data_6DNB
#
_model_server_result.job_id            VtiNx9AjLiSK1ApqJF9WnQ 
_model_server_result.datetime_utc      '2024-11-24 11:33:26' 
_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          6dnb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":505}' 
#
_entry.id    6DNB 
#
_exptl.entry_id    6DNB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            6DNB 
_cell.length_a            84.085 
_cell.length_b            84.085 
_cell.length_c            210.128 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DNB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_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 
_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
? 3 D N N 
? 3 E N N 
? 3 F 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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     6DNB 
_atom_sites.fract_transf_matrix[1][1]    0.011893 
_atom_sites.fract_transf_matrix[1][2]    0.006866 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013733 
_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]    0.004759 
_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 PG4 A 1 501 1 PG4 PG4 . 
C 2 PG4 A 1 502 2 PG4 PG4 . 
D 3 GOL A 1 503 1 GOL GOL . 
E 3 GOL A 1 504 2 GOL GOL . 
F 3 GOL A 1 505 3 GOL GOL . 
G 4 PO4 A 1 506 2001 PO4 PO4 . 
H 5 HOH A 1 601 115 HOH HOH . 
H 5 HOH A 2 602 134 HOH HOH . 
H 5 HOH A 3 603 102 HOH HOH . 
H 5 HOH A 4 604 190 HOH HOH . 
H 5 HOH A 5 605 116 HOH HOH . 
H 5 HOH A 6 606 193 HOH HOH . 
H 5 HOH A 7 607 91 HOH HOH . 
H 5 HOH A 8 608 72 HOH HOH . 
H 5 HOH A 9 609 191 HOH HOH . 
H 5 HOH A 10 610 82 HOH HOH . 
H 5 HOH A 11 611 135 HOH HOH . 
H 5 HOH A 12 612 204 HOH HOH . 
H 5 HOH A 13 613 154 HOH HOH . 
H 5 HOH A 14 614 220 HOH HOH . 
H 5 HOH A 15 615 40 HOH HOH . 
H 5 HOH A 16 616 65 HOH HOH . 
H 5 HOH A 17 617 4 HOH HOH . 
H 5 HOH A 18 618 218 HOH HOH . 
H 5 HOH A 19 619 222 HOH HOH . 
H 5 HOH A 20 620 233 HOH HOH . 
H 5 HOH A 21 621 95 HOH HOH . 
H 5 HOH A 22 622 148 HOH HOH . 
H 5 HOH A 23 623 43 HOH HOH . 
H 5 HOH A 24 624 100 HOH HOH . 
H 5 HOH A 25 625 111 HOH HOH . 
H 5 HOH A 26 626 140 HOH HOH . 
H 5 HOH A 27 627 56 HOH HOH . 
H 5 HOH A 28 628 66 HOH HOH . 
H 5 HOH A 29 629 108 HOH HOH . 
H 5 HOH A 30 630 38 HOH HOH . 
H 5 HOH A 31 631 180 HOH HOH . 
H 5 HOH A 32 632 13 HOH HOH . 
H 5 HOH A 33 633 97 HOH HOH . 
H 5 HOH A 34 634 221 HOH HOH . 
H 5 HOH A 35 635 194 HOH HOH . 
H 5 HOH A 36 636 158 HOH HOH . 
H 5 HOH A 37 637 231 HOH HOH . 
H 5 HOH A 38 638 189 HOH HOH . 
H 5 HOH A 39 639 142 HOH HOH . 
H 5 HOH A 40 640 22 HOH HOH . 
H 5 HOH A 41 641 173 HOH HOH . 
H 5 HOH A 42 642 104 HOH HOH . 
H 5 HOH A 43 643 141 HOH HOH . 
H 5 HOH A 44 644 64 HOH HOH . 
H 5 HOH A 45 645 195 HOH HOH . 
H 5 HOH A 46 646 29 HOH HOH . 
H 5 HOH A 47 647 27 HOH HOH . 
H 5 HOH A 48 648 44 HOH HOH . 
H 5 HOH A 49 649 124 HOH HOH . 
H 5 HOH A 50 650 87 HOH HOH . 
H 5 HOH A 51 651 144 HOH HOH . 
H 5 HOH A 52 652 35 HOH HOH . 
H 5 HOH A 53 653 185 HOH HOH . 
H 5 HOH A 54 654 113 HOH HOH . 
H 5 HOH A 55 655 28 HOH HOH . 
H 5 HOH A 56 656 203 HOH HOH . 
H 5 HOH A 57 657 79 HOH HOH . 
H 5 HOH A 58 658 137 HOH HOH . 
H 5 HOH A 59 659 7 HOH HOH . 
H 5 HOH A 60 660 156 HOH HOH . 
H 5 HOH A 61 661 8 HOH HOH . 
H 5 HOH A 62 662 105 HOH HOH . 
H 5 HOH A 63 663 75 HOH HOH . 
H 5 HOH A 64 664 1 HOH HOH . 
H 5 HOH A 65 665 9 HOH HOH . 
H 5 HOH A 66 666 98 HOH HOH . 
H 5 HOH A 67 667 225 HOH HOH . 
H 5 HOH A 68 668 169 HOH HOH . 
H 5 HOH A 69 669 34 HOH HOH . 
H 5 HOH A 70 670 96 HOH HOH . 
H 5 HOH A 71 671 150 HOH HOH . 
H 5 HOH A 72 672 175 HOH HOH . 
H 5 HOH A 73 673 236 HOH HOH . 
H 5 HOH A 74 674 48 HOH HOH . 
H 5 HOH A 75 675 20 HOH HOH . 
H 5 HOH A 76 676 74 HOH HOH . 
H 5 HOH A 77 677 119 HOH HOH . 
H 5 HOH A 78 678 214 HOH HOH . 
H 5 HOH A 79 679 31 HOH HOH . 
H 5 HOH A 80 680 89 HOH HOH . 
H 5 HOH A 81 681 45 HOH HOH . 
H 5 HOH A 82 682 145 HOH HOH . 
H 5 HOH A 83 683 174 HOH HOH . 
H 5 HOH A 84 684 80 HOH HOH . 
H 5 HOH A 85 685 32 HOH HOH . 
H 5 HOH A 86 686 176 HOH HOH . 
H 5 HOH A 87 687 26 HOH HOH . 
H 5 HOH A 88 688 215 HOH HOH . 
H 5 HOH A 89 689 14 HOH HOH . 
H 5 HOH A 90 690 67 HOH HOH . 
H 5 HOH A 91 691 94 HOH HOH . 
H 5 HOH A 92 692 152 HOH HOH . 
H 5 HOH A 93 693 151 HOH HOH . 
H 5 HOH A 94 694 62 HOH HOH . 
H 5 HOH A 95 695 49 HOH HOH . 
H 5 HOH A 96 696 71 HOH HOH . 
H 5 HOH A 97 697 23 HOH HOH . 
H 5 HOH A 98 698 224 HOH HOH . 
H 5 HOH A 99 699 78 HOH HOH . 
H 5 HOH A 100 700 54 HOH HOH . 
H 5 HOH A 101 701 129 HOH HOH . 
H 5 HOH A 102 702 46 HOH HOH . 
H 5 HOH A 103 703 36 HOH HOH . 
H 5 HOH A 104 704 3 HOH HOH . 
H 5 HOH A 105 705 168 HOH HOH . 
H 5 HOH A 106 706 121 HOH HOH . 
H 5 HOH A 107 707 47 HOH HOH . 
H 5 HOH A 108 708 90 HOH HOH . 
H 5 HOH A 109 709 61 HOH HOH . 
H 5 HOH A 110 710 171 HOH HOH . 
H 5 HOH A 111 711 42 HOH HOH . 
H 5 HOH A 112 712 120 HOH HOH . 
H 5 HOH A 113 713 93 HOH HOH . 
H 5 HOH A 114 714 68 HOH HOH . 
H 5 HOH A 115 715 133 HOH HOH . 
H 5 HOH A 116 716 21 HOH HOH . 
H 5 HOH A 117 717 143 HOH HOH . 
H 5 HOH A 118 718 84 HOH HOH . 
H 5 HOH A 119 719 33 HOH HOH . 
H 5 HOH A 120 720 110 HOH HOH . 
H 5 HOH A 121 721 230 HOH HOH . 
H 5 HOH A 122 722 37 HOH HOH . 
H 5 HOH A 123 723 73 HOH HOH . 
H 5 HOH A 124 724 52 HOH HOH . 
H 5 HOH A 125 725 25 HOH HOH . 
H 5 HOH A 126 726 112 HOH HOH . 
H 5 HOH A 127 727 101 HOH HOH . 
H 5 HOH A 128 728 228 HOH HOH . 
H 5 HOH A 129 729 172 HOH HOH . 
H 5 HOH A 130 730 2 HOH HOH . 
H 5 HOH A 131 731 232 HOH HOH . 
H 5 HOH A 132 732 17 HOH HOH . 
H 5 HOH A 133 733 146 HOH HOH . 
H 5 HOH A 134 734 60 HOH HOH . 
H 5 HOH A 135 735 229 HOH HOH . 
H 5 HOH A 136 736 136 HOH HOH . 
H 5 HOH A 137 737 157 HOH HOH . 
H 5 HOH A 138 738 39 HOH HOH . 
H 5 HOH A 139 739 125 HOH HOH . 
H 5 HOH A 140 740 138 HOH HOH . 
H 5 HOH A 141 741 85 HOH HOH . 
H 5 HOH A 142 742 12 HOH HOH . 
H 5 HOH A 143 743 128 HOH HOH . 
H 5 HOH A 144 744 70 HOH HOH . 
H 5 HOH A 145 745 207 HOH HOH . 
H 5 HOH A 146 746 10 HOH HOH . 
H 5 HOH A 147 747 164 HOH HOH . 
H 5 HOH A 148 748 63 HOH HOH . 
H 5 HOH A 149 749 41 HOH HOH . 
H 5 HOH A 150 750 15 HOH HOH . 
H 5 HOH A 151 751 196 HOH HOH . 
H 5 HOH A 152 752 178 HOH HOH . 
H 5 HOH A 153 753 167 HOH HOH . 
H 5 HOH A 154 754 114 HOH HOH . 
H 5 HOH A 155 755 99 HOH HOH . 
H 5 HOH A 156 756 30 HOH HOH . 
H 5 HOH A 157 757 181 HOH HOH . 
H 5 HOH A 158 758 147 HOH HOH . 
H 5 HOH A 159 759 107 HOH HOH . 
H 5 HOH A 160 760 197 HOH HOH . 
H 5 HOH A 161 761 198 HOH HOH . 
H 5 HOH A 162 762 237 HOH HOH . 
H 5 HOH A 163 763 18 HOH HOH . 
H 5 HOH A 164 764 55 HOH HOH . 
H 5 HOH A 165 765 11 HOH HOH . 
H 5 HOH A 166 766 131 HOH HOH . 
H 5 HOH A 167 767 76 HOH HOH . 
H 5 HOH A 168 768 227 HOH HOH . 
H 5 HOH A 169 769 86 HOH HOH . 
H 5 HOH A 170 770 122 HOH HOH . 
H 5 HOH A 171 771 182 HOH HOH . 
H 5 HOH A 172 772 58 HOH HOH . 
H 5 HOH A 173 773 81 HOH HOH . 
H 5 HOH A 174 774 57 HOH HOH . 
H 5 HOH A 175 775 59 HOH HOH . 
H 5 HOH A 176 776 139 HOH HOH . 
H 5 HOH A 177 777 109 HOH HOH . 
H 5 HOH A 178 778 202 HOH HOH . 
H 5 HOH A 179 779 19 HOH HOH . 
H 5 HOH A 180 780 6 HOH HOH . 
H 5 HOH A 181 781 24 HOH HOH . 
H 5 HOH A 182 782 126 HOH HOH . 
H 5 HOH A 183 783 50 HOH HOH . 
H 5 HOH A 184 784 106 HOH HOH . 
H 5 HOH A 185 785 209 HOH HOH . 
H 5 HOH A 186 786 5 HOH HOH . 
H 5 HOH A 187 787 213 HOH HOH . 
H 5 HOH A 188 788 226 HOH HOH . 
H 5 HOH A 189 789 103 HOH HOH . 
H 5 HOH A 190 790 179 HOH HOH . 
H 5 HOH A 191 791 117 HOH HOH . 
H 5 HOH A 192 792 234 HOH HOH . 
H 5 HOH A 193 793 51 HOH HOH . 
H 5 HOH A 194 794 88 HOH HOH . 
H 5 HOH A 195 795 206 HOH HOH . 
H 5 HOH A 196 796 235 HOH HOH . 
H 5 HOH A 197 797 223 HOH HOH . 
H 5 HOH A 198 798 16 HOH HOH . 
H 5 HOH A 199 799 199 HOH HOH . 
H 5 HOH A 200 800 153 HOH HOH . 
H 5 HOH A 201 801 201 HOH HOH . 
H 5 HOH A 202 802 217 HOH HOH . 
H 5 HOH A 203 803 165 HOH HOH . 
H 5 HOH A 204 804 200 HOH HOH . 
H 5 HOH A 205 805 69 HOH HOH . 
H 5 HOH A 206 806 219 HOH HOH . 
H 5 HOH A 207 807 211 HOH HOH . 
H 5 HOH A 208 808 183 HOH HOH . 
H 5 HOH A 209 809 208 HOH HOH . 
H 5 HOH A 210 810 92 HOH HOH . 
H 5 HOH A 211 811 155 HOH HOH . 
H 5 HOH A 212 812 130 HOH HOH . 
H 5 HOH A 213 813 188 HOH HOH . 
H 5 HOH A 214 814 216 HOH HOH . 
H 5 HOH A 215 815 127 HOH HOH . 
H 5 HOH A 216 816 166 HOH HOH . 
H 5 HOH A 217 817 118 HOH HOH . 
H 5 HOH A 218 818 186 HOH HOH . 
H 5 HOH A 219 819 132 HOH HOH . 
H 5 HOH A 220 820 161 HOH HOH . 
H 5 HOH A 221 821 160 HOH HOH . 
H 5 HOH A 222 822 205 HOH HOH . 
H 5 HOH A 223 823 159 HOH HOH . 
H 5 HOH A 224 824 177 HOH HOH . 
H 5 HOH A 225 825 83 HOH HOH . 
H 5 HOH A 226 826 170 HOH HOH . 
H 5 HOH A 227 827 192 HOH HOH . 
H 5 HOH A 228 828 162 HOH HOH . 
H 5 HOH A 229 829 149 HOH HOH . 
H 5 HOH A 230 830 210 HOH HOH . 
H 5 HOH A 231 831 77 HOH HOH . 
H 5 HOH A 232 832 212 HOH HOH . 
H 5 HOH A 233 833 187 HOH HOH . 
H 5 HOH A 234 834 53 HOH HOH . 
H 5 HOH A 235 835 163 HOH HOH . 
H 5 HOH A 236 836 184 HOH HOH . 
H 5 HOH A 237 837 123 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 3 15.326 40.464 25.825 1 54.4 ? C1 GOL 505 A 1 
HETATM 2 O O1 GOL . . . F 3 16.496 39.629 25.893 1 55.98 ? O1 GOL 505 A 1 
HETATM 3 C C2 GOL . . . F 3 14.694 40.213 24.451 1 50.81 ? C2 GOL 505 A 1 
HETATM 4 O O2 GOL . . . F 3 15.729 40.331 23.482 1 60.59 ? O2 GOL 505 A 1 
HETATM 5 C C3 GOL . . . F 3 13.537 41.149 24.08 1 49.49 ? C3 GOL 505 A 1 
HETATM 6 O O3 GOL . . . F 3 12.813 41.62 25.221 1 39.11 ? O3 GOL 505 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           6 
#