data_8YDQ
#
_model_server_result.job_id            VV1kABSxMiZHN5EpEpfLCg 
_model_server_result.datetime_utc      '2025-08-28 10:35:16' 
_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          8ydq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":601}' 
#
_entry.id    8YDQ 
#
_exptl.entry_id    8YDQ 
_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            8YDQ 
_cell.length_a            74.86 
_cell.length_b            74.86 
_cell.length_c            100.58 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YDQ 
_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        ? 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf2 B SG CYS 47 B CYS 379 1_555 B SG CYS 100 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf3 B SG CYS 59 B CYS 391 1_555 B SG CYS 193 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 B SG CYS 148 B CYS 480 1_555 B SG CYS 156 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
#
_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                     8YDQ 
_atom_sites.fract_transf_matrix[1][1]    0.013358 
_atom_sites.fract_transf_matrix[1][2]    0.007712 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015425 
_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]    0.009942 
_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 56 HOH HOH . 
D 4 HOH A 2 102 103 HOH HOH . 
D 4 HOH A 3 103 29 HOH HOH . 
D 4 HOH A 4 104 52 HOH HOH . 
D 4 HOH A 5 105 4 HOH HOH . 
D 4 HOH A 6 106 104 HOH HOH . 
D 4 HOH A 7 107 71 HOH HOH . 
D 4 HOH A 8 108 45 HOH HOH . 
D 4 HOH A 9 109 111 HOH HOH . 
D 4 HOH A 10 110 2 HOH HOH . 
D 4 HOH A 11 111 33 HOH HOH . 
D 4 HOH A 12 112 34 HOH HOH . 
D 4 HOH A 13 113 63 HOH HOH . 
D 4 HOH A 14 114 64 HOH HOH . 
D 4 HOH A 15 115 92 HOH HOH . 
D 4 HOH A 16 116 115 HOH HOH . 
D 4 HOH A 17 117 142 HOH HOH . 
D 4 HOH A 18 118 108 HOH HOH . 
D 4 HOH A 19 119 62 HOH HOH . 
D 4 HOH A 20 120 74 HOH HOH . 
D 4 HOH A 21 121 102 HOH HOH . 
D 4 HOH A 22 122 26 HOH HOH . 
D 4 HOH A 23 123 94 HOH HOH . 
E 4 HOH B 1 701 46 HOH HOH . 
E 4 HOH B 2 702 132 HOH HOH . 
E 4 HOH B 3 703 37 HOH HOH . 
E 4 HOH B 4 704 1 HOH HOH . 
E 4 HOH B 5 705 85 HOH HOH . 
E 4 HOH B 6 706 36 HOH HOH . 
E 4 HOH B 7 707 23 HOH HOH . 
E 4 HOH B 8 708 58 HOH HOH . 
E 4 HOH B 9 709 3 HOH HOH . 
E 4 HOH B 10 710 88 HOH HOH . 
E 4 HOH B 11 711 99 HOH HOH . 
E 4 HOH B 12 712 40 HOH HOH . 
E 4 HOH B 13 713 65 HOH HOH . 
E 4 HOH B 14 714 129 HOH HOH . 
E 4 HOH B 15 715 12 HOH HOH . 
E 4 HOH B 16 716 109 HOH HOH . 
E 4 HOH B 17 717 11 HOH HOH . 
E 4 HOH B 18 718 20 HOH HOH . 
E 4 HOH B 19 719 28 HOH HOH . 
E 4 HOH B 20 720 13 HOH HOH . 
E 4 HOH B 21 721 106 HOH HOH . 
E 4 HOH B 22 722 41 HOH HOH . 
E 4 HOH B 23 723 47 HOH HOH . 
E 4 HOH B 24 724 112 HOH HOH . 
E 4 HOH B 25 725 128 HOH HOH . 
E 4 HOH B 26 726 67 HOH HOH . 
E 4 HOH B 27 727 27 HOH HOH . 
E 4 HOH B 28 728 96 HOH HOH . 
E 4 HOH B 29 729 16 HOH HOH . 
E 4 HOH B 30 730 18 HOH HOH . 
E 4 HOH B 31 731 72 HOH HOH . 
E 4 HOH B 32 732 8 HOH HOH . 
E 4 HOH B 33 733 51 HOH HOH . 
E 4 HOH B 34 734 48 HOH HOH . 
E 4 HOH B 35 735 55 HOH HOH . 
E 4 HOH B 36 736 19 HOH HOH . 
E 4 HOH B 37 737 145 HOH HOH . 
E 4 HOH B 38 738 10 HOH HOH . 
E 4 HOH B 39 739 32 HOH HOH . 
E 4 HOH B 40 740 39 HOH HOH . 
E 4 HOH B 41 741 5 HOH HOH . 
E 4 HOH B 42 742 14 HOH HOH . 
E 4 HOH B 43 743 25 HOH HOH . 
E 4 HOH B 44 744 22 HOH HOH . 
E 4 HOH B 45 745 97 HOH HOH . 
E 4 HOH B 46 746 107 HOH HOH . 
E 4 HOH B 47 747 7 HOH HOH . 
E 4 HOH B 48 748 6 HOH HOH . 
E 4 HOH B 49 749 30 HOH HOH . 
E 4 HOH B 50 750 136 HOH HOH . 
E 4 HOH B 51 751 110 HOH HOH . 
E 4 HOH B 52 752 105 HOH HOH . 
E 4 HOH B 53 753 123 HOH HOH . 
E 4 HOH B 54 754 130 HOH HOH . 
E 4 HOH B 55 755 15 HOH HOH . 
E 4 HOH B 56 756 100 HOH HOH . 
E 4 HOH B 57 757 59 HOH HOH . 
E 4 HOH B 58 758 89 HOH HOH . 
E 4 HOH B 59 759 17 HOH HOH . 
E 4 HOH B 60 760 90 HOH HOH . 
E 4 HOH B 61 761 124 HOH HOH . 
E 4 HOH B 62 762 24 HOH HOH . 
E 4 HOH B 63 763 93 HOH HOH . 
E 4 HOH B 64 764 21 HOH HOH . 
E 4 HOH B 65 765 101 HOH HOH . 
E 4 HOH B 66 766 60 HOH HOH . 
E 4 HOH B 67 767 44 HOH HOH . 
E 4 HOH B 68 768 49 HOH HOH . 
E 4 HOH B 69 769 35 HOH HOH . 
E 4 HOH B 70 770 87 HOH HOH . 
E 4 HOH B 71 771 38 HOH HOH . 
E 4 HOH B 72 772 66 HOH HOH . 
E 4 HOH B 73 773 121 HOH HOH . 
E 4 HOH B 74 774 75 HOH HOH . 
E 4 HOH B 75 775 9 HOH HOH . 
E 4 HOH B 76 776 57 HOH HOH . 
E 4 HOH B 77 777 79 HOH HOH . 
E 4 HOH B 78 778 69 HOH HOH . 
E 4 HOH B 79 779 137 HOH HOH . 
E 4 HOH B 80 780 73 HOH HOH . 
E 4 HOH B 81 781 83 HOH HOH . 
E 4 HOH B 82 782 50 HOH HOH . 
E 4 HOH B 83 783 43 HOH HOH . 
E 4 HOH B 84 784 140 HOH HOH . 
E 4 HOH B 85 785 143 HOH HOH . 
E 4 HOH B 86 786 117 HOH HOH . 
E 4 HOH B 87 787 120 HOH HOH . 
E 4 HOH B 88 788 82 HOH HOH . 
E 4 HOH B 89 789 31 HOH HOH . 
E 4 HOH B 90 790 70 HOH HOH . 
E 4 HOH B 91 791 127 HOH HOH . 
E 4 HOH B 92 792 144 HOH HOH . 
E 4 HOH B 93 793 118 HOH HOH . 
E 4 HOH B 94 794 54 HOH HOH . 
E 4 HOH B 95 795 119 HOH HOH . 
E 4 HOH B 96 796 122 HOH HOH . 
E 4 HOH B 97 797 42 HOH HOH . 
E 4 HOH B 98 798 77 HOH HOH . 
E 4 HOH B 99 799 81 HOH HOH . 
E 4 HOH B 100 800 76 HOH HOH . 
E 4 HOH B 101 801 113 HOH HOH . 
E 4 HOH B 102 802 80 HOH HOH . 
E 4 HOH B 103 803 53 HOH HOH . 
E 4 HOH B 104 804 141 HOH HOH . 
E 4 HOH B 105 805 84 HOH HOH . 
E 4 HOH B 106 806 86 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 23.324 -24.442 -27.562 1 47.05 ? C1 GOL 601 B 1 
HETATM 2 O O1 GOL . . . C 3 23.265 -23.232 -28.256 1 51.88 ? O1 GOL 601 B 1 
HETATM 3 C C2 GOL . . . C 3 24.748 -25.027 -27.754 1 45.23 ? C2 GOL 601 B 1 
HETATM 4 O O2 GOL . . . C 3 25.002 -25.384 -29.068 1 47.42 ? O2 GOL 601 B 1 
HETATM 5 C C3 GOL . . . C 3 24.792 -26.25 -26.82 1 46.63 ? C3 GOL 601 B 1 
HETATM 6 O O3 GOL . . . C 3 25.927 -26.975 -27.171 1 49.53 ? O3 GOL 601 B 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#