data_4Y5B # _model_server_result.job_id U4-jbi8smfweirpmrAtPaA _model_server_result.datetime_utc '2024-10-12 14:25:47' _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 4y5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4Y5B # _exptl.entry_id 4Y5B _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.48 _cell.angle_gamma 90 _cell.entry_id 4Y5B _cell.length_a 45.404 _cell.length_b 73.09 _cell.length_c 52.764 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y5B _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 _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 255 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 255 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 290 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 290 _struct_conn.ptnr2_symmetry 1_555 _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 2.042 _struct_conn.pdbx_value_order ? # _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 184 n n C1 C2 GOL sing 185 n n C1 H11 GOL sing 186 n n C1 H12 GOL sing 187 n n O1 HO1 GOL sing 188 n n C2 O2 GOL sing 189 n n C2 C3 GOL sing 190 n n C2 H2 GOL sing 191 n n O2 HO2 GOL sing 192 n n C3 O3 GOL sing 193 n n C3 H31 GOL sing 194 n n C3 H32 GOL sing 195 n n O3 HO3 GOL sing 196 n n # _atom_sites.entry_id 4Y5B _atom_sites.fract_transf_matrix[1][1] 0.022024 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007792 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013682 _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] 0.020104 _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 3 47P A 1 403 403 47P 47P . E 3 47P A 1 404 404 47P 47P . F 3 47P A 1 405 405 47P 47P . G 4 DMS A 1 406 406 DMS DMS . H 5 ACT A 1 407 407 ACT ACT . I 5 ACT A 1 408 408 ACT ACT . J 6 HOH A 1 501 501 HOH HOH . J 6 HOH A 2 515 515 HOH HOH . J 6 HOH A 3 569 569 HOH HOH . J 6 HOH A 4 582 582 HOH HOH . J 6 HOH A 5 588 588 HOH HOH . J 6 HOH A 6 589 589 HOH HOH . J 6 HOH A 7 612 612 HOH HOH . J 6 HOH A 8 621 621 HOH HOH . J 6 HOH A 9 629 629 HOH HOH . J 6 HOH A 10 638 638 HOH HOH . J 6 HOH A 11 645 645 HOH HOH . J 6 HOH A 12 677 677 HOH HOH . J 6 HOH A 13 678 678 HOH HOH . J 6 HOH A 14 686 686 HOH HOH . J 6 HOH A 15 690 690 HOH HOH . J 6 HOH A 16 708 708 HOH HOH . J 6 HOH A 17 731 731 HOH HOH . J 6 HOH A 18 733 733 HOH HOH . J 6 HOH A 19 738 738 HOH HOH . J 6 HOH A 20 744 744 HOH HOH . J 6 HOH A 21 747 747 HOH HOH . J 6 HOH A 22 748 748 HOH HOH . J 6 HOH A 23 760 760 HOH HOH . J 6 HOH A 24 775 775 HOH HOH . J 6 HOH A 25 786 786 HOH HOH . J 6 HOH A 26 798 798 HOH HOH . J 6 HOH A 27 804 804 HOH HOH . J 6 HOH A 28 807 807 HOH HOH . J 6 HOH A 29 813 813 HOH HOH . J 6 HOH A 30 817 817 HOH HOH . J 6 HOH A 31 819 819 HOH HOH . J 6 HOH A 32 826 826 HOH HOH . J 6 HOH A 33 830 830 HOH HOH . J 6 HOH A 34 835 835 HOH HOH . J 6 HOH A 35 852 852 HOH HOH . J 6 HOH A 36 858 858 HOH HOH . J 6 HOH A 37 864 864 HOH HOH . J 6 HOH A 38 867 867 HOH HOH . J 6 HOH A 39 877 877 HOH HOH . J 6 HOH A 40 881 881 HOH HOH . J 6 HOH A 41 883 883 HOH HOH . J 6 HOH A 42 895 895 HOH HOH . J 6 HOH A 43 896 896 HOH HOH . J 6 HOH A 44 897 897 HOH HOH . J 6 HOH A 45 905 905 HOH HOH . J 6 HOH A 46 925 925 HOH HOH . J 6 HOH A 47 932 932 HOH HOH . J 6 HOH A 48 938 938 HOH HOH . J 6 HOH A 49 948 948 HOH HOH . J 6 HOH A 50 955 955 HOH HOH . J 6 HOH A 51 957 957 HOH HOH . J 6 HOH A 52 959 959 HOH HOH . J 6 HOH A 53 971 971 HOH HOH . J 6 HOH A 54 978 978 HOH HOH . J 6 HOH A 55 988 988 HOH HOH . J 6 HOH A 56 992 992 HOH HOH . J 6 HOH A 57 995 995 HOH HOH . J 6 HOH A 58 996 996 HOH HOH . J 6 HOH A 59 1005 1005 HOH HOH . J 6 HOH A 60 1010 1010 HOH HOH . J 6 HOH A 61 1014 1014 HOH HOH . J 6 HOH A 62 1015 1015 HOH HOH . J 6 HOH A 63 1026 1026 HOH HOH . J 6 HOH A 64 1038 1038 HOH HOH . J 6 HOH A 65 1058 1058 HOH HOH . J 6 HOH A 66 1070 1070 HOH HOH . J 6 HOH A 67 1071 1071 HOH HOH . J 6 HOH A 68 1079 1079 HOH HOH . J 6 HOH A 69 1081 1081 HOH HOH . J 6 HOH A 70 1089 1089 HOH HOH . J 6 HOH A 71 1092 1092 HOH HOH . J 6 HOH A 72 1095 1095 HOH HOH . J 6 HOH A 73 1096 1096 HOH HOH . J 6 HOH A 74 1107 1107 HOH HOH . J 6 HOH A 75 1110 1110 HOH HOH . J 6 HOH A 76 1111 1111 HOH HOH . J 6 HOH A 77 1115 1115 HOH HOH . J 6 HOH A 78 1116 1116 HOH HOH . J 6 HOH A 79 1124 1124 HOH HOH . J 6 HOH A 80 1125 1125 HOH HOH . J 6 HOH A 81 1149 1149 HOH HOH . J 6 HOH A 82 1161 1161 HOH HOH . J 6 HOH A 83 1167 1167 HOH HOH . J 6 HOH A 84 1172 1172 HOH HOH . J 6 HOH A 85 1173 1173 HOH HOH . J 6 HOH A 86 1180 1180 HOH HOH . J 6 HOH A 87 1190 1190 HOH HOH . J 6 HOH A 88 1207 1207 HOH HOH . J 6 HOH A 89 1210 1210 HOH HOH . J 6 HOH A 90 1221 1221 HOH HOH . J 6 HOH A 91 1223 1223 HOH HOH . J 6 HOH A 92 1225 1225 HOH HOH . J 6 HOH A 93 1226 1226 HOH HOH . J 6 HOH A 94 1227 1227 HOH HOH . J 6 HOH A 95 1232 1232 HOH HOH . J 6 HOH A 96 1236 1236 HOH HOH . J 6 HOH A 97 1237 1237 HOH HOH . J 6 HOH A 98 1244 1244 HOH HOH . J 6 HOH A 99 1260 1260 HOH HOH . J 6 HOH A 100 1282 1282 HOH HOH . J 6 HOH A 101 1286 1286 HOH HOH . J 6 HOH A 102 1290 1290 HOH HOH . J 6 HOH A 103 1292 1292 HOH HOH . J 6 HOH A 104 1299 1299 HOH HOH . J 6 HOH A 105 1302 1302 HOH HOH . J 6 HOH A 106 1304 1304 HOH HOH . J 6 HOH A 107 1306 1306 HOH HOH . J 6 HOH A 108 1317 1317 HOH HOH . J 6 HOH A 109 1340 1340 HOH HOH . J 6 HOH A 110 1346 1346 HOH HOH . J 6 HOH A 111 1359 1359 HOH HOH . J 6 HOH A 112 1361 1361 HOH HOH . J 6 HOH A 113 1365 1365 HOH HOH . J 6 HOH A 114 1369 1369 HOH HOH . J 6 HOH A 115 1384 1384 HOH HOH . J 6 HOH A 116 1391 1391 HOH HOH . J 6 HOH A 117 1394 1394 HOH HOH . J 6 HOH A 118 1401 1401 HOH HOH . J 6 HOH A 119 1410 1410 HOH HOH . J 6 HOH A 120 1417 1417 HOH HOH . J 6 HOH A 121 1419 1419 HOH HOH . J 6 HOH A 122 1421 1421 HOH HOH . J 6 HOH A 123 1427 1427 HOH HOH . J 6 HOH A 124 1441 1441 HOH HOH . J 6 HOH A 125 1459 1459 HOH HOH . J 6 HOH A 126 1461 1461 HOH HOH . J 6 HOH A 127 1463 1463 HOH HOH . J 6 HOH A 128 1475 1475 HOH HOH . J 6 HOH A 129 1503 1503 HOH HOH . J 6 HOH A 130 1515 1515 HOH HOH . J 6 HOH A 131 1523 1523 HOH HOH . J 6 HOH A 132 1534 1534 HOH HOH . J 6 HOH A 133 1535 1535 HOH HOH . J 6 HOH A 134 1538 1538 HOH HOH . J 6 HOH A 135 1540 1540 HOH HOH . J 6 HOH A 136 1547 1547 HOH HOH . J 6 HOH A 137 1555 1555 HOH HOH . J 6 HOH A 138 1562 1562 HOH HOH . J 6 HOH A 139 1565 1565 HOH HOH . J 6 HOH A 140 1566 1566 HOH HOH . J 6 HOH A 141 1569 1569 HOH HOH . J 6 HOH A 142 1572 1572 HOH HOH . J 6 HOH A 143 1581 1581 HOH HOH . J 6 HOH A 144 1593 1593 HOH HOH . J 6 HOH A 145 1594 1594 HOH HOH . J 6 HOH A 146 1601 1601 HOH HOH . J 6 HOH A 147 1610 1610 HOH HOH . J 6 HOH A 148 1612 1612 HOH HOH . J 6 HOH A 149 1619 1619 HOH HOH . J 6 HOH A 150 1627 1627 HOH HOH . J 6 HOH A 151 1631 1631 HOH HOH . J 6 HOH A 152 1637 1637 HOH HOH . J 6 HOH A 153 1638 1638 HOH HOH . J 6 HOH A 154 1640 1640 HOH HOH . J 6 HOH A 155 1641 1641 HOH HOH . J 6 HOH A 156 1645 1645 HOH HOH . J 6 HOH A 157 1651 1651 HOH HOH . J 6 HOH A 158 1658 1658 HOH HOH . J 6 HOH A 159 1659 1659 HOH HOH . J 6 HOH A 160 1665 1665 HOH HOH . J 6 HOH A 161 1672 1672 HOH HOH . J 6 HOH A 162 1684 1684 HOH HOH . J 6 HOH A 163 1689 1689 HOH HOH . J 6 HOH A 164 1690 1690 HOH HOH . J 6 HOH A 165 1694 1694 HOH HOH . J 6 HOH A 166 1699 1699 HOH HOH . J 6 HOH A 167 1700 1700 HOH HOH . J 6 HOH A 168 1706 1706 HOH HOH . J 6 HOH A 169 1709 1709 HOH HOH . J 6 HOH A 170 1716 1716 HOH HOH . J 6 HOH A 171 1718 1718 HOH HOH . J 6 HOH A 172 1724 1724 HOH HOH . J 6 HOH A 173 1731 1731 HOH HOH . J 6 HOH A 174 1738 1738 HOH HOH . J 6 HOH A 175 1739 1739 HOH HOH . J 6 HOH A 176 1745 1745 HOH HOH . J 6 HOH A 177 1757 1757 HOH HOH . J 6 HOH A 178 1772 1772 HOH HOH . J 6 HOH A 179 1776 1776 HOH HOH . J 6 HOH A 180 1782 1782 HOH HOH . J 6 HOH A 181 1784 1784 HOH HOH . J 6 HOH A 182 1792 1792 HOH HOH . J 6 HOH A 183 1805 1805 HOH HOH . J 6 HOH A 184 1820 1820 HOH HOH . J 6 HOH A 185 1832 1832 HOH HOH . J 6 HOH A 186 1836 1836 HOH HOH . J 6 HOH A 187 1839 1839 HOH HOH . J 6 HOH A 188 1840 1840 HOH HOH . J 6 HOH A 189 1844 1844 HOH HOH . J 6 HOH A 190 1850 1850 HOH HOH . J 6 HOH A 191 1853 1853 HOH HOH . J 6 HOH A 192 1857 1857 HOH HOH . J 6 HOH A 193 1883 1883 HOH HOH . J 6 HOH A 194 1906 1906 HOH HOH . J 6 HOH A 195 1936 1936 HOH HOH . J 6 HOH A 196 1958 1958 HOH HOH . J 6 HOH A 197 1964 1964 HOH HOH . J 6 HOH A 198 1969 1969 HOH HOH . J 6 HOH A 199 1977 1977 HOH HOH . J 6 HOH A 200 1980 1980 HOH HOH . J 6 HOH A 201 1987 1987 HOH HOH . J 6 HOH A 202 1999 1999 HOH HOH . J 6 HOH A 203 2026 2026 HOH HOH . J 6 HOH A 204 2057 2057 HOH HOH . J 6 HOH A 205 2060 2060 HOH HOH . J 6 HOH A 206 2070 2070 HOH HOH . J 6 HOH A 207 2085 2085 HOH HOH . J 6 HOH A 208 2093 2093 HOH HOH . J 6 HOH A 209 2102 2102 HOH HOH . J 6 HOH A 210 2103 2103 HOH HOH . J 6 HOH A 211 2107 2107 HOH HOH . J 6 HOH A 212 2125 2125 HOH HOH . J 6 HOH A 213 2137 2137 HOH HOH . J 6 HOH A 214 2151 2151 HOH HOH . J 6 HOH A 215 2159 2159 HOH HOH . J 6 HOH A 216 2162 2162 HOH HOH . J 6 HOH A 217 2163 2163 HOH HOH . J 6 HOH A 218 2166 2166 HOH HOH . J 6 HOH A 219 2167 2167 HOH HOH . J 6 HOH A 220 2168 2168 HOH HOH . J 6 HOH A 221 2180 2180 HOH HOH . J 6 HOH A 222 2185 2185 HOH HOH . J 6 HOH A 223 2198 2198 HOH HOH . J 6 HOH A 224 2216 2216 HOH HOH . J 6 HOH A 225 2227 2227 HOH HOH . J 6 HOH A 226 2247 2247 HOH HOH . J 6 HOH A 227 2250 2250 HOH HOH . J 6 HOH A 228 2274 2274 HOH HOH . J 6 HOH A 229 2283 2283 HOH HOH . J 6 HOH A 230 2307 2307 HOH HOH . J 6 HOH A 231 2308 2308 HOH HOH . J 6 HOH A 232 2327 2327 HOH HOH . J 6 HOH A 233 2331 2331 HOH HOH . J 6 HOH A 234 2339 2339 HOH HOH . J 6 HOH A 235 2344 2344 HOH HOH . J 6 HOH A 236 2354 2354 HOH HOH . J 6 HOH A 237 2357 2357 HOH HOH . J 6 HOH A 238 2364 2364 HOH HOH . J 6 HOH A 239 2387 2387 HOH HOH . J 6 HOH A 240 2404 2404 HOH HOH . J 6 HOH A 241 2445 2445 HOH HOH . J 6 HOH A 242 2451 2451 HOH HOH . J 6 HOH A 243 2459 2459 HOH HOH . J 6 HOH A 244 2467 2467 HOH HOH . J 6 HOH A 245 2478 2478 HOH HOH . J 6 HOH A 246 2483 2483 HOH HOH . J 6 HOH A 247 2518 2518 HOH HOH . J 6 HOH A 248 2520 2520 HOH HOH . J 6 HOH A 249 2524 2524 HOH HOH . J 6 HOH A 250 2533 2533 HOH HOH . J 6 HOH A 251 2535 2535 HOH HOH . J 6 HOH A 252 2539 2539 HOH HOH . J 6 HOH A 253 2540 2540 HOH HOH . J 6 HOH A 254 2611 2611 HOH HOH . J 6 HOH A 255 2623 2623 HOH HOH . J 6 HOH A 256 2625 2625 HOH HOH . J 6 HOH A 257 2630 2630 HOH HOH . J 6 HOH A 258 2643 2643 HOH HOH . J 6 HOH A 259 2657 2657 HOH HOH . J 6 HOH A 260 2660 2660 HOH HOH . J 6 HOH A 261 2669 2669 HOH HOH . J 6 HOH A 262 2677 2677 HOH HOH . J 6 HOH A 263 2688 2688 HOH HOH . J 6 HOH A 264 2735 2735 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 8.068 -3.581 -11.46 1 18.45 ? C1 GOL 401 A 1 HETATM 2 O O1 GOL . . . B 2 9.089 -2.71 -11.02 1 14.87 ? O1 GOL 401 A 1 HETATM 3 C C2 GOL . . . B 2 6.776 -2.797 -11.684 1 20.38 ? C2 GOL 401 A 1 HETATM 4 O O2 GOL . . . B 2 6.976 -1.838 -12.712 1 20.98 ? O2 GOL 401 A 1 HETATM 5 C C3 GOL . . . B 2 5.641 -3.769 -12.02 1 22.04 ? C3 GOL 401 A 1 HETATM 6 O O3 GOL . . . B 2 5.902 -4.408 -13.251 1 24.57 ? O3 GOL 401 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 6 #