXU . A . I 5 -23.375 5.639 17.491 0.3 16.49 ? C8 VXU 1253 A 1 HETATM 14 C C8 VXU . B . I 5 -23.455 5.742 17.56 0.6 16.18 ? C8 VXU 1253 A 1 HETATM 15 C C9 VXU . A . I 5 -22.997 5.656 16.029 0.3 16.42 ? C9 VXU 1253 A 1 HETATM 16 C C9 VXU . B . I 5 -23.021 5.865 16.107 0.6 15.98 ? C9 VXU 1253 A 1 HETATM 17 C C7 VXU . A . I 5 -23.471 4.189 17.913 0.3 15.73 ? C7 VXU 1253 A 1 HETATM 18 C C7 VXU . B . I 5 -23.34 4.276 17.981 0.6 14.99 ? C7 VXU 1253 A 1 HETATM 19 C C12 VXU . A . I 5 -20.43 1.705 17.559 0.3 16.27 ? C12 VXU 1253 A 1 HETATM 20 C C12 VXU . B . I 5 -20.062 1.808 17.383 0.6 14.84 ? C12 VXU 1253 A 1 HETATM 21 N N13 VXU . A . I 5 -19.129 1.159 17.201 0.3 14.5 ? N13 VXU 1253 A 1 HETATM 22 N N13 VXU . B . I 5 -19.465 2.956 18.124 0.6 12.4 ? N13 VXU 1253 A 1 HETATM 23 O O10 VXU . A . I 5 -23.673 4.569 15.387 0.3 18.21 ? O10 VXU 1253 A 1 HETATM 24 O O10 VXU . B . I 5 -23.577 4.762 15.366 0.6 19.7 ? O10 VXU 1253 A 1 HETATM 25 O O6 VXU . A . I 5 -22.169 3.665 17.741 0.3 16.88 ? O6 VXU 1253 A 1 HETATM 26 O O6 VXU . B . I 5 -21.985 3.908 17.705 0.6 17.91 ? O6 VXU 1253 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #