data_5DBH # _model_server_result.job_id Hnzt9FY9sBIVGRBPpDsH2g _model_server_result.datetime_utc '2025-07-27 04:46:10' _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 5dbh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5DBH # _exptl.entry_id 5DBH _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 1 _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 5DBH _cell.length_a 112.66 _cell.length_b 112.66 _cell.length_c 43.369 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DBH _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _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 _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' 6_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 163 n n C1 C2 GOL sing 164 n n C1 H11 GOL sing 165 n n C1 H12 GOL sing 166 n n O1 HO1 GOL sing 167 n n C2 O2 GOL sing 168 n n C2 C3 GOL sing 169 n n C2 H2 GOL sing 170 n n O2 HO2 GOL sing 171 n n C3 O3 GOL sing 172 n n C3 H31 GOL sing 173 n n C3 H32 GOL sing 174 n n O3 HO3 GOL sing 175 n n # _atom_sites.entry_id 5DBH _atom_sites.fract_transf_matrix[1][1] 0.008876 _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] 0.008876 _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] 0.023058 _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 X 1 401 402 GOL GOL . C 3 0JO X 1 402 1 0JO P1T . D 4 HOH X 1 501 502 HOH HOH . D 4 HOH X 2 502 551 HOH HOH . D 4 HOH X 3 503 554 HOH HOH . D 4 HOH X 4 504 531 HOH HOH . D 4 HOH X 5 505 591 HOH HOH . D 4 HOH X 6 506 544 HOH HOH . D 4 HOH X 7 507 584 HOH HOH . D 4 HOH X 8 508 593 HOH HOH . D 4 HOH X 9 509 508 HOH HOH . D 4 HOH X 10 510 576 HOH HOH . D 4 HOH X 11 511 523 HOH HOH . D 4 HOH X 12 512 543 HOH HOH . D 4 HOH X 13 513 570 HOH HOH . D 4 HOH X 14 514 555 HOH HOH . D 4 HOH X 15 515 548 HOH HOH . D 4 HOH X 16 516 524 HOH HOH . D 4 HOH X 17 517 536 HOH HOH . D 4 HOH X 18 518 542 HOH HOH . D 4 HOH X 19 519 545 HOH HOH . D 4 HOH X 20 520 566 HOH HOH . D 4 HOH X 21 521 515 HOH HOH . D 4 HOH X 22 522 560 HOH HOH . D 4 HOH X 23 523 505 HOH HOH . D 4 HOH X 24 524 514 HOH HOH . D 4 HOH X 25 525 541 HOH HOH . D 4 HOH X 26 526 567 HOH HOH . D 4 HOH X 27 527 503 HOH HOH . D 4 HOH X 28 528 516 HOH HOH . D 4 HOH X 29 529 530 HOH HOH . D 4 HOH X 30 530 552 HOH HOH . D 4 HOH X 31 531 525 HOH HOH . D 4 HOH X 32 532 569 HOH HOH . D 4 HOH X 33 533 553 HOH HOH . D 4 HOH X 34 534 558 HOH HOH . D 4 HOH X 35 535 583 HOH HOH . D 4 HOH X 36 536 556 HOH HOH . D 4 HOH X 37 537 528 HOH HOH . D 4 HOH X 38 538 527 HOH HOH . D 4 HOH X 39 539 549 HOH HOH . D 4 HOH X 40 540 550 HOH HOH . D 4 HOH X 41 541 580 HOH HOH . D 4 HOH X 42 542 511 HOH HOH . D 4 HOH X 43 543 504 HOH HOH . D 4 HOH X 44 544 572 HOH HOH . D 4 HOH X 45 545 587 HOH HOH . D 4 HOH X 46 546 512 HOH HOH . D 4 HOH X 47 547 540 HOH HOH . D 4 HOH X 48 548 501 HOH HOH . D 4 HOH X 49 549 575 HOH HOH . D 4 HOH X 50 550 563 HOH HOH . D 4 HOH X 51 551 537 HOH HOH . D 4 HOH X 52 552 571 HOH HOH . D 4 HOH X 53 553 519 HOH HOH . D 4 HOH X 54 554 509 HOH HOH . D 4 HOH X 55 555 529 HOH HOH . D 4 HOH X 56 556 532 HOH HOH . D 4 HOH X 57 557 564 HOH HOH . D 4 HOH X 58 558 535 HOH HOH . D 4 HOH X 59 559 592 HOH HOH . D 4 HOH X 60 560 585 HOH HOH . D 4 HOH X 61 561 517 HOH HOH . D 4 HOH X 62 562 513 HOH HOH . D 4 HOH X 63 563 506 HOH HOH . D 4 HOH X 64 564 538 HOH HOH . D 4 HOH X 65 565 582 HOH HOH . D 4 HOH X 66 566 539 HOH HOH . D 4 HOH X 67 567 510 HOH HOH . D 4 HOH X 68 568 518 HOH HOH . D 4 HOH X 69 569 526 HOH HOH . D 4 HOH X 70 570 581 HOH HOH . D 4 HOH X 71 571 578 HOH HOH . D 4 HOH X 72 572 520 HOH HOH . D 4 HOH X 73 573 534 HOH HOH . D 4 HOH X 74 574 562 HOH HOH . D 4 HOH X 75 575 573 HOH HOH . D 4 HOH X 76 576 522 HOH HOH . D 4 HOH X 77 577 546 HOH HOH . D 4 HOH X 78 578 574 HOH HOH . D 4 HOH X 79 579 507 HOH HOH . D 4 HOH X 80 580 559 HOH HOH . D 4 HOH X 81 581 579 HOH HOH . D 4 HOH X 82 582 533 HOH HOH . D 4 HOH X 83 583 521 HOH HOH . D 4 HOH X 84 584 577 HOH HOH . D 4 HOH X 85 585 590 HOH HOH . D 4 HOH X 86 586 568 HOH HOH . D 4 HOH X 87 587 588 HOH HOH . D 4 HOH X 88 588 547 HOH HOH . D 4 HOH X 89 589 557 HOH HOH . D 4 HOH X 90 590 586 HOH HOH . D 4 HOH X 91 591 561 HOH HOH . D 4 HOH X 92 592 589 HOH HOH . D 4 HOH X 93 593 565 HOH HOH . D 4 HOH X 94 594 1 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 -14.663 -22.013 0.125 1 30.12 ? C1 GOL 401 X 1 HETATM 2 O O1 GOL . . . B 2 -15.186 -22.66 -1.018 1 29.32 ? O1 GOL 401 X 1 HETATM 3 C C2 GOL . . . B 2 -14.371 -23.04 1.216 1 31.82 ? C2 GOL 401 X 1 HETATM 4 O O2 GOL . . . B 2 -13.329 -23.876 0.773 1 32.12 ? O2 GOL 401 X 1 HETATM 5 C C3 GOL . . . B 2 -13.912 -22.308 2.473 1 32.05 ? C3 GOL 401 X 1 HETATM 6 O O3 GOL . . . B 2 -15.013 -21.724 3.144 1 27.16 ? O3 GOL 401 X 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #