data_5K4V # _model_server_result.job_id 80pNUIGZXKx27xMPAw1-Uw _model_server_result.datetime_utc '2024-12-02 20:50:34' _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 5k4v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":1406}' # _entry.id 5K4V # _exptl.entry_id 5K4V _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 8 _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 90 _cell.entry_id 5K4V _cell.length_a 90.399 _cell.length_b 131.53 _cell.length_c 55.02 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K4V _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,M,N,O,P,Q,R,S,T,U,V,W,X _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 J N N ? 4 K N N ? 4 L N N ? 4 Q N N ? 4 R N N ? 4 S N N ? 4 T N N ? 4 U 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 metalc ? metalc1 A OD1 ASP 186 A ASP 1187 1_555 M NA NA . A NA 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc2 M NA NA . A NA 1411 1_555 W O HOH . A HOH 1523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc3 M NA NA . A NA 1411 1_555 W O HOH . A HOH 1540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? metalc ? metalc4 B OD1 ASP 186 C ASP 1187 1_555 V NA NA . C NA 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc5 V NA NA . C NA 1409 1_555 X O HOH . C HOH 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.017 ? metalc ? metalc6 V NA NA . C NA 1409 1_555 X O HOH . C HOH 1530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? # _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 135 n n C1 C2 GOL sing 136 n n C1 H11 GOL sing 137 n n C1 H12 GOL sing 138 n n O1 HO1 GOL sing 139 n n C2 O2 GOL sing 140 n n C2 C3 GOL sing 141 n n C2 H2 GOL sing 142 n n O2 HO2 GOL sing 143 n n C3 O3 GOL sing 144 n n C3 H31 GOL sing 145 n n C3 H32 GOL sing 146 n n O3 HO3 GOL sing 147 n n # _atom_sites.entry_id 5K4V _atom_sites.fract_transf_matrix[1][1] 0.011062 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007603 _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] 0.018175 _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 C 2 NAD A 1 1401 1400 NAD NAD . D 3 ACT A 1 1402 5 ACT ACT . E 3 ACT A 1 1403 6 ACT ACT . F 3 ACT A 1 1404 7 ACT ACT . G 3 ACT A 1 1405 9 ACT ACT . H 3 ACT A 1 1406 10 ACT ACT . I 3 ACT A 1 1407 11 ACT ACT . J 4 GOL A 1 1408 1 GOL GOL . K 4 GOL A 1 1409 3 GOL GOL . L 4 GOL A 1 1410 5 GOL GOL . M 5 NA A 1 1411 2 NA NA . N 2 NAD C 1 1401 1400 NAD NAD . O 3 ACT C 1 1402 1 ACT ACT . P 3 ACT C 1 1403 3 ACT ACT . Q 4 GOL C 1 1404 2 GOL GOL . R 4 GOL C 1 1405 4 GOL GOL . S 4 GOL C 1 1406 6 GOL GOL . T 4 GOL C 1 1407 7 GOL GOL . U 4 GOL C 1 1408 8 GOL GOL . V 5 NA C 1 1409 1 NA NA . W 6 HOH A 1 1501 126 HOH HOH . W 6 HOH A 2 1502 429 HOH HOH . W 6 HOH A 3 1503 225 HOH HOH . W 6 HOH A 4 1504 170 HOH HOH . W 6 HOH A 5 1505 120 HOH HOH . W 6 HOH A 6 1506 32 HOH HOH . W 6 HOH A 7 1507 154 HOH HOH . W 6 HOH A 8 1508 192 HOH HOH . W 6 HOH A 9 1509 59 HOH HOH . W 6 HOH A 10 1510 177 HOH HOH . W 6 HOH A 11 1511 127 HOH HOH . W 6 HOH A 12 1512 420 HOH HOH . W 6 HOH A 13 1513 104 HOH HOH . W 6 HOH A 14 1514 182 HOH HOH . W 6 HOH A 15 1515 16 HOH HOH . W 6 HOH A 16 1516 198 HOH HOH . W 6 HOH A 17 1517 284 HOH HOH . W 6 HOH A 18 1518 63 HOH HOH . W 6 HOH A 19 1519 39 HOH HOH . W 6 HOH A 20 1520 223 HOH HOH . W 6 HOH A 21 1521 117 HOH HOH . W 6 HOH A 22 1522 194 HOH HOH . W 6 HOH A 23 1523 3 HOH HOH . W 6 HOH A 24 1524 195 HOH HOH . W 6 HOH A 25 1525 492 HOH HOH . W 6 HOH A 26 1526 34 HOH HOH . W 6 HOH A 27 1527 44 HOH HOH . W 6 HOH A 28 1528 69 HOH HOH . W 6 HOH A 29 1529 26 HOH HOH . W 6 HOH A 30 1530 164 HOH HOH . W 6 HOH A 31 1531 28 HOH HOH . W 6 HOH A 32 1532 60 HOH HOH . W 6 HOH A 33 1533 235 HOH HOH . W 6 HOH A 34 1534 304 HOH HOH . W 6 HOH A 35 1535 14 HOH HOH . W 6 HOH A 36 1536 64 HOH HOH . W 6 HOH A 37 1537 160 HOH HOH . W 6 HOH A 38 1538 41 HOH HOH . W 6 HOH A 39 1539 233 HOH HOH . W 6 HOH A 40 1540 447 HOH HOH . W 6 HOH A 41 1541 169 HOH HOH . W 6 HOH A 42 1542 42 HOH HOH . W 6 HOH A 43 1543 490 HOH HOH . W 6 HOH A 44 1544 317 HOH HOH . W 6 HOH A 45 1545 35 HOH HOH . W 6 HOH A 46 1546 146 HOH HOH . W 6 HOH A 47 1547 150 HOH HOH . W 6 HOH A 48 1548 171 HOH HOH . W 6 HOH A 49 1549 48 HOH HOH . W 6 HOH A 50 1550 145 HOH HOH . W 6 HOH A 51 1551 174 HOH HOH . W 6 HOH A 52 1552 70 HOH HOH . W 6 HOH A 53 1553 62 HOH HOH . W 6 HOH A 54 1554 15 HOH HOH . W 6 HOH A 55 1555 17 HOH HOH . W 6 HOH A 56 1556 115 HOH HOH . W 6 HOH A 57 1557 268 HOH HOH . W 6 HOH A 58 1558 494 HOH HOH . W 6 HOH A 59 1559 413 HOH HOH . W 6 HOH A 60 1560 102 HOH HOH . W 6 HOH A 61 1561 13 HOH HOH . W 6 HOH A 62 1562 51 HOH HOH . W 6 HOH A 63 1563 206 HOH HOH . W 6 HOH A 64 1564 61 HOH HOH . W 6 HOH A 65 1565 495 HOH HOH . W 6 HOH A 66 1566 45 HOH HOH . W 6 HOH A 67 1567 151 HOH HOH . W 6 HOH A 68 1568 433 HOH HOH . W 6 HOH A 69 1569 149 HOH HOH . W 6 HOH A 70 1570 162 HOH HOH . W 6 HOH A 71 1571 167 HOH HOH . W 6 HOH A 72 1572 190 HOH HOH . W 6 HOH A 73 1573 124 HOH HOH . W 6 HOH A 74 1574 232 HOH HOH . W 6 HOH A 75 1575 236 HOH HOH . W 6 HOH A 76 1576 133 HOH HOH . W 6 HOH A 77 1577 243 HOH HOH . W 6 HOH A 78 1578 52 HOH HOH . W 6 HOH A 79 1579 66 HOH HOH . W 6 HOH A 80 1580 152 HOH HOH . W 6 HOH A 81 1581 38 HOH HOH . W 6 HOH A 82 1582 155 HOH HOH . W 6 HOH A 83 1583 25 HOH HOH . W 6 HOH A 84 1584 220 HOH HOH . W 6 HOH A 85 1585 412 HOH HOH . W 6 HOH A 86 1586 37 HOH HOH . W 6 HOH A 87 1587 464 HOH HOH . W 6 HOH A 88 1588 210 HOH HOH . W 6 HOH A 89 1589 200 HOH HOH . W 6 HOH A 90 1590 460 HOH HOH . W 6 HOH A 91 1591 47 HOH HOH . W 6 HOH A 92 1592 156 HOH HOH . W 6 HOH A 93 1593 43 HOH HOH . W 6 HOH A 94 1594 406 HOH HOH . W 6 HOH A 95 1595 157 HOH HOH . W 6 HOH A 96 1596 287 HOH HOH . W 6 HOH A 97 1597 158 HOH HOH . W 6 HOH A 98 1598 218 HOH HOH . W 6 HOH A 99 1599 226 HOH HOH . W 6 HOH A 100 1600 427 HOH HOH . W 6 HOH A 101 1601 203 HOH HOH . W 6 HOH A 102 1602 46 HOH HOH . W 6 HOH A 103 1603 231 HOH HOH . W 6 HOH A 104 1604 424 HOH HOH . W 6 HOH A 105 1605 176 HOH HOH . W 6 HOH A 106 1606 98 HOH HOH . W 6 HOH A 107 1607 199 HOH HOH . W 6 HOH A 108 1608 105 HOH HOH . W 6 HOH A 109 1609 65 HOH HOH . W 6 HOH A 110 1610 142 HOH HOH . W 6 HOH A 111 1611 306 HOH HOH . W 6 HOH A 112 1612 248 HOH HOH . W 6 HOH A 113 1613 386 HOH HOH . W 6 HOH A 114 1614 229 HOH HOH . W 6 HOH A 115 1615 97 HOH HOH . W 6 HOH A 116 1616 50 HOH HOH . W 6 HOH A 117 1617 49 HOH HOH . W 6 HOH A 118 1618 205 HOH HOH . W 6 HOH A 119 1619 136 HOH HOH . W 6 HOH A 120 1620 130 HOH HOH . W 6 HOH A 121 1621 237 HOH HOH . W 6 HOH A 122 1622 197 HOH HOH . X 6 HOH C 1 1501 259 HOH HOH . X 6 HOH C 2 1502 74 HOH HOH . X 6 HOH C 3 1503 312 HOH HOH . X 6 HOH C 4 1504 338 HOH HOH . X 6 HOH C 5 1505 316 HOH HOH . X 6 HOH C 6 1506 82 HOH HOH . X 6 HOH C 7 1507 99 HOH HOH . X 6 HOH C 8 1508 83 HOH HOH . X 6 HOH C 9 1509 309 HOH HOH . X 6 HOH C 10 1510 258 HOH HOH . X 6 HOH C 11 1511 77 HOH HOH . X 6 HOH C 12 1512 12 HOH HOH . X 6 HOH C 13 1513 90 HOH HOH . X 6 HOH C 14 1514 276 HOH HOH . X 6 HOH C 15 1515 96 HOH HOH . X 6 HOH C 16 1516 496 HOH HOH . X 6 HOH C 17 1517 252 HOH HOH . X 6 HOH C 18 1518 95 HOH HOH . X 6 HOH C 19 1519 251 HOH HOH . X 6 HOH C 20 1520 19 HOH HOH . X 6 HOH C 21 1521 92 HOH HOH . X 6 HOH C 22 1522 302 HOH HOH . X 6 HOH C 23 1523 381 HOH HOH . X 6 HOH C 24 1524 368 HOH HOH . X 6 HOH C 25 1525 6 HOH HOH . X 6 HOH C 26 1526 253 HOH HOH . X 6 HOH C 27 1527 191 HOH HOH . X 6 HOH C 28 1528 299 HOH HOH . X 6 HOH C 29 1529 345 HOH HOH . X 6 HOH C 30 1530 7 HOH HOH . X 6 HOH C 31 1531 344 HOH HOH . X 6 HOH C 32 1532 340 HOH HOH . X 6 HOH C 33 1533 76 HOH HOH . X 6 HOH C 34 1534 72 HOH HOH . X 6 HOH C 35 1535 10 HOH HOH . X 6 HOH C 36 1536 80 HOH HOH . X 6 HOH C 37 1537 346 HOH HOH . X 6 HOH C 38 1538 488 HOH HOH . X 6 HOH C 39 1539 18 HOH HOH . X 6 HOH C 40 1540 71 HOH HOH . X 6 HOH C 41 1541 318 HOH HOH . X 6 HOH C 42 1542 325 HOH HOH . X 6 HOH C 43 1543 367 HOH HOH . X 6 HOH C 44 1544 257 HOH HOH . X 6 HOH C 45 1545 266 HOH HOH . X 6 HOH C 46 1546 68 HOH HOH . X 6 HOH C 47 1547 84 HOH HOH . X 6 HOH C 48 1548 351 HOH HOH . X 6 HOH C 49 1549 85 HOH HOH . X 6 HOH C 50 1550 336 HOH HOH . X 6 HOH C 51 1551 270 HOH HOH . X 6 HOH C 52 1552 337 HOH HOH . X 6 HOH C 53 1553 477 HOH HOH . X 6 HOH C 54 1554 86 HOH HOH . X 6 HOH C 55 1555 308 HOH HOH . X 6 HOH C 56 1556 73 HOH HOH . X 6 HOH C 57 1557 93 HOH HOH . X 6 HOH C 58 1558 78 HOH HOH . X 6 HOH C 59 1559 265 HOH HOH . X 6 HOH C 60 1560 392 HOH HOH . X 6 HOH C 61 1561 79 HOH HOH . X 6 HOH C 62 1562 327 HOH HOH . X 6 HOH C 63 1563 394 HOH HOH . X 6 HOH C 64 1564 139 HOH HOH . X 6 HOH C 65 1565 163 HOH HOH . X 6 HOH C 66 1566 475 HOH HOH . X 6 HOH C 67 1567 356 HOH HOH . X 6 HOH C 68 1568 341 HOH HOH . X 6 HOH C 69 1569 349 HOH HOH . X 6 HOH C 70 1570 385 HOH HOH . X 6 HOH C 71 1571 279 HOH HOH . X 6 HOH C 72 1572 315 HOH HOH . X 6 HOH C 73 1573 332 HOH HOH . X 6 HOH C 74 1574 260 HOH HOH . X 6 HOH C 75 1575 440 HOH HOH . X 6 HOH C 76 1576 9 HOH HOH . X 6 HOH C 77 1577 331 HOH HOH . X 6 HOH C 78 1578 314 HOH HOH . X 6 HOH C 79 1579 310 HOH HOH . X 6 HOH C 80 1580 295 HOH HOH . X 6 HOH C 81 1581 487 HOH HOH . X 6 HOH C 82 1582 53 HOH HOH . X 6 HOH C 83 1583 372 HOH HOH . X 6 HOH C 84 1584 91 HOH HOH . X 6 HOH C 85 1585 387 HOH HOH . X 6 HOH C 86 1586 497 HOH HOH . X 6 HOH C 87 1587 380 HOH HOH . X 6 HOH C 88 1588 320 HOH HOH . X 6 HOH C 89 1589 485 HOH HOH . X 6 HOH C 90 1590 364 HOH HOH . X 6 HOH C 91 1591 382 HOH HOH . X 6 HOH C 92 1592 473 HOH HOH . X 6 HOH C 93 1593 267 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 . . . S 4 23.631 31.299 -17 1 47.25 ? C1 GOL 1406 C 1 HETATM 2 O O1 GOL . . . S 4 23.925 29.937 -16.688 1 39.17 ? O1 GOL 1406 C 1 HETATM 3 C C2 GOL . . . S 4 24.671 32.092 -16.234 1 50.22 ? C2 GOL 1406 C 1 HETATM 4 O O2 GOL . . . S 4 24.176 32.323 -14.925 1 55.6 ? O2 GOL 1406 C 1 HETATM 5 C C3 GOL . . . S 4 24.993 33.404 -16.932 1 53.97 ? C3 GOL 1406 C 1 HETATM 6 O O3 GOL . . . S 4 26.328 33.302 -17.488 1 55.96 ? O3 GOL 1406 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #