data_4YD4 # _model_server_result.job_id PQyXUm0Xhk9LkE4oJeF70w _model_server_result.datetime_utc '2024-11-22 05:48:35' _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 4yd4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4YD4 # _exptl.entry_id 4YD4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.56 _cell.angle_gamma 90 _cell.entry_id 4YD4 _cell.length_a 45.342 _cell.length_b 73.49 _cell.length_c 53.026 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YD4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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,K _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N 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 255 A CYS 255 1_555 A SG CYS 290 A CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? covale ? covale1 A OD1 ASP 279 A ASP 279 1_555 F C 4AY . A 4AY 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 165 n n C1 C2 GOL sing 166 n n C1 H11 GOL sing 167 n n C1 H12 GOL sing 168 n n O1 HO1 GOL sing 169 n n C2 O2 GOL sing 170 n n C2 C3 GOL sing 171 n n C2 H2 GOL sing 172 n n O2 HO2 GOL sing 173 n n C3 O3 GOL sing 174 n n C3 H31 GOL sing 175 n n C3 H32 GOL sing 176 n n O3 HO3 GOL sing 177 n n # _atom_sites.entry_id 4YD4 _atom_sites.fract_transf_matrix[1][1] 0.022055 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007834 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013607 _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] 0.020013 _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 1 401 401 GOL GOL . C 2 GOL A 1 402 402 GOL GOL . D 2 GOL A 1 403 403 GOL GOL . E 2 GOL A 1 404 404 GOL GOL . F 3 4AY A 1 405 405 4AY 4AY . G 4 BR A 1 406 406 BR BR . H 5 DMS A 1 407 407 DMS DMS . I 6 EDO A 1 408 408 EDO EDO . J 7 PG4 A 1 409 409 PG4 PG4 . K 8 HOH A 1 501 501 HOH HOH . K 8 HOH A 2 515 515 HOH HOH . K 8 HOH A 3 569 569 HOH HOH . K 8 HOH A 4 582 582 HOH HOH . K 8 HOH A 5 588 588 HOH HOH . K 8 HOH A 6 589 589 HOH HOH . K 8 HOH A 7 612 612 HOH HOH . K 8 HOH A 8 621 621 HOH HOH . K 8 HOH A 9 629 629 HOH HOH . K 8 HOH A 10 630 630 HOH HOH . K 8 HOH A 11 638 638 HOH HOH . K 8 HOH A 12 677 677 HOH HOH . K 8 HOH A 13 678 678 HOH HOH . K 8 HOH A 14 686 686 HOH HOH . K 8 HOH A 15 690 690 HOH HOH . K 8 HOH A 16 731 731 HOH HOH . K 8 HOH A 17 733 733 HOH HOH . K 8 HOH A 18 738 738 HOH HOH . K 8 HOH A 19 744 744 HOH HOH . K 8 HOH A 20 747 747 HOH HOH . K 8 HOH A 21 748 748 HOH HOH . K 8 HOH A 22 760 760 HOH HOH . K 8 HOH A 23 775 775 HOH HOH . K 8 HOH A 24 786 786 HOH HOH . K 8 HOH A 25 798 798 HOH HOH . K 8 HOH A 26 804 804 HOH HOH . K 8 HOH A 27 807 807 HOH HOH . K 8 HOH A 28 813 813 HOH HOH . K 8 HOH A 29 817 817 HOH HOH . K 8 HOH A 30 819 819 HOH HOH . K 8 HOH A 31 826 826 HOH HOH . K 8 HOH A 32 830 830 HOH HOH . K 8 HOH A 33 835 835 HOH HOH . K 8 HOH A 34 852 852 HOH HOH . K 8 HOH A 35 864 864 HOH HOH . K 8 HOH A 36 867 867 HOH HOH . K 8 HOH A 37 877 877 HOH HOH . K 8 HOH A 38 883 883 HOH HOH . K 8 HOH A 39 895 895 HOH HOH . K 8 HOH A 40 896 896 HOH HOH . K 8 HOH A 41 897 897 HOH HOH . K 8 HOH A 42 905 905 HOH HOH . K 8 HOH A 43 913 913 HOH HOH . K 8 HOH A 44 925 925 HOH HOH . K 8 HOH A 45 938 938 HOH HOH . K 8 HOH A 46 948 948 HOH HOH . K 8 HOH A 47 955 955 HOH HOH . K 8 HOH A 48 957 957 HOH HOH . K 8 HOH A 49 959 959 HOH HOH . K 8 HOH A 50 970 970 HOH HOH . K 8 HOH A 51 971 971 HOH HOH . K 8 HOH A 52 978 978 HOH HOH . K 8 HOH A 53 988 988 HOH HOH . K 8 HOH A 54 992 992 HOH HOH . K 8 HOH A 55 996 996 HOH HOH . K 8 HOH A 56 1010 1010 HOH HOH . K 8 HOH A 57 1014 1014 HOH HOH . K 8 HOH A 58 1038 1038 HOH HOH . K 8 HOH A 59 1058 1058 HOH HOH . K 8 HOH A 60 1070 1070 HOH HOH . K 8 HOH A 61 1071 1071 HOH HOH . K 8 HOH A 62 1081 1081 HOH HOH . K 8 HOH A 63 1085 1085 HOH HOH . K 8 HOH A 64 1086 1086 HOH HOH . K 8 HOH A 65 1092 1092 HOH HOH . K 8 HOH A 66 1095 1095 HOH HOH . K 8 HOH A 67 1102 1102 HOH HOH . K 8 HOH A 68 1107 1107 HOH HOH . K 8 HOH A 69 1110 1110 HOH HOH . K 8 HOH A 70 1111 1111 HOH HOH . K 8 HOH A 71 1115 1115 HOH HOH . K 8 HOH A 72 1118 1118 HOH HOH . K 8 HOH A 73 1124 1124 HOH HOH . K 8 HOH A 74 1133 1133 HOH HOH . K 8 HOH A 75 1149 1149 HOH HOH . K 8 HOH A 76 1161 1161 HOH HOH . K 8 HOH A 77 1172 1172 HOH HOH . K 8 HOH A 78 1173 1173 HOH HOH . K 8 HOH A 79 1177 1177 HOH HOH . K 8 HOH A 80 1180 1180 HOH HOH . K 8 HOH A 81 1190 1190 HOH HOH . K 8 HOH A 82 1207 1207 HOH HOH . K 8 HOH A 83 1210 1210 HOH HOH . K 8 HOH A 84 1219 1219 HOH HOH . K 8 HOH A 85 1223 1223 HOH HOH . K 8 HOH A 86 1226 1226 HOH HOH . K 8 HOH A 87 1232 1232 HOH HOH . K 8 HOH A 88 1236 1236 HOH HOH . K 8 HOH A 89 1237 1237 HOH HOH . K 8 HOH A 90 1239 1239 HOH HOH . K 8 HOH A 91 1244 1244 HOH HOH . K 8 HOH A 92 1260 1260 HOH HOH . K 8 HOH A 93 1269 1269 HOH HOH . K 8 HOH A 94 1282 1282 HOH HOH . K 8 HOH A 95 1286 1286 HOH HOH . K 8 HOH A 96 1290 1290 HOH HOH . K 8 HOH A 97 1292 1292 HOH HOH . K 8 HOH A 98 1302 1302 HOH HOH . K 8 HOH A 99 1304 1304 HOH HOH . K 8 HOH A 100 1306 1306 HOH HOH . K 8 HOH A 101 1316 1316 HOH HOH . K 8 HOH A 102 1329 1329 HOH HOH . K 8 HOH A 103 1340 1340 HOH HOH . K 8 HOH A 104 1345 1345 HOH HOH . K 8 HOH A 105 1349 1349 HOH HOH . K 8 HOH A 106 1354 1354 HOH HOH . K 8 HOH A 107 1359 1359 HOH HOH . K 8 HOH A 108 1365 1365 HOH HOH . K 8 HOH A 109 1369 1369 HOH HOH . K 8 HOH A 110 1384 1384 HOH HOH . K 8 HOH A 111 1385 1385 HOH HOH . K 8 HOH A 112 1392 1392 HOH HOH . K 8 HOH A 113 1394 1394 HOH HOH . K 8 HOH A 114 1401 1401 HOH HOH . K 8 HOH A 115 1408 1408 HOH HOH . K 8 HOH A 116 1410 1410 HOH HOH . K 8 HOH A 117 1417 1417 HOH HOH . K 8 HOH A 118 1419 1419 HOH HOH . K 8 HOH A 119 1421 1421 HOH HOH . K 8 HOH A 120 1441 1441 HOH HOH . K 8 HOH A 121 1459 1459 HOH HOH . K 8 HOH A 122 1461 1461 HOH HOH . K 8 HOH A 123 1463 1463 HOH HOH . K 8 HOH A 124 1475 1475 HOH HOH . K 8 HOH A 125 1486 1486 HOH HOH . K 8 HOH A 126 1507 1507 HOH HOH . K 8 HOH A 127 1515 1515 HOH HOH . K 8 HOH A 128 1535 1535 HOH HOH . K 8 HOH A 129 1538 1538 HOH HOH . K 8 HOH A 130 1540 1540 HOH HOH . K 8 HOH A 131 1550 1550 HOH HOH . K 8 HOH A 132 1555 1555 HOH HOH . K 8 HOH A 133 1562 1562 HOH HOH . K 8 HOH A 134 1565 1565 HOH HOH . K 8 HOH A 135 1566 1566 HOH HOH . K 8 HOH A 136 1572 1572 HOH HOH . K 8 HOH A 137 1581 1581 HOH HOH . K 8 HOH A 138 1593 1593 HOH HOH . K 8 HOH A 139 1594 1594 HOH HOH . K 8 HOH A 140 1600 1600 HOH HOH . K 8 HOH A 141 1610 1610 HOH HOH . K 8 HOH A 142 1612 1612 HOH HOH . K 8 HOH A 143 1614 1614 HOH HOH . K 8 HOH A 144 1619 1619 HOH HOH . K 8 HOH A 145 1627 1627 HOH HOH . K 8 HOH A 146 1637 1637 HOH HOH . K 8 HOH A 147 1638 1638 HOH HOH . K 8 HOH A 148 1651 1651 HOH HOH . K 8 HOH A 149 1689 1689 HOH HOH . K 8 HOH A 150 1690 1690 HOH HOH . K 8 HOH A 151 1694 1694 HOH HOH . K 8 HOH A 152 1699 1699 HOH HOH . K 8 HOH A 153 1700 1700 HOH HOH . K 8 HOH A 154 1706 1706 HOH HOH . K 8 HOH A 155 1709 1709 HOH HOH . K 8 HOH A 156 1718 1718 HOH HOH . K 8 HOH A 157 1731 1731 HOH HOH . K 8 HOH A 158 1738 1738 HOH HOH . K 8 HOH A 159 1739 1739 HOH HOH . K 8 HOH A 160 1757 1757 HOH HOH . K 8 HOH A 161 1772 1772 HOH HOH . K 8 HOH A 162 1776 1776 HOH HOH . K 8 HOH A 163 1782 1782 HOH HOH . K 8 HOH A 164 1784 1784 HOH HOH . K 8 HOH A 165 1792 1792 HOH HOH . K 8 HOH A 166 1805 1805 HOH HOH . K 8 HOH A 167 1807 1807 HOH HOH . K 8 HOH A 168 1820 1820 HOH HOH . K 8 HOH A 169 1833 1833 HOH HOH . K 8 HOH A 170 1839 1839 HOH HOH . K 8 HOH A 171 1840 1840 HOH HOH . K 8 HOH A 172 1844 1844 HOH HOH . K 8 HOH A 173 1846 1846 HOH HOH . K 8 HOH A 174 1851 1851 HOH HOH . K 8 HOH A 175 1853 1853 HOH HOH . K 8 HOH A 176 1894 1894 HOH HOH . K 8 HOH A 177 1897 1897 HOH HOH . K 8 HOH A 178 1906 1906 HOH HOH . K 8 HOH A 179 1951 1951 HOH HOH . K 8 HOH A 180 1954 1954 HOH HOH . K 8 HOH A 181 1958 1958 HOH HOH . K 8 HOH A 182 1977 1977 HOH HOH . K 8 HOH A 183 1980 1980 HOH HOH . K 8 HOH A 184 1987 1987 HOH HOH . K 8 HOH A 185 1999 1999 HOH HOH . K 8 HOH A 186 2015 2015 HOH HOH . K 8 HOH A 187 2041 2041 HOH HOH . K 8 HOH A 188 2055 2055 HOH HOH . K 8 HOH A 189 2057 2057 HOH HOH . K 8 HOH A 190 2060 2060 HOH HOH . K 8 HOH A 191 2070 2070 HOH HOH . K 8 HOH A 192 2085 2085 HOH HOH . K 8 HOH A 193 2093 2093 HOH HOH . K 8 HOH A 194 2102 2102 HOH HOH . K 8 HOH A 195 2107 2107 HOH HOH . K 8 HOH A 196 2110 2110 HOH HOH . K 8 HOH A 197 2137 2137 HOH HOH . K 8 HOH A 198 2151 2151 HOH HOH . K 8 HOH A 199 2152 2152 HOH HOH . K 8 HOH A 200 2159 2159 HOH HOH . K 8 HOH A 201 2162 2162 HOH HOH . K 8 HOH A 202 2163 2163 HOH HOH . K 8 HOH A 203 2164 2164 HOH HOH . K 8 HOH A 204 2166 2166 HOH HOH . K 8 HOH A 205 2167 2167 HOH HOH . K 8 HOH A 206 2177 2177 HOH HOH . K 8 HOH A 207 2180 2180 HOH HOH . K 8 HOH A 208 2185 2185 HOH HOH . K 8 HOH A 209 2216 2216 HOH HOH . K 8 HOH A 210 2227 2227 HOH HOH . K 8 HOH A 211 2247 2247 HOH HOH . K 8 HOH A 212 2283 2283 HOH HOH . K 8 HOH A 213 2307 2307 HOH HOH . K 8 HOH A 214 2308 2308 HOH HOH . K 8 HOH A 215 2312 2312 HOH HOH . K 8 HOH A 216 2331 2331 HOH HOH . K 8 HOH A 217 2339 2339 HOH HOH . K 8 HOH A 218 2344 2344 HOH HOH . K 8 HOH A 219 2355 2355 HOH HOH . K 8 HOH A 220 2357 2357 HOH HOH . K 8 HOH A 221 2364 2364 HOH HOH . K 8 HOH A 222 2384 2384 HOH HOH . K 8 HOH A 223 2404 2404 HOH HOH . K 8 HOH A 224 2451 2451 HOH HOH . K 8 HOH A 225 2459 2459 HOH HOH . K 8 HOH A 226 2483 2483 HOH HOH . K 8 HOH A 227 2520 2520 HOH HOH . K 8 HOH A 228 2533 2533 HOH HOH . K 8 HOH A 229 2535 2535 HOH HOH . K 8 HOH A 230 2539 2539 HOH HOH . K 8 HOH A 231 2540 2540 HOH HOH . K 8 HOH A 232 2611 2611 HOH HOH . K 8 HOH A 233 2625 2625 HOH HOH . K 8 HOH A 234 2657 2657 HOH HOH . K 8 HOH A 235 2660 2660 HOH HOH . K 8 HOH A 236 2704 2704 HOH HOH . K 8 HOH A 237 2727 2727 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 C1 GOL . . . B 2 7.879 -1.417 -11.382 0.83 15.02 ? C1 GOL 401 A 1 HETATM 2 O O1 GOL . . . B 2 8.937 -0.596 -10.913 0.83 11.68 ? O1 GOL 401 A 1 HETATM 3 C C2 GOL . . . B 2 6.606 -0.585 -11.553 0.83 16.37 ? C2 GOL 401 A 1 HETATM 4 O O2 GOL . . . B 2 6.791 0.342 -12.609 0.83 17.28 ? O2 GOL 401 A 1 HETATM 5 C C3 GOL . . . B 2 5.434 -1.512 -11.852 0.83 18.32 ? C3 GOL 401 A 1 HETATM 6 O O3 GOL . . . B 2 5.699 -2.244 -13.029 0.83 19.63 ? O3 GOL 401 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #