data_6PDI # _model_server_result.job_id 3bYqcQuYd29XPyV9UHo2IQ _model_server_result.datetime_utc '2025-03-04 15:18:43' _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 6pdi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":504}' # _entry.id 6PDI # _exptl.entry_id 6PDI _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 4 _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 120 _cell.entry_id 6PDI _cell.length_a 96.961 _cell.length_b 96.961 _cell.length_c 80.065 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 D N N ? 4 E N N ? 4 F N N ? 4 G N 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 138 n n C1 C2 GOL sing 139 n n C1 H11 GOL sing 140 n n C1 H12 GOL sing 141 n n O1 HO1 GOL sing 142 n n C2 O2 GOL sing 143 n n C2 C3 GOL sing 144 n n C2 H2 GOL sing 145 n n O2 HO2 GOL sing 146 n n C3 O3 GOL sing 147 n n C3 H31 GOL sing 148 n n C3 H32 GOL sing 149 n n O3 HO3 GOL sing 150 n n # _atom_sites.entry_id 6PDI _atom_sites.fract_transf_matrix[1][1] 0.010313 _atom_sites.fract_transf_matrix[1][2] 0.005954 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011909 _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] 0.01249 _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 3 OCJ A 1 501 501 OCJ UNL . D 4 GOL A 1 502 502 GOL GOL . E 4 GOL A 1 503 503 GOL GOL . F 4 GOL A 1 504 504 GOL GOL . G 4 GOL A 1 505 505 GOL GOL . H 5 EDO A 1 506 506 EDO EDO . I 5 EDO A 1 507 507 EDO EDO . J 6 HOH A 1 601 719 HOH HOH . J 6 HOH A 2 602 734 HOH HOH . J 6 HOH A 3 603 705 HOH HOH . J 6 HOH A 4 604 686 HOH HOH . J 6 HOH A 5 605 654 HOH HOH . J 6 HOH A 6 606 684 HOH HOH . J 6 HOH A 7 607 679 HOH HOH . J 6 HOH A 8 608 687 HOH HOH . J 6 HOH A 9 609 640 HOH HOH . J 6 HOH A 10 610 673 HOH HOH . J 6 HOH A 11 611 678 HOH HOH . J 6 HOH A 12 612 671 HOH HOH . J 6 HOH A 13 613 712 HOH HOH . J 6 HOH A 14 614 728 HOH HOH . J 6 HOH A 15 615 733 HOH HOH . J 6 HOH A 16 616 714 HOH HOH . J 6 HOH A 17 617 680 HOH HOH . J 6 HOH A 18 618 692 HOH HOH . J 6 HOH A 19 619 604 HOH HOH . J 6 HOH A 20 620 731 HOH HOH . J 6 HOH A 21 621 641 HOH HOH . J 6 HOH A 22 622 732 HOH HOH . J 6 HOH A 23 623 636 HOH HOH . J 6 HOH A 24 624 697 HOH HOH . J 6 HOH A 25 625 612 HOH HOH . J 6 HOH A 26 626 688 HOH HOH . J 6 HOH A 27 627 665 HOH HOH . J 6 HOH A 28 628 657 HOH HOH . J 6 HOH A 29 629 730 HOH HOH . J 6 HOH A 30 630 718 HOH HOH . J 6 HOH A 31 631 727 HOH HOH . J 6 HOH A 32 632 683 HOH HOH . J 6 HOH A 33 633 647 HOH HOH . J 6 HOH A 34 634 642 HOH HOH . J 6 HOH A 35 635 634 HOH HOH . J 6 HOH A 36 636 652 HOH HOH . J 6 HOH A 37 637 674 HOH HOH . J 6 HOH A 38 638 607 HOH HOH . J 6 HOH A 39 639 655 HOH HOH . J 6 HOH A 40 640 702 HOH HOH . J 6 HOH A 41 641 742 HOH HOH . J 6 HOH A 42 642 645 HOH HOH . J 6 HOH A 43 643 632 HOH HOH . J 6 HOH A 44 644 704 HOH HOH . J 6 HOH A 45 645 740 HOH HOH . J 6 HOH A 46 646 737 HOH HOH . J 6 HOH A 47 647 691 HOH HOH . J 6 HOH A 48 648 610 HOH HOH . J 6 HOH A 49 649 614 HOH HOH . J 6 HOH A 50 650 615 HOH HOH . J 6 HOH A 51 651 706 HOH HOH . J 6 HOH A 52 652 675 HOH HOH . J 6 HOH A 53 653 635 HOH HOH . J 6 HOH A 54 654 637 HOH HOH . J 6 HOH A 55 655 618 HOH HOH . J 6 HOH A 56 656 628 HOH HOH . J 6 HOH A 57 657 633 HOH HOH . J 6 HOH A 58 658 717 HOH HOH . J 6 HOH A 59 659 723 HOH HOH . J 6 HOH A 60 660 716 HOH HOH . J 6 HOH A 61 661 603 HOH HOH . J 6 HOH A 62 662 643 HOH HOH . J 6 HOH A 63 663 601 HOH HOH . J 6 HOH A 64 664 608 HOH HOH . J 6 HOH A 65 665 711 HOH HOH . J 6 HOH A 66 666 695 HOH HOH . J 6 HOH A 67 667 672 HOH HOH . J 6 HOH A 68 668 681 HOH HOH . J 6 HOH A 69 669 682 HOH HOH . J 6 HOH A 70 670 630 HOH HOH . J 6 HOH A 71 671 708 HOH HOH . J 6 HOH A 72 672 707 HOH HOH . J 6 HOH A 73 673 658 HOH HOH . J 6 HOH A 74 674 710 HOH HOH . J 6 HOH A 75 675 720 HOH HOH . J 6 HOH A 76 676 666 HOH HOH . J 6 HOH A 77 677 622 HOH HOH . J 6 HOH A 78 678 648 HOH HOH . J 6 HOH A 79 679 602 HOH HOH . J 6 HOH A 80 680 625 HOH HOH . J 6 HOH A 81 681 605 HOH HOH . J 6 HOH A 82 682 735 HOH HOH . J 6 HOH A 83 683 656 HOH HOH . J 6 HOH A 84 684 620 HOH HOH . J 6 HOH A 85 685 649 HOH HOH . J 6 HOH A 86 686 659 HOH HOH . J 6 HOH A 87 687 715 HOH HOH . J 6 HOH A 88 688 600 HOH HOH . J 6 HOH A 89 689 609 HOH HOH . J 6 HOH A 90 690 689 HOH HOH . J 6 HOH A 91 691 724 HOH HOH . J 6 HOH A 92 692 713 HOH HOH . J 6 HOH A 93 693 646 HOH HOH . J 6 HOH A 94 694 626 HOH HOH . J 6 HOH A 95 695 703 HOH HOH . J 6 HOH A 96 696 700 HOH HOH . J 6 HOH A 97 697 621 HOH HOH . J 6 HOH A 98 698 631 HOH HOH . J 6 HOH A 99 699 664 HOH HOH . J 6 HOH A 100 700 611 HOH HOH . J 6 HOH A 101 701 639 HOH HOH . J 6 HOH A 102 702 638 HOH HOH . J 6 HOH A 103 703 619 HOH HOH . J 6 HOH A 104 704 663 HOH HOH . J 6 HOH A 105 705 721 HOH HOH . J 6 HOH A 106 706 744 HOH HOH . J 6 HOH A 107 707 660 HOH HOH . J 6 HOH A 108 708 739 HOH HOH . J 6 HOH A 109 709 616 HOH HOH . J 6 HOH A 110 710 668 HOH HOH . J 6 HOH A 111 711 651 HOH HOH . J 6 HOH A 112 712 613 HOH HOH . J 6 HOH A 113 713 627 HOH HOH . J 6 HOH A 114 714 606 HOH HOH . J 6 HOH A 115 715 743 HOH HOH . J 6 HOH A 116 716 696 HOH HOH . J 6 HOH A 117 717 676 HOH HOH . J 6 HOH A 118 718 738 HOH HOH . J 6 HOH A 119 719 677 HOH HOH . J 6 HOH A 120 720 653 HOH HOH . J 6 HOH A 121 721 629 HOH HOH . J 6 HOH A 122 722 650 HOH HOH . J 6 HOH A 123 723 617 HOH HOH . J 6 HOH A 124 724 729 HOH HOH . J 6 HOH A 125 725 741 HOH HOH . J 6 HOH A 126 726 725 HOH HOH . J 6 HOH A 127 727 661 HOH HOH . J 6 HOH A 128 728 699 HOH HOH . J 6 HOH A 129 729 698 HOH HOH . J 6 HOH A 130 730 644 HOH HOH . J 6 HOH A 131 731 667 HOH HOH . J 6 HOH A 132 732 694 HOH HOH . J 6 HOH A 133 733 685 HOH HOH . J 6 HOH A 134 734 722 HOH HOH . J 6 HOH A 135 735 670 HOH HOH . J 6 HOH A 136 736 709 HOH HOH . J 6 HOH A 137 737 690 HOH HOH . J 6 HOH A 138 738 701 HOH HOH . J 6 HOH A 139 739 726 HOH HOH . K 6 HOH B 1 101 669 HOH HOH . K 6 HOH B 2 102 624 HOH HOH . K 6 HOH B 3 103 693 HOH HOH . K 6 HOH B 4 104 623 HOH HOH . K 6 HOH B 5 105 662 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 . . . F 4 82.272 76.58 -21.858 1 91.85 ? C1 GOL 504 A 1 HETATM 2 O O1 GOL . . . F 4 81.879 75.686 -20.818 1 94.57 ? O1 GOL 504 A 1 HETATM 3 C C2 GOL . . . F 4 83.531 77.341 -21.497 1 87.78 ? C2 GOL 504 A 1 HETATM 4 O O2 GOL . . . F 4 84.548 76.425 -21.094 1 93.7 ? O2 GOL 504 A 1 HETATM 5 C C3 GOL . . . F 4 84.053 78.208 -22.623 1 90.84 ? C3 GOL 504 A 1 HETATM 6 O O3 GOL . . . F 4 85.39 78.641 -22.379 1 84.87 ? O3 GOL 504 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #