data_5M6D # _model_server_result.job_id qftlp-WXuZNWhauCWMO7-w _model_server_result.datetime_utc '2025-03-05 20:36:37' _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 5m6d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 5M6D # _exptl.entry_id 5M6D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 119.64 _cell.angle_gamma 90 _cell.entry_id 5M6D _cell.length_a 81.041 _cell.length_b 130.237 _cell.length_c 79.837 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M6D _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 41.55771 0 69.390319 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 G N N ? 5 H 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 covale ? covale1 A C SER 170 A SER 170 1_555 A N CSU 171 A CSU 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C CSU 171 A CSU 171 1_555 A N THR 172 A THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 B C SER 170 B SER 170 1_555 B N CSU 171 B CSU 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 B C CSU 171 B CSU 171 1_555 B N THR 172 B THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? metalc ? metalc1 A O ILE 41 A ILE 41 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc2 A O VAL 44 A VAL 44 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc3 A O VAL 47 A VAL 47 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc4 D CA CA . A CA 402 1_555 K O HOH . A HOH 580 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc5 D CA CA . A CA 402 1_555 K O HOH . A HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? # _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 153 n n C1 C2 GOL sing 154 n n C1 H11 GOL sing 155 n n C1 H12 GOL sing 156 n n O1 HO1 GOL sing 157 n n C2 O2 GOL sing 158 n n C2 C3 GOL sing 159 n n C2 H2 GOL sing 160 n n O2 HO2 GOL sing 161 n n C3 O3 GOL sing 162 n n C3 H31 GOL sing 163 n n C3 H32 GOL sing 164 n n O3 HO3 GOL sing 165 n n # _atom_sites.entry_id 5M6D _atom_sites.fract_transf_matrix[1][1] 0.012339 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007022 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007678 _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] 0.014412 _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 CL A 1 401 4 CL CL . D 3 CA A 1 402 5 CA CA . E 4 ACY A 1 403 2 ACY ACY . F 5 GOL B 1 401 1 GOL GOL . G 5 GOL B 1 402 2 GOL GOL . H 5 GOL B 1 403 3 GOL GOL . I 2 CL B 1 404 6 CL CL . J 4 ACY B 1 405 1 ACY ACY . K 6 HOH A 1 501 319 HOH HOH . K 6 HOH A 2 502 185 HOH HOH . K 6 HOH A 3 503 168 HOH HOH . K 6 HOH A 4 504 30 HOH HOH . K 6 HOH A 5 505 70 HOH HOH . K 6 HOH A 6 506 81 HOH HOH . K 6 HOH A 7 507 98 HOH HOH . K 6 HOH A 8 508 112 HOH HOH . K 6 HOH A 9 509 133 HOH HOH . K 6 HOH A 10 510 189 HOH HOH . K 6 HOH A 11 511 4 HOH HOH . K 6 HOH A 12 512 96 HOH HOH . K 6 HOH A 13 513 152 HOH HOH . K 6 HOH A 14 514 87 HOH HOH . K 6 HOH A 15 515 63 HOH HOH . K 6 HOH A 16 516 33 HOH HOH . K 6 HOH A 17 517 71 HOH HOH . K 6 HOH A 18 518 304 HOH HOH . K 6 HOH A 19 519 149 HOH HOH . K 6 HOH A 20 520 48 HOH HOH . K 6 HOH A 21 521 223 HOH HOH . K 6 HOH A 22 522 203 HOH HOH . K 6 HOH A 23 523 91 HOH HOH . K 6 HOH A 24 524 159 HOH HOH . K 6 HOH A 25 525 27 HOH HOH . K 6 HOH A 26 526 269 HOH HOH . K 6 HOH A 27 527 29 HOH HOH . K 6 HOH A 28 528 88 HOH HOH . K 6 HOH A 29 529 84 HOH HOH . K 6 HOH A 30 530 3 HOH HOH . K 6 HOH A 31 531 251 HOH HOH . K 6 HOH A 32 532 247 HOH HOH . K 6 HOH A 33 533 53 HOH HOH . K 6 HOH A 34 534 110 HOH HOH . K 6 HOH A 35 535 320 HOH HOH . K 6 HOH A 36 536 200 HOH HOH . K 6 HOH A 37 537 89 HOH HOH . K 6 HOH A 38 538 49 HOH HOH . K 6 HOH A 39 539 12 HOH HOH . K 6 HOH A 40 540 164 HOH HOH . K 6 HOH A 41 541 255 HOH HOH . K 6 HOH A 42 542 260 HOH HOH . K 6 HOH A 43 543 43 HOH HOH . K 6 HOH A 44 544 314 HOH HOH . K 6 HOH A 45 545 61 HOH HOH . K 6 HOH A 46 546 94 HOH HOH . K 6 HOH A 47 547 188 HOH HOH . K 6 HOH A 48 548 24 HOH HOH . K 6 HOH A 49 549 298 HOH HOH . K 6 HOH A 50 550 121 HOH HOH . K 6 HOH A 51 551 113 HOH HOH . K 6 HOH A 52 552 56 HOH HOH . K 6 HOH A 53 553 83 HOH HOH . K 6 HOH A 54 554 69 HOH HOH . K 6 HOH A 55 555 289 HOH HOH . K 6 HOH A 56 556 18 HOH HOH . K 6 HOH A 57 557 205 HOH HOH . K 6 HOH A 58 558 252 HOH HOH . K 6 HOH A 59 559 40 HOH HOH . K 6 HOH A 60 560 58 HOH HOH . K 6 HOH A 61 561 68 HOH HOH . K 6 HOH A 62 562 316 HOH HOH . K 6 HOH A 63 563 101 HOH HOH . K 6 HOH A 64 564 131 HOH HOH . K 6 HOH A 65 565 282 HOH HOH . K 6 HOH A 66 566 303 HOH HOH . K 6 HOH A 67 567 25 HOH HOH . K 6 HOH A 68 568 210 HOH HOH . K 6 HOH A 69 569 235 HOH HOH . K 6 HOH A 70 570 45 HOH HOH . K 6 HOH A 71 571 15 HOH HOH . K 6 HOH A 72 572 195 HOH HOH . K 6 HOH A 73 573 76 HOH HOH . K 6 HOH A 74 574 39 HOH HOH . K 6 HOH A 75 575 92 HOH HOH . K 6 HOH A 76 576 11 HOH HOH . K 6 HOH A 77 577 32 HOH HOH . K 6 HOH A 78 578 120 HOH HOH . K 6 HOH A 79 579 212 HOH HOH . K 6 HOH A 80 580 144 HOH HOH . K 6 HOH A 81 581 42 HOH HOH . K 6 HOH A 82 582 249 HOH HOH . K 6 HOH A 83 583 82 HOH HOH . K 6 HOH A 84 584 184 HOH HOH . K 6 HOH A 85 585 52 HOH HOH . K 6 HOH A 86 586 163 HOH HOH . K 6 HOH A 87 587 99 HOH HOH . K 6 HOH A 88 588 38 HOH HOH . K 6 HOH A 89 589 36 HOH HOH . K 6 HOH A 90 590 148 HOH HOH . K 6 HOH A 91 591 72 HOH HOH . K 6 HOH A 92 592 115 HOH HOH . K 6 HOH A 93 593 238 HOH HOH . K 6 HOH A 94 594 176 HOH HOH . K 6 HOH A 95 595 74 HOH HOH . K 6 HOH A 96 596 132 HOH HOH . K 6 HOH A 97 597 196 HOH HOH . K 6 HOH A 98 598 280 HOH HOH . K 6 HOH A 99 599 67 HOH HOH . K 6 HOH A 100 600 129 HOH HOH . K 6 HOH A 101 601 306 HOH HOH . K 6 HOH A 102 602 309 HOH HOH . K 6 HOH A 103 603 213 HOH HOH . K 6 HOH A 104 604 145 HOH HOH . K 6 HOH A 105 605 259 HOH HOH . K 6 HOH A 106 606 117 HOH HOH . K 6 HOH A 107 607 263 HOH HOH . K 6 HOH A 108 608 216 HOH HOH . K 6 HOH A 109 609 73 HOH HOH . K 6 HOH A 110 610 302 HOH HOH . K 6 HOH A 111 611 225 HOH HOH . K 6 HOH A 112 612 14 HOH HOH . K 6 HOH A 113 613 246 HOH HOH . K 6 HOH A 114 614 95 HOH HOH . K 6 HOH A 115 615 124 HOH HOH . K 6 HOH A 116 616 286 HOH HOH . K 6 HOH A 117 617 90 HOH HOH . K 6 HOH A 118 618 141 HOH HOH . K 6 HOH A 119 619 128 HOH HOH . K 6 HOH A 120 620 257 HOH HOH . K 6 HOH A 121 621 226 HOH HOH . K 6 HOH A 122 622 288 HOH HOH . K 6 HOH A 123 623 165 HOH HOH . K 6 HOH A 124 624 180 HOH HOH . K 6 HOH A 125 625 300 HOH HOH . K 6 HOH A 126 626 153 HOH HOH . K 6 HOH A 127 627 206 HOH HOH . K 6 HOH A 128 628 275 HOH HOH . K 6 HOH A 129 629 193 HOH HOH . K 6 HOH A 130 630 295 HOH HOH . K 6 HOH A 131 631 170 HOH HOH . K 6 HOH A 132 632 315 HOH HOH . K 6 HOH A 133 633 266 HOH HOH . K 6 HOH A 134 634 241 HOH HOH . K 6 HOH A 135 635 228 HOH HOH . K 6 HOH A 136 636 136 HOH HOH . K 6 HOH A 137 637 126 HOH HOH . K 6 HOH A 138 638 178 HOH HOH . K 6 HOH A 139 639 217 HOH HOH . K 6 HOH A 140 640 312 HOH HOH . K 6 HOH A 141 641 271 HOH HOH . L 6 HOH B 1 501 294 HOH HOH . L 6 HOH B 2 502 57 HOH HOH . L 6 HOH B 3 503 161 HOH HOH . L 6 HOH B 4 504 123 HOH HOH . L 6 HOH B 5 505 157 HOH HOH . L 6 HOH B 6 506 46 HOH HOH . L 6 HOH B 7 507 7 HOH HOH . L 6 HOH B 8 508 97 HOH HOH . L 6 HOH B 9 509 64 HOH HOH . L 6 HOH B 10 510 119 HOH HOH . L 6 HOH B 11 511 80 HOH HOH . L 6 HOH B 12 512 111 HOH HOH . L 6 HOH B 13 513 16 HOH HOH . L 6 HOH B 14 514 2 HOH HOH . L 6 HOH B 15 515 139 HOH HOH . L 6 HOH B 16 516 103 HOH HOH . L 6 HOH B 17 517 17 HOH HOH . L 6 HOH B 18 518 262 HOH HOH . L 6 HOH B 19 519 138 HOH HOH . L 6 HOH B 20 520 54 HOH HOH . L 6 HOH B 21 521 37 HOH HOH . L 6 HOH B 22 522 297 HOH HOH . L 6 HOH B 23 523 62 HOH HOH . L 6 HOH B 24 524 65 HOH HOH . L 6 HOH B 25 525 59 HOH HOH . L 6 HOH B 26 526 137 HOH HOH . L 6 HOH B 27 527 55 HOH HOH . L 6 HOH B 28 528 108 HOH HOH . L 6 HOH B 29 529 6 HOH HOH . L 6 HOH B 30 530 41 HOH HOH . L 6 HOH B 31 531 28 HOH HOH . L 6 HOH B 32 532 258 HOH HOH . L 6 HOH B 33 533 122 HOH HOH . L 6 HOH B 34 534 77 HOH HOH . L 6 HOH B 35 535 219 HOH HOH . L 6 HOH B 36 536 248 HOH HOH . L 6 HOH B 37 537 102 HOH HOH . L 6 HOH B 38 538 9 HOH HOH . L 6 HOH B 39 539 20 HOH HOH . L 6 HOH B 40 540 177 HOH HOH . L 6 HOH B 41 541 155 HOH HOH . L 6 HOH B 42 542 5 HOH HOH . L 6 HOH B 43 543 270 HOH HOH . L 6 HOH B 44 544 130 HOH HOH . L 6 HOH B 45 545 26 HOH HOH . L 6 HOH B 46 546 186 HOH HOH . L 6 HOH B 47 547 44 HOH HOH . L 6 HOH B 48 548 146 HOH HOH . L 6 HOH B 49 549 34 HOH HOH . L 6 HOH B 50 550 114 HOH HOH . L 6 HOH B 51 551 8 HOH HOH . L 6 HOH B 52 552 107 HOH HOH . L 6 HOH B 53 553 50 HOH HOH . L 6 HOH B 54 554 35 HOH HOH . L 6 HOH B 55 555 21 HOH HOH . L 6 HOH B 56 556 118 HOH HOH . L 6 HOH B 57 557 211 HOH HOH . L 6 HOH B 58 558 51 HOH HOH . L 6 HOH B 59 559 240 HOH HOH . L 6 HOH B 60 560 1 HOH HOH . L 6 HOH B 61 561 272 HOH HOH . L 6 HOH B 62 562 93 HOH HOH . L 6 HOH B 63 563 187 HOH HOH . L 6 HOH B 64 564 31 HOH HOH . L 6 HOH B 65 565 104 HOH HOH . L 6 HOH B 66 566 78 HOH HOH . L 6 HOH B 67 567 305 HOH HOH . L 6 HOH B 68 568 13 HOH HOH . L 6 HOH B 69 569 10 HOH HOH . L 6 HOH B 70 570 109 HOH HOH . L 6 HOH B 71 571 22 HOH HOH . L 6 HOH B 72 572 19 HOH HOH . L 6 HOH B 73 573 47 HOH HOH . L 6 HOH B 74 574 172 HOH HOH . L 6 HOH B 75 575 268 HOH HOH . L 6 HOH B 76 576 66 HOH HOH . L 6 HOH B 77 577 75 HOH HOH . L 6 HOH B 78 578 116 HOH HOH . L 6 HOH B 79 579 160 HOH HOH . L 6 HOH B 80 580 135 HOH HOH . L 6 HOH B 81 581 290 HOH HOH . L 6 HOH B 82 582 60 HOH HOH . L 6 HOH B 83 583 291 HOH HOH . L 6 HOH B 84 584 318 HOH HOH . L 6 HOH B 85 585 214 HOH HOH . L 6 HOH B 86 586 285 HOH HOH . L 6 HOH B 87 587 281 HOH HOH . L 6 HOH B 88 588 308 HOH HOH . L 6 HOH B 89 589 273 HOH HOH . L 6 HOH B 90 590 197 HOH HOH . L 6 HOH B 91 591 100 HOH HOH . L 6 HOH B 92 592 85 HOH HOH . L 6 HOH B 93 593 293 HOH HOH . L 6 HOH B 94 594 174 HOH HOH . L 6 HOH B 95 595 230 HOH HOH . L 6 HOH B 96 596 143 HOH HOH . L 6 HOH B 97 597 209 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 . . . G 5 20.659 88.183 54.788 1 75.08 ? C1 GOL 402 B 1 HETATM 2 O O1 GOL . . . G 5 20.273 87.971 53.448 1 74.37 ? O1 GOL 402 B 1 HETATM 3 C C2 GOL . . . G 5 22.163 88.018 54.895 1 76.05 ? C2 GOL 402 B 1 HETATM 4 O O2 GOL . . . G 5 22.786 89.234 55.237 1 76.28 ? O2 GOL 402 B 1 HETATM 5 C C3 GOL . . . G 5 22.519 86.93 55.902 1 76.54 ? C3 GOL 402 B 1 HETATM 6 O O3 GOL . . . G 5 23.907 86.957 56.156 1 76.77 ? O3 GOL 402 B 1 HETATM 7 H H11 GOL . . . G 5 20.16 87.463 55.437 1 90.09 ? H11 GOL 402 B 1 HETATM 8 H H12 GOL . . . G 5 20.373 89.186 55.103 1 90.09 ? H12 GOL 402 B 1 HETATM 9 H HO1 GOL . . . G 5 19.296 88.01 53.38 1 89.24 ? HO1 GOL 402 B 1 HETATM 10 H H2 GOL . . . G 5 22.53 87.698 53.919 1 91.26 ? H2 GOL 402 B 1 HETATM 11 H HO2 GOL . . . G 5 22.496 89.509 56.132 1 91.53 ? HO2 GOL 402 B 1 HETATM 12 H H31 GOL . . . G 5 22.236 85.954 55.506 1 91.85 ? H31 GOL 402 B 1 HETATM 13 H H32 GOL . . . G 5 21.972 87.093 56.83 1 91.85 ? H32 GOL 402 B 1 HETATM 14 H HO3 GOL . . . G 5 24.082 86.595 57.049 1 92.12 ? HO3 GOL 402 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #