data_9D3Y # _model_server_result.job_id ugszXX_MCwQQNndmosjSWQ _model_server_result.datetime_utc '2025-07-01 11:38:09' _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 9d3y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":702}' # _entry.id 9D3Y # _exptl.entry_id 9D3Y _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 98.01 _cell.angle_gamma 90 _cell.entry_id 9D3Y _cell.length_a 72.77 _cell.length_b 41.05 _cell.length_c 102.92 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9D3Y _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,F,G,H,I _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 ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 34 A CYS 396 1_555 A SG CYS 68 A CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 72 A CYS 434 1_555 A SG CYS 190 A CYS 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 236 A CYS 598 1_555 A SG CYS 256 A CYS 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 267 A CYS 629 1_555 A SG CYS 298 A CYS 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _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 196 n n C1 C2 GOL sing 197 n n C1 H11 GOL sing 198 n n C1 H12 GOL sing 199 n n O1 HO1 GOL sing 200 n n C2 O2 GOL sing 201 n n C2 C3 GOL sing 202 n n C2 H2 GOL sing 203 n n O2 HO2 GOL sing 204 n n C3 O3 GOL sing 205 n n C3 H31 GOL sing 206 n n C3 H32 GOL sing 207 n n O3 HO3 GOL sing 208 n n # _atom_sites.entry_id 9D3Y _atom_sites.fract_transf_matrix[1][1] 0.013742 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001934 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024361 _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] 0.009812 _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 2 GOL A 1 703 3 GOL GOL . E 2 GOL A 1 704 4 GOL GOL . F 2 GOL A 1 705 5 GOL GOL . G 2 GOL A 1 706 7 GOL GOL . H 3 A1A1Y A 1 707 1 A1A1Y SJ0 . I 4 HOH A 1 801 33 HOH HOH . I 4 HOH A 2 802 34 HOH HOH . I 4 HOH A 3 803 5 HOH HOH . I 4 HOH A 4 804 36 HOH HOH . I 4 HOH A 5 805 53 HOH HOH . I 4 HOH A 6 806 57 HOH HOH . I 4 HOH A 7 807 17 HOH HOH . I 4 HOH A 8 808 29 HOH HOH . I 4 HOH A 9 809 3 HOH HOH . I 4 HOH A 10 810 38 HOH HOH . I 4 HOH A 11 811 51 HOH HOH . I 4 HOH A 12 812 50 HOH HOH . I 4 HOH A 13 813 15 HOH HOH . I 4 HOH A 14 814 12 HOH HOH . I 4 HOH A 15 815 43 HOH HOH . I 4 HOH A 16 816 10 HOH HOH . I 4 HOH A 17 817 26 HOH HOH . I 4 HOH A 18 818 32 HOH HOH . I 4 HOH A 19 819 13 HOH HOH . I 4 HOH A 20 820 39 HOH HOH . I 4 HOH A 21 821 47 HOH HOH . I 4 HOH A 22 822 31 HOH HOH . I 4 HOH A 23 823 48 HOH HOH . I 4 HOH A 24 824 25 HOH HOH . I 4 HOH A 25 825 7 HOH HOH . I 4 HOH A 26 826 37 HOH HOH . I 4 HOH A 27 827 18 HOH HOH . I 4 HOH A 28 828 8 HOH HOH . I 4 HOH A 29 829 22 HOH HOH . I 4 HOH A 30 830 59 HOH HOH . I 4 HOH A 31 831 2 HOH HOH . I 4 HOH A 32 832 41 HOH HOH . I 4 HOH A 33 833 28 HOH HOH . I 4 HOH A 34 834 30 HOH HOH . I 4 HOH A 35 835 20 HOH HOH . I 4 HOH A 36 836 61 HOH HOH . I 4 HOH A 37 837 11 HOH HOH . I 4 HOH A 38 838 4 HOH HOH . I 4 HOH A 39 839 14 HOH HOH . I 4 HOH A 40 840 54 HOH HOH . I 4 HOH A 41 841 45 HOH HOH . I 4 HOH A 42 842 16 HOH HOH . I 4 HOH A 43 843 1 HOH HOH . I 4 HOH A 44 844 42 HOH HOH . I 4 HOH A 45 845 21 HOH HOH . I 4 HOH A 46 846 6 HOH HOH . I 4 HOH A 47 847 35 HOH HOH . I 4 HOH A 48 848 27 HOH HOH . I 4 HOH A 49 849 24 HOH HOH . I 4 HOH A 50 850 65 HOH HOH . I 4 HOH A 51 851 23 HOH HOH . I 4 HOH A 52 852 44 HOH HOH . I 4 HOH A 53 853 63 HOH HOH . I 4 HOH A 54 854 58 HOH HOH . I 4 HOH A 55 855 52 HOH HOH . I 4 HOH A 56 856 46 HOH HOH . I 4 HOH A 57 857 62 HOH HOH . I 4 HOH A 58 858 19 HOH HOH . I 4 HOH A 59 859 67 HOH HOH . I 4 HOH A 60 860 40 HOH HOH . I 4 HOH A 61 861 55 HOH HOH . I 4 HOH A 62 862 64 HOH HOH . I 4 HOH A 63 863 56 HOH HOH . I 4 HOH A 64 864 49 HOH HOH . I 4 HOH A 65 865 66 HOH HOH . I 4 HOH A 66 866 9 HOH HOH . I 4 HOH A 67 867 60 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 2 2.741 -6.318 22.741 1 38.19 ? C1 GOL 702 A 1 HETATM 2 O O1 GOL . . . C 2 3.915 -7.064 22.609 1 37.61 ? O1 GOL 702 A 1 HETATM 3 C C2 GOL . . . C 2 2.766 -5.165 21.7 1 34.73 ? C2 GOL 702 A 1 HETATM 4 O O2 GOL . . . C 2 3.753 -4.225 21.977 1 32.58 ? O2 GOL 702 A 1 HETATM 5 C C3 GOL . . . C 2 2.97 -5.839 20.314 1 43.36 ? C3 GOL 702 A 1 HETATM 6 O O3 GOL . . . C 2 2.904 -4.817 19.357 1 43.93 ? O3 GOL 702 A 1 HETATM 7 H H11 GOL . . . C 2 2.646 -5.937 23.628 1 45.87 ? H11 GOL 702 A 1 HETATM 8 H H12 GOL . . . C 2 1.946 -6.854 22.596 1 45.87 ? H12 GOL 702 A 1 HETATM 9 H HO1 GOL . . . C 2 3.708 -7.768 22.178 1 45.17 ? HO1 GOL 702 A 1 HETATM 10 H H2 GOL . . . C 2 1.922 -4.687 21.722 1 41.71 ? H2 GOL 702 A 1 HETATM 11 H HO2 GOL . . . C 2 4.474 -4.643 22.142 1 39.13 ? HO2 GOL 702 A 1 HETATM 12 H H31 GOL . . . C 2 2.294 -6.524 20.194 1 52.08 ? H31 GOL 702 A 1 HETATM 13 H H32 GOL . . . C 2 3.817 -6.312 20.315 1 52.08 ? H32 GOL 702 A 1 HETATM 14 H HO3 GOL . . . C 2 3.028 -5.178 18.598 1 52.75 ? HO3 GOL 702 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #