data_8YDU
#
_model_server_result.job_id            d47ByAUwpRGP21ZXYz3P7w 
_model_server_result.datetime_utc      '2025-08-28 14:46:11' 
_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          8ydu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":601}' 
#
_entry.id    8YDU 
#
_exptl.entry_id    8YDU 
_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    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         120 
_cell.entry_id            8YDU 
_cell.length_a            74.26 
_cell.length_b            74.26 
_cell.length_c            99.76 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YDU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    'P 31 2"' 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 B SG CYS 4 B CYS 336 1_555 B SG CYS 29 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf2 B SG CYS 47 B CYS 379 1_555 B SG CYS 100 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf3 B SG CYS 59 B CYS 391 1_555 B SG CYS 193 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf4 B SG CYS 148 B CYS 480 1_555 B SG CYS 156 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
#
_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                     8YDU 
_atom_sites.fract_transf_matrix[1][1]    0.013466 
_atom_sites.fract_transf_matrix[1][2]    0.007775 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015549 
_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]    0.010024 
_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 GOL B 1 601 101 GOL GOL . 
D 4 HOH A 1 101 203 HOH HOH . 
D 4 HOH A 2 102 8 HOH HOH . 
D 4 HOH A 3 103 81 HOH HOH . 
D 4 HOH A 4 104 65 HOH HOH . 
D 4 HOH A 5 105 6 HOH HOH . 
D 4 HOH A 6 106 3 HOH HOH . 
D 4 HOH A 7 107 36 HOH HOH . 
D 4 HOH A 8 108 108 HOH HOH . 
D 4 HOH A 9 109 16 HOH HOH . 
D 4 HOH A 10 110 28 HOH HOH . 
D 4 HOH A 11 111 34 HOH HOH . 
D 4 HOH A 12 112 185 HOH HOH . 
D 4 HOH A 13 113 123 HOH HOH . 
D 4 HOH A 14 114 52 HOH HOH . 
D 4 HOH A 15 115 41 HOH HOH . 
D 4 HOH A 16 116 120 HOH HOH . 
D 4 HOH A 17 117 124 HOH HOH . 
D 4 HOH A 18 118 152 HOH HOH . 
D 4 HOH A 19 119 205 HOH HOH . 
D 4 HOH A 20 120 125 HOH HOH . 
D 4 HOH A 21 121 195 HOH HOH . 
D 4 HOH A 22 122 122 HOH HOH . 
D 4 HOH A 23 123 79 HOH HOH . 
D 4 HOH A 24 124 68 HOH HOH . 
E 4 HOH B 1 701 133 HOH HOH . 
E 4 HOH B 2 702 70 HOH HOH . 
E 4 HOH B 3 703 4 HOH HOH . 
E 4 HOH B 4 704 56 HOH HOH . 
E 4 HOH B 5 705 186 HOH HOH . 
E 4 HOH B 6 706 96 HOH HOH . 
E 4 HOH B 7 707 93 HOH HOH . 
E 4 HOH B 8 708 39 HOH HOH . 
E 4 HOH B 9 709 10 HOH HOH . 
E 4 HOH B 10 710 66 HOH HOH . 
E 4 HOH B 11 711 5 HOH HOH . 
E 4 HOH B 12 712 15 HOH HOH . 
E 4 HOH B 13 713 71 HOH HOH . 
E 4 HOH B 14 714 21 HOH HOH . 
E 4 HOH B 15 715 154 HOH HOH . 
E 4 HOH B 16 716 26 HOH HOH . 
E 4 HOH B 17 717 24 HOH HOH . 
E 4 HOH B 18 718 23 HOH HOH . 
E 4 HOH B 19 719 136 HOH HOH . 
E 4 HOH B 20 720 42 HOH HOH . 
E 4 HOH B 21 721 60 HOH HOH . 
E 4 HOH B 22 722 61 HOH HOH . 
E 4 HOH B 23 723 25 HOH HOH . 
E 4 HOH B 24 724 45 HOH HOH . 
E 4 HOH B 25 725 20 HOH HOH . 
E 4 HOH B 26 726 83 HOH HOH . 
E 4 HOH B 27 727 199 HOH HOH . 
E 4 HOH B 28 728 43 HOH HOH . 
E 4 HOH B 29 729 48 HOH HOH . 
E 4 HOH B 30 730 2 HOH HOH . 
E 4 HOH B 31 731 11 HOH HOH . 
E 4 HOH B 32 732 160 HOH HOH . 
E 4 HOH B 33 733 57 HOH HOH . 
E 4 HOH B 34 734 146 HOH HOH . 
E 4 HOH B 35 735 17 HOH HOH . 
E 4 HOH B 36 736 9 HOH HOH . 
E 4 HOH B 37 737 1 HOH HOH . 
E 4 HOH B 38 738 18 HOH HOH . 
E 4 HOH B 39 739 40 HOH HOH . 
E 4 HOH B 40 740 182 HOH HOH . 
E 4 HOH B 41 741 99 HOH HOH . 
E 4 HOH B 42 742 50 HOH HOH . 
E 4 HOH B 43 743 32 HOH HOH . 
E 4 HOH B 44 744 14 HOH HOH . 
E 4 HOH B 45 745 35 HOH HOH . 
E 4 HOH B 46 746 27 HOH HOH . 
E 4 HOH B 47 747 13 HOH HOH . 
E 4 HOH B 48 748 7 HOH HOH . 
E 4 HOH B 49 749 77 HOH HOH . 
E 4 HOH B 50 750 30 HOH HOH . 
E 4 HOH B 51 751 112 HOH HOH . 
E 4 HOH B 52 752 97 HOH HOH . 
E 4 HOH B 53 753 115 HOH HOH . 
E 4 HOH B 54 754 75 HOH HOH . 
E 4 HOH B 55 755 78 HOH HOH . 
E 4 HOH B 56 756 139 HOH HOH . 
E 4 HOH B 57 757 140 HOH HOH . 
E 4 HOH B 58 758 62 HOH HOH . 
E 4 HOH B 59 759 204 HOH HOH . 
E 4 HOH B 60 760 31 HOH HOH . 
E 4 HOH B 61 761 169 HOH HOH . 
E 4 HOH B 62 762 85 HOH HOH . 
E 4 HOH B 63 763 88 HOH HOH . 
E 4 HOH B 64 764 22 HOH HOH . 
E 4 HOH B 65 765 12 HOH HOH . 
E 4 HOH B 66 766 69 HOH HOH . 
E 4 HOH B 67 767 130 HOH HOH . 
E 4 HOH B 68 768 19 HOH HOH . 
E 4 HOH B 69 769 47 HOH HOH . 
E 4 HOH B 70 770 67 HOH HOH . 
E 4 HOH B 71 771 114 HOH HOH . 
E 4 HOH B 72 772 116 HOH HOH . 
E 4 HOH B 73 773 177 HOH HOH . 
E 4 HOH B 74 774 207 HOH HOH . 
E 4 HOH B 75 775 54 HOH HOH . 
E 4 HOH B 76 776 55 HOH HOH . 
E 4 HOH B 77 777 49 HOH HOH . 
E 4 HOH B 78 778 64 HOH HOH . 
E 4 HOH B 79 779 137 HOH HOH . 
E 4 HOH B 80 780 103 HOH HOH . 
E 4 HOH B 81 781 87 HOH HOH . 
E 4 HOH B 82 782 171 HOH HOH . 
E 4 HOH B 83 783 98 HOH HOH . 
E 4 HOH B 84 784 37 HOH HOH . 
E 4 HOH B 85 785 29 HOH HOH . 
E 4 HOH B 86 786 95 HOH HOH . 
E 4 HOH B 87 787 63 HOH HOH . 
E 4 HOH B 88 788 181 HOH HOH . 
E 4 HOH B 89 789 198 HOH HOH . 
E 4 HOH B 90 790 135 HOH HOH . 
E 4 HOH B 91 791 196 HOH HOH . 
E 4 HOH B 92 792 58 HOH HOH . 
E 4 HOH B 93 793 91 HOH HOH . 
E 4 HOH B 94 794 163 HOH HOH . 
E 4 HOH B 95 795 101 HOH HOH . 
E 4 HOH B 96 796 53 HOH HOH . 
E 4 HOH B 97 797 158 HOH HOH . 
E 4 HOH B 98 798 74 HOH HOH . 
E 4 HOH B 99 799 168 HOH HOH . 
E 4 HOH B 100 800 46 HOH HOH . 
E 4 HOH B 101 801 82 HOH HOH . 
E 4 HOH B 102 802 51 HOH HOH . 
E 4 HOH B 103 803 38 HOH HOH . 
E 4 HOH B 104 804 173 HOH HOH . 
E 4 HOH B 105 805 110 HOH HOH . 
E 4 HOH B 106 806 209 HOH HOH . 
E 4 HOH B 107 807 104 HOH HOH . 
E 4 HOH B 108 808 170 HOH HOH . 
E 4 HOH B 109 809 76 HOH HOH . 
E 4 HOH B 110 810 165 HOH HOH . 
E 4 HOH B 111 811 143 HOH HOH . 
E 4 HOH B 112 812 113 HOH HOH . 
E 4 HOH B 113 813 117 HOH HOH . 
E 4 HOH B 114 814 141 HOH HOH . 
E 4 HOH B 115 815 92 HOH HOH . 
E 4 HOH B 116 816 164 HOH HOH . 
E 4 HOH B 117 817 80 HOH HOH . 
E 4 HOH B 118 818 118 HOH HOH . 
E 4 HOH B 119 819 176 HOH HOH . 
E 4 HOH B 120 820 206 HOH HOH . 
E 4 HOH B 121 821 44 HOH HOH . 
E 4 HOH B 122 822 200 HOH HOH . 
E 4 HOH B 123 823 73 HOH HOH . 
E 4 HOH B 124 824 72 HOH HOH . 
E 4 HOH B 125 825 33 HOH HOH . 
E 4 HOH B 126 826 180 HOH HOH . 
E 4 HOH B 127 827 179 HOH HOH . 
E 4 HOH B 128 828 208 HOH HOH . 
E 4 HOH B 129 829 84 HOH HOH . 
E 4 HOH B 130 830 197 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 . . . C 3 -41.579 7.814 -10.55 1 50.09 ? C1 GOL 601 B 1 
HETATM 2 O O1 GOL . . . C 3 -42.665 8.331 -11.254 1 54.26 ? O1 GOL 601 B 1 
HETATM 3 C C2 GOL . . . C 3 -40.418 8.835 -10.656 1 48.07 ? C2 GOL 601 B 1 
HETATM 4 O O2 GOL . . . C 3 -39.852 8.858 -11.921 1 48.59 ? O2 GOL 601 B 1 
HETATM 5 C C3 GOL . . . C 3 -39.414 8.371 -9.591 1 44.11 ? C3 GOL 601 B 1 
HETATM 6 O O3 GOL . . . C 3 -38.215 9.023 -9.809 1 49.13 ? O3 GOL 601 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#