data_9D40
#
_model_server_result.job_id            MYTI-QTuPUxDf0cqgN5VKg 
_model_server_result.datetime_utc      '2025-07-04 21:18:07' 
_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          9d40 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":701}' 
#
_entry.id    9D40 
#
_exptl.entry_id    9D40 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          97.82 
_cell.angle_gamma         90 
_cell.entry_id            9D40 
_cell.length_a            72.52 
_cell.length_b            40.98 
_cell.length_c            101.87 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9D40 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_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 
_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
? 2 B N N 
? 2 C N 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 A SG CYS 4 A CYS 366 1_555 A SG CYS 50 A CYS 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf2 A SG CYS 34 A CYS 396 1_555 A SG CYS 68 A CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf3 A SG CYS 72 A CYS 434 1_555 A SG CYS 190 A CYS 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
disulf ? disulf4 A SG CYS 236 A CYS 598 1_555 A SG CYS 256 A CYS 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? 
disulf ? disulf5 A SG CYS 267 A CYS 629 1_555 A SG CYS 298 A CYS 660 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf6 A SG CYS 267 A CYS 629 1_555 A SG CYS 298 A CYS 660 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.037 ? 
#
_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 188 n n 
C1 C2 GOL sing 189 n n 
C1 H11 GOL sing 190 n n 
C1 H12 GOL sing 191 n n 
O1 HO1 GOL sing 192 n n 
C2 O2 GOL sing 193 n n 
C2 C3 GOL sing 194 n n 
C2 H2 GOL sing 195 n n 
O2 HO2 GOL sing 196 n n 
C3 O3 GOL sing 197 n n 
C3 H31 GOL sing 198 n n 
C3 H32 GOL sing 199 n n 
O3 HO3 GOL sing 200 n n 
#
_atom_sites.entry_id                     9D40 
_atom_sites.fract_transf_matrix[1][1]    0.013789 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001894 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.024402 
_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]    0.009909 
_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 A 1 701 1 GOL GOL . 
C 2 GOL A 1 702 2 GOL GOL . 
D 3 A1A1Z A 1 703 1 A1A1Z SD0 . 
E 4 HOH A 1 801 76 HOH HOH . 
E 4 HOH A 2 802 61 HOH HOH . 
E 4 HOH A 3 803 57 HOH HOH . 
E 4 HOH A 4 804 75 HOH HOH . 
E 4 HOH A 5 805 82 HOH HOH . 
E 4 HOH A 6 806 141 HOH HOH . 
E 4 HOH A 7 807 68 HOH HOH . 
E 4 HOH A 8 808 37 HOH HOH . 
E 4 HOH A 9 809 107 HOH HOH . 
E 4 HOH A 10 810 16 HOH HOH . 
E 4 HOH A 11 811 35 HOH HOH . 
E 4 HOH A 12 812 45 HOH HOH . 
E 4 HOH A 13 813 17 HOH HOH . 
E 4 HOH A 14 814 31 HOH HOH . 
E 4 HOH A 15 815 63 HOH HOH . 
E 4 HOH A 16 816 84 HOH HOH . 
E 4 HOH A 17 817 22 HOH HOH . 
E 4 HOH A 18 818 101 HOH HOH . 
E 4 HOH A 19 819 43 HOH HOH . 
E 4 HOH A 20 820 120 HOH HOH . 
E 4 HOH A 21 821 110 HOH HOH . 
E 4 HOH A 22 822 12 HOH HOH . 
E 4 HOH A 23 823 97 HOH HOH . 
E 4 HOH A 24 824 112 HOH HOH . 
E 4 HOH A 25 825 64 HOH HOH . 
E 4 HOH A 26 826 2 HOH HOH . 
E 4 HOH A 27 827 93 HOH HOH . 
E 4 HOH A 28 828 52 HOH HOH . 
E 4 HOH A 29 829 32 HOH HOH . 
E 4 HOH A 30 830 4 HOH HOH . 
E 4 HOH A 31 831 53 HOH HOH . 
E 4 HOH A 32 832 41 HOH HOH . 
E 4 HOH A 33 833 95 HOH HOH . 
E 4 HOH A 34 834 66 HOH HOH . 
E 4 HOH A 35 835 47 HOH HOH . 
E 4 HOH A 36 836 74 HOH HOH . 
E 4 HOH A 37 837 69 HOH HOH . 
E 4 HOH A 38 838 55 HOH HOH . 
E 4 HOH A 39 839 40 HOH HOH . 
E 4 HOH A 40 840 128 HOH HOH . 
E 4 HOH A 41 841 126 HOH HOH . 
E 4 HOH A 42 842 51 HOH HOH . 
E 4 HOH A 43 843 29 HOH HOH . 
E 4 HOH A 44 844 124 HOH HOH . 
E 4 HOH A 45 845 71 HOH HOH . 
E 4 HOH A 46 846 118 HOH HOH . 
E 4 HOH A 47 847 87 HOH HOH . 
E 4 HOH A 48 848 24 HOH HOH . 
E 4 HOH A 49 849 67 HOH HOH . 
E 4 HOH A 50 850 11 HOH HOH . 
E 4 HOH A 51 851 36 HOH HOH . 
E 4 HOH A 52 852 6 HOH HOH . 
E 4 HOH A 53 853 3 HOH HOH . 
E 4 HOH A 54 854 8 HOH HOH . 
E 4 HOH A 55 855 114 HOH HOH . 
E 4 HOH A 56 856 50 HOH HOH . 
E 4 HOH A 57 857 130 HOH HOH . 
E 4 HOH A 58 858 9 HOH HOH . 
E 4 HOH A 59 859 92 HOH HOH . 
E 4 HOH A 60 860 5 HOH HOH . 
E 4 HOH A 61 861 33 HOH HOH . 
E 4 HOH A 62 862 14 HOH HOH . 
E 4 HOH A 63 863 13 HOH HOH . 
E 4 HOH A 64 864 79 HOH HOH . 
E 4 HOH A 65 865 23 HOH HOH . 
E 4 HOH A 66 866 113 HOH HOH . 
E 4 HOH A 67 867 81 HOH HOH . 
E 4 HOH A 68 868 18 HOH HOH . 
E 4 HOH A 69 869 7 HOH HOH . 
E 4 HOH A 70 870 15 HOH HOH . 
E 4 HOH A 71 871 49 HOH HOH . 
E 4 HOH A 72 872 56 HOH HOH . 
E 4 HOH A 73 873 54 HOH HOH . 
E 4 HOH A 74 874 80 HOH HOH . 
E 4 HOH A 75 875 133 HOH HOH . 
E 4 HOH A 76 876 65 HOH HOH . 
E 4 HOH A 77 877 34 HOH HOH . 
E 4 HOH A 78 878 19 HOH HOH . 
E 4 HOH A 79 879 21 HOH HOH . 
E 4 HOH A 80 880 48 HOH HOH . 
E 4 HOH A 81 881 26 HOH HOH . 
E 4 HOH A 82 882 108 HOH HOH . 
E 4 HOH A 83 883 94 HOH HOH . 
E 4 HOH A 84 884 38 HOH HOH . 
E 4 HOH A 85 885 30 HOH HOH . 
E 4 HOH A 86 886 60 HOH HOH . 
E 4 HOH A 87 887 104 HOH HOH . 
E 4 HOH A 88 888 122 HOH HOH . 
E 4 HOH A 89 889 77 HOH HOH . 
E 4 HOH A 90 890 25 HOH HOH . 
E 4 HOH A 91 891 73 HOH HOH . 
E 4 HOH A 92 892 98 HOH HOH . 
E 4 HOH A 93 893 85 HOH HOH . 
E 4 HOH A 94 894 59 HOH HOH . 
E 4 HOH A 95 895 127 HOH HOH . 
E 4 HOH A 96 896 1 HOH HOH . 
E 4 HOH A 97 897 140 HOH HOH . 
E 4 HOH A 98 898 100 HOH HOH . 
E 4 HOH A 99 899 138 HOH HOH . 
E 4 HOH A 100 900 129 HOH HOH . 
E 4 HOH A 101 901 83 HOH HOH . 
E 4 HOH A 102 902 27 HOH HOH . 
E 4 HOH A 103 903 116 HOH HOH . 
E 4 HOH A 104 904 136 HOH HOH . 
E 4 HOH A 105 905 86 HOH HOH . 
E 4 HOH A 106 906 117 HOH HOH . 
E 4 HOH A 107 907 44 HOH HOH . 
E 4 HOH A 108 908 134 HOH HOH . 
E 4 HOH A 109 909 102 HOH HOH . 
E 4 HOH A 110 910 139 HOH HOH . 
E 4 HOH A 111 911 20 HOH HOH . 
E 4 HOH A 112 912 58 HOH HOH . 
E 4 HOH A 113 913 62 HOH HOH . 
E 4 HOH A 114 914 121 HOH HOH . 
E 4 HOH A 115 915 78 HOH HOH . 
E 4 HOH A 116 916 103 HOH HOH . 
E 4 HOH A 117 917 10 HOH HOH . 
E 4 HOH A 118 918 111 HOH HOH . 
E 4 HOH A 119 919 109 HOH HOH . 
E 4 HOH A 120 920 137 HOH HOH . 
E 4 HOH A 121 921 123 HOH HOH . 
E 4 HOH A 122 922 42 HOH HOH . 
E 4 HOH A 123 923 28 HOH HOH . 
E 4 HOH A 124 924 89 HOH HOH . 
E 4 HOH A 125 925 70 HOH HOH . 
E 4 HOH A 126 926 46 HOH HOH . 
E 4 HOH A 127 927 135 HOH HOH . 
E 4 HOH A 128 928 105 HOH HOH . 
E 4 HOH A 129 929 90 HOH HOH . 
E 4 HOH A 130 930 91 HOH HOH . 
E 4 HOH A 131 931 115 HOH HOH . 
E 4 HOH A 132 932 99 HOH HOH . 
E 4 HOH A 133 933 88 HOH HOH . 
E 4 HOH A 134 934 125 HOH HOH . 
E 4 HOH A 135 935 119 HOH HOH . 
E 4 HOH A 136 936 132 HOH HOH . 
E 4 HOH A 137 937 131 HOH HOH . 
E 4 HOH A 138 938 96 HOH HOH . 
E 4 HOH A 139 939 72 HOH HOH . 
E 4 HOH A 140 940 39 HOH HOH . 
E 4 HOH A 141 941 106 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 2.913 -5.731 22.365 1 31.21 ? C1 GOL 701 A 1 
HETATM 2 O O1 GOL . . . B 2 4.066 -6.537 22.263 1 35.86 ? O1 GOL 701 A 1 
HETATM 3 C C2 GOL . . . B 2 2.916 -4.651 21.251 1 29.05 ? C2 GOL 701 A 1 
HETATM 4 O O2 GOL . . . B 2 3.827 -3.574 21.551 1 23.49 ? O2 GOL 701 A 1 
HETATM 5 C C3 GOL . . . B 2 3.175 -5.415 19.909 1 33.39 ? C3 GOL 701 A 1 
HETATM 6 O O3 GOL . . . B 2 3.002 -4.475 18.839 1 33.6 ? O3 GOL 701 A 1 
HETATM 7 H H11 GOL . . . B 2 2.858 -5.284 23.224 1 37.4 ? H11 GOL 701 A 1 
HETATM 8 H H12 GOL . . . B 2 2.099 -6.251 22.284 1 37.4 ? H12 GOL 701 A 1 
HETATM 9 H HO1 GOL . . . B 2 4.675 -6.039 21.975 1 42.99 ? HO1 GOL 701 A 1 
HETATM 10 H H2 GOL . . . B 2 2.055 -4.212 21.178 1 34.82 ? H2 GOL 701 A 1 
HETATM 11 H HO2 GOL . . . B 2 4.241 -3.385 20.837 1 28.14 ? HO2 GOL 701 A 1 
HETATM 12 H H31 GOL . . . B 2 2.567 -6.169 19.859 1 40.02 ? H31 GOL 701 A 1 
HETATM 13 H H32 GOL . . . B 2 4.063 -5.804 19.939 1 40.02 ? H32 GOL 701 A 1 
HETATM 14 H HO3 GOL . . . B 2 2.184 -4.261 18.831 1 40.27 ? HO3 GOL 701 A 1 
#
_model_server_stats.io_time_ms              121 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           401 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#