data_4YD5
#
_model_server_result.job_id            LRE8aXK6XYb6rexMBQpVWw 
_model_server_result.datetime_utc      '2024-11-28 00:52:57' 
_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          4yd5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":404}' 
#
_entry.id    4YD5 
#
_exptl.entry_id    4YD5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          109.27 
_cell.angle_gamma         90 
_cell.entry_id            4YD5 
_cell.length_a            45.326 
_cell.length_b            72.966 
_cell.length_c            52.673 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YD5 
_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,L 
_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
? 4 E N N 
? 4 F N N 
? 4 G N N 
? 4 H N N 
? 4 I 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                2.039 
_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 166 n n 
C1 C2 GOL sing 167 n n 
C1 H11 GOL sing 168 n n 
C1 H12 GOL sing 169 n n 
O1 HO1 GOL sing 170 n n 
C2 O2 GOL sing 171 n n 
C2 C3 GOL sing 172 n n 
C2 H2 GOL sing 173 n n 
O2 HO2 GOL sing 174 n n 
C3 O3 GOL sing 175 n n 
C3 H31 GOL sing 176 n n 
C3 H32 GOL sing 177 n n 
O3 HO3 GOL sing 178 n n 
#
_atom_sites.entry_id                     4YD5 
_atom_sites.fract_transf_matrix[1][1]    0.022062 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.007714 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013705 
_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]    0.020112 
_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 4AV A 1 401 401 4AV 4AV . 
C 3 DMS A 1 402 402 DMS DMS . 
D 3 DMS A 1 403 403 DMS DMS . 
E 4 GOL A 1 404 404 GOL GOL . 
F 4 GOL A 1 405 405 GOL GOL . 
G 4 GOL A 1 406 406 GOL GOL . 
H 4 GOL A 1 407 407 GOL GOL . 
I 4 GOL A 1 408 408 GOL GOL . 
J 5 ACT A 1 409 409 ACT ACT . 
K 5 ACT A 1 410 410 ACT ACT . 
L 6 HOH A 1 531 531 HOH HOH . 
L 6 HOH A 2 569 569 HOH HOH . 
L 6 HOH A 3 582 582 HOH HOH . 
L 6 HOH A 4 588 588 HOH HOH . 
L 6 HOH A 5 589 589 HOH HOH . 
L 6 HOH A 6 612 612 HOH HOH . 
L 6 HOH A 7 621 621 HOH HOH . 
L 6 HOH A 8 629 629 HOH HOH . 
L 6 HOH A 9 638 638 HOH HOH . 
L 6 HOH A 10 677 677 HOH HOH . 
L 6 HOH A 11 678 678 HOH HOH . 
L 6 HOH A 12 686 686 HOH HOH . 
L 6 HOH A 13 690 690 HOH HOH . 
L 6 HOH A 14 697 697 HOH HOH . 
L 6 HOH A 15 731 731 HOH HOH . 
L 6 HOH A 16 733 733 HOH HOH . 
L 6 HOH A 17 738 738 HOH HOH . 
L 6 HOH A 18 744 744 HOH HOH . 
L 6 HOH A 19 747 747 HOH HOH . 
L 6 HOH A 20 748 748 HOH HOH . 
L 6 HOH A 21 760 760 HOH HOH . 
L 6 HOH A 22 775 775 HOH HOH . 
L 6 HOH A 23 786 786 HOH HOH . 
L 6 HOH A 24 787 787 HOH HOH . 
L 6 HOH A 25 798 798 HOH HOH . 
L 6 HOH A 26 804 804 HOH HOH . 
L 6 HOH A 27 807 807 HOH HOH . 
L 6 HOH A 28 813 813 HOH HOH . 
L 6 HOH A 29 819 819 HOH HOH . 
L 6 HOH A 30 826 826 HOH HOH . 
L 6 HOH A 31 830 830 HOH HOH . 
L 6 HOH A 32 835 835 HOH HOH . 
L 6 HOH A 33 864 864 HOH HOH . 
L 6 HOH A 34 867 867 HOH HOH . 
L 6 HOH A 35 877 877 HOH HOH . 
L 6 HOH A 36 883 883 HOH HOH . 
L 6 HOH A 37 895 895 HOH HOH . 
L 6 HOH A 38 896 896 HOH HOH . 
L 6 HOH A 39 897 897 HOH HOH . 
L 6 HOH A 40 905 905 HOH HOH . 
L 6 HOH A 41 925 925 HOH HOH . 
L 6 HOH A 42 932 932 HOH HOH . 
L 6 HOH A 43 938 938 HOH HOH . 
L 6 HOH A 44 948 948 HOH HOH . 
L 6 HOH A 45 955 955 HOH HOH . 
L 6 HOH A 46 957 957 HOH HOH . 
L 6 HOH A 47 959 959 HOH HOH . 
L 6 HOH A 48 971 971 HOH HOH . 
L 6 HOH A 49 978 978 HOH HOH . 
L 6 HOH A 50 988 988 HOH HOH . 
L 6 HOH A 51 992 992 HOH HOH . 
L 6 HOH A 52 996 996 HOH HOH . 
L 6 HOH A 53 1005 1005 HOH HOH . 
L 6 HOH A 54 1010 1010 HOH HOH . 
L 6 HOH A 55 1014 1014 HOH HOH . 
L 6 HOH A 56 1038 1038 HOH HOH . 
L 6 HOH A 57 1058 1058 HOH HOH . 
L 6 HOH A 58 1070 1070 HOH HOH . 
L 6 HOH A 59 1071 1071 HOH HOH . 
L 6 HOH A 60 1079 1079 HOH HOH . 
L 6 HOH A 61 1081 1081 HOH HOH . 
L 6 HOH A 62 1086 1086 HOH HOH . 
L 6 HOH A 63 1089 1089 HOH HOH . 
L 6 HOH A 64 1092 1092 HOH HOH . 
L 6 HOH A 65 1095 1095 HOH HOH . 
L 6 HOH A 66 1107 1107 HOH HOH . 
L 6 HOH A 67 1110 1110 HOH HOH . 
L 6 HOH A 68 1111 1111 HOH HOH . 
L 6 HOH A 69 1115 1115 HOH HOH . 
L 6 HOH A 70 1118 1118 HOH HOH . 
L 6 HOH A 71 1124 1124 HOH HOH . 
L 6 HOH A 72 1125 1125 HOH HOH . 
L 6 HOH A 73 1149 1149 HOH HOH . 
L 6 HOH A 74 1167 1167 HOH HOH . 
L 6 HOH A 75 1172 1172 HOH HOH . 
L 6 HOH A 76 1173 1173 HOH HOH . 
L 6 HOH A 77 1180 1180 HOH HOH . 
L 6 HOH A 78 1188 1188 HOH HOH . 
L 6 HOH A 79 1190 1190 HOH HOH . 
L 6 HOH A 80 1207 1207 HOH HOH . 
L 6 HOH A 81 1210 1210 HOH HOH . 
L 6 HOH A 82 1219 1219 HOH HOH . 
L 6 HOH A 83 1223 1223 HOH HOH . 
L 6 HOH A 84 1226 1226 HOH HOH . 
L 6 HOH A 85 1232 1232 HOH HOH . 
L 6 HOH A 86 1236 1236 HOH HOH . 
L 6 HOH A 87 1237 1237 HOH HOH . 
L 6 HOH A 88 1239 1239 HOH HOH . 
L 6 HOH A 89 1244 1244 HOH HOH . 
L 6 HOH A 90 1260 1260 HOH HOH . 
L 6 HOH A 91 1282 1282 HOH HOH . 
L 6 HOH A 92 1286 1286 HOH HOH . 
L 6 HOH A 93 1290 1290 HOH HOH . 
L 6 HOH A 94 1292 1292 HOH HOH . 
L 6 HOH A 95 1299 1299 HOH HOH . 
L 6 HOH A 96 1304 1304 HOH HOH . 
L 6 HOH A 97 1306 1306 HOH HOH . 
L 6 HOH A 98 1316 1316 HOH HOH . 
L 6 HOH A 99 1317 1317 HOH HOH . 
L 6 HOH A 100 1329 1329 HOH HOH . 
L 6 HOH A 101 1340 1340 HOH HOH . 
L 6 HOH A 102 1345 1345 HOH HOH . 
L 6 HOH A 103 1346 1346 HOH HOH . 
L 6 HOH A 104 1359 1359 HOH HOH . 
L 6 HOH A 105 1365 1365 HOH HOH . 
L 6 HOH A 106 1369 1369 HOH HOH . 
L 6 HOH A 107 1384 1384 HOH HOH . 
L 6 HOH A 108 1385 1385 HOH HOH . 
L 6 HOH A 109 1392 1392 HOH HOH . 
L 6 HOH A 110 1394 1394 HOH HOH . 
L 6 HOH A 111 1401 1401 HOH HOH . 
L 6 HOH A 112 1410 1410 HOH HOH . 
L 6 HOH A 113 1417 1417 HOH HOH . 
L 6 HOH A 114 1421 1421 HOH HOH . 
L 6 HOH A 115 1427 1427 HOH HOH . 
L 6 HOH A 116 1441 1441 HOH HOH . 
L 6 HOH A 117 1447 1447 HOH HOH . 
L 6 HOH A 118 1459 1459 HOH HOH . 
L 6 HOH A 119 1460 1460 HOH HOH . 
L 6 HOH A 120 1461 1461 HOH HOH . 
L 6 HOH A 121 1463 1463 HOH HOH . 
L 6 HOH A 122 1475 1475 HOH HOH . 
L 6 HOH A 123 1515 1515 HOH HOH . 
L 6 HOH A 124 1534 1534 HOH HOH . 
L 6 HOH A 125 1535 1535 HOH HOH . 
L 6 HOH A 126 1538 1538 HOH HOH . 
L 6 HOH A 127 1540 1540 HOH HOH . 
L 6 HOH A 128 1562 1562 HOH HOH . 
L 6 HOH A 129 1566 1566 HOH HOH . 
L 6 HOH A 130 1572 1572 HOH HOH . 
L 6 HOH A 131 1581 1581 HOH HOH . 
L 6 HOH A 132 1593 1593 HOH HOH . 
L 6 HOH A 133 1594 1594 HOH HOH . 
L 6 HOH A 134 1610 1610 HOH HOH . 
L 6 HOH A 135 1612 1612 HOH HOH . 
L 6 HOH A 136 1627 1627 HOH HOH . 
L 6 HOH A 137 1633 1633 HOH HOH . 
L 6 HOH A 138 1637 1637 HOH HOH . 
L 6 HOH A 139 1638 1638 HOH HOH . 
L 6 HOH A 140 1640 1640 HOH HOH . 
L 6 HOH A 141 1645 1645 HOH HOH . 
L 6 HOH A 142 1651 1651 HOH HOH . 
L 6 HOH A 143 1658 1658 HOH HOH . 
L 6 HOH A 144 1683 1683 HOH HOH . 
L 6 HOH A 145 1689 1689 HOH HOH . 
L 6 HOH A 146 1690 1690 HOH HOH . 
L 6 HOH A 147 1706 1706 HOH HOH . 
L 6 HOH A 148 1709 1709 HOH HOH . 
L 6 HOH A 149 1718 1718 HOH HOH . 
L 6 HOH A 150 1731 1731 HOH HOH . 
L 6 HOH A 151 1739 1739 HOH HOH . 
L 6 HOH A 152 1745 1745 HOH HOH . 
L 6 HOH A 153 1757 1757 HOH HOH . 
L 6 HOH A 154 1772 1772 HOH HOH . 
L 6 HOH A 155 1776 1776 HOH HOH . 
L 6 HOH A 156 1782 1782 HOH HOH . 
L 6 HOH A 157 1784 1784 HOH HOH . 
L 6 HOH A 158 1792 1792 HOH HOH . 
L 6 HOH A 159 1805 1805 HOH HOH . 
L 6 HOH A 160 1820 1820 HOH HOH . 
L 6 HOH A 161 1832 1832 HOH HOH . 
L 6 HOH A 162 1839 1839 HOH HOH . 
L 6 HOH A 163 1840 1840 HOH HOH . 
L 6 HOH A 164 1844 1844 HOH HOH . 
L 6 HOH A 165 1846 1846 HOH HOH . 
L 6 HOH A 166 1851 1851 HOH HOH . 
L 6 HOH A 167 1853 1853 HOH HOH . 
L 6 HOH A 168 1883 1883 HOH HOH . 
L 6 HOH A 169 1894 1894 HOH HOH . 
L 6 HOH A 170 1906 1906 HOH HOH . 
L 6 HOH A 171 1954 1954 HOH HOH . 
L 6 HOH A 172 1971 1971 HOH HOH . 
L 6 HOH A 173 1977 1977 HOH HOH . 
L 6 HOH A 174 1980 1980 HOH HOH . 
L 6 HOH A 175 1987 1987 HOH HOH . 
L 6 HOH A 176 1999 1999 HOH HOH . 
L 6 HOH A 177 2026 2026 HOH HOH . 
L 6 HOH A 178 2041 2041 HOH HOH . 
L 6 HOH A 179 2057 2057 HOH HOH . 
L 6 HOH A 180 2060 2060 HOH HOH . 
L 6 HOH A 181 2073 2073 HOH HOH . 
L 6 HOH A 182 2085 2085 HOH HOH . 
L 6 HOH A 183 2093 2093 HOH HOH . 
L 6 HOH A 184 2095 2095 HOH HOH . 
L 6 HOH A 185 2102 2102 HOH HOH . 
L 6 HOH A 186 2107 2107 HOH HOH . 
L 6 HOH A 187 2110 2110 HOH HOH . 
L 6 HOH A 188 2137 2137 HOH HOH . 
L 6 HOH A 189 2159 2159 HOH HOH . 
L 6 HOH A 190 2162 2162 HOH HOH . 
L 6 HOH A 191 2163 2163 HOH HOH . 
L 6 HOH A 192 2166 2166 HOH HOH . 
L 6 HOH A 193 2167 2167 HOH HOH . 
L 6 HOH A 194 2180 2180 HOH HOH . 
L 6 HOH A 195 2198 2198 HOH HOH . 
L 6 HOH A 196 2216 2216 HOH HOH . 
L 6 HOH A 197 2227 2227 HOH HOH . 
L 6 HOH A 198 2247 2247 HOH HOH . 
L 6 HOH A 199 2274 2274 HOH HOH . 
L 6 HOH A 200 2283 2283 HOH HOH . 
L 6 HOH A 201 2307 2307 HOH HOH . 
L 6 HOH A 202 2308 2308 HOH HOH . 
L 6 HOH A 203 2327 2327 HOH HOH . 
L 6 HOH A 204 2330 2330 HOH HOH . 
L 6 HOH A 205 2331 2331 HOH HOH . 
L 6 HOH A 206 2339 2339 HOH HOH . 
L 6 HOH A 207 2344 2344 HOH HOH . 
L 6 HOH A 208 2354 2354 HOH HOH . 
L 6 HOH A 209 2355 2355 HOH HOH . 
L 6 HOH A 210 2357 2357 HOH HOH . 
L 6 HOH A 211 2364 2364 HOH HOH . 
L 6 HOH A 212 2445 2445 HOH HOH . 
L 6 HOH A 213 2451 2451 HOH HOH . 
L 6 HOH A 214 2459 2459 HOH HOH . 
L 6 HOH A 215 2467 2467 HOH HOH . 
L 6 HOH A 216 2483 2483 HOH HOH . 
L 6 HOH A 217 2520 2520 HOH HOH . 
L 6 HOH A 218 2533 2533 HOH HOH . 
L 6 HOH A 219 2535 2535 HOH HOH . 
L 6 HOH A 220 2539 2539 HOH HOH . 
L 6 HOH A 221 2540 2540 HOH HOH . 
L 6 HOH A 222 2611 2611 HOH HOH . 
L 6 HOH A 223 2625 2625 HOH HOH . 
L 6 HOH A 224 2657 2657 HOH HOH . 
L 6 HOH A 225 2660 2660 HOH HOH . 
L 6 HOH A 226 2704 2704 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 . . . E 4 8.07 -2.586 -11.479 0.79 16.01 ? C1 GOL 404 A 1 
HETATM 2 O O1 GOL . . . E 4 9.14 -1.77 -11.027 0.79 13.49 ? O1 GOL 404 A 1 
HETATM 3 C C2 GOL . . . E 4 6.79 -1.774 -11.678 0.79 17.96 ? C2 GOL 404 A 1 
HETATM 4 O O2 GOL . . . E 4 6.981 -0.825 -12.714 0.79 18.56 ? O2 GOL 404 A 1 
HETATM 5 C C3 GOL . . . E 4 5.65 -2.742 -12.003 0.79 19.55 ? C3 GOL 404 A 1 
HETATM 6 O O3 GOL . . . E 4 5.876 -3.395 -13.234 0.79 20.89 ? O3 GOL 404 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           436 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#