data_9R4O # _model_server_result.job_id b5Cby9iZZWzVdyEzWlHLIw _model_server_result.datetime_utc '2025-07-26 20:47:03' _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 9r4o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 9R4O # _exptl.entry_id 9R4O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _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 9R4O _cell.length_a 107.024 _cell.length_b 107.024 _cell.length_c 127.541 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9R4O _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 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 MAN _pdbx_entity_branch_link.comp_id_2 MAN _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B MAN 1 B 1 MAN A 550 MAN 2 n B MAN 2 B 2 MAN A 551 MAN # 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 204 A CYS 204 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 339 A CYS 339 1_555 A SG CYS 345 A CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 B O6 MAN . B MAN 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 9R4O _atom_sites.fract_transf_matrix[1][1] 0.009344 _atom_sites.fract_transf_matrix[1][2] 0.005395 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010789 _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] 0.007841 _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 MAN A 1 501 552 MAN MAN . D 4 GOL A 1 502 553 GOL GOL . E 5 HOH A 1 601 4 HOH HOH . E 5 HOH A 2 602 7 HOH HOH . E 5 HOH A 3 603 30 HOH HOH . E 5 HOH A 4 604 35 HOH HOH . E 5 HOH A 5 605 20 HOH HOH . E 5 HOH A 6 606 26 HOH HOH . E 5 HOH A 7 607 19 HOH HOH . E 5 HOH A 8 608 12 HOH HOH . E 5 HOH A 9 609 27 HOH HOH . E 5 HOH A 10 610 5 HOH HOH . E 5 HOH A 11 611 10 HOH HOH . E 5 HOH A 12 612 11 HOH HOH . E 5 HOH A 13 613 21 HOH HOH . E 5 HOH A 14 614 25 HOH HOH . E 5 HOH A 15 615 34 HOH HOH . E 5 HOH A 16 616 2 HOH HOH . E 5 HOH A 17 617 15 HOH HOH . E 5 HOH A 18 618 23 HOH HOH . E 5 HOH A 19 619 41 HOH HOH . E 5 HOH A 20 620 1 HOH HOH . E 5 HOH A 21 621 13 HOH HOH . E 5 HOH A 22 622 3 HOH HOH . E 5 HOH A 23 623 56 HOH HOH . E 5 HOH A 24 624 8 HOH HOH . E 5 HOH A 25 625 38 HOH HOH . E 5 HOH A 26 626 9 HOH HOH . E 5 HOH A 27 627 18 HOH HOH . E 5 HOH A 28 628 44 HOH HOH . E 5 HOH A 29 629 17 HOH HOH . E 5 HOH A 30 630 43 HOH HOH . E 5 HOH A 31 631 55 HOH HOH . E 5 HOH A 32 632 58 HOH HOH . E 5 HOH A 33 633 14 HOH HOH . E 5 HOH A 34 634 37 HOH HOH . E 5 HOH A 35 635 59 HOH HOH . E 5 HOH A 36 636 32 HOH HOH . E 5 HOH A 37 637 6 HOH HOH . E 5 HOH A 38 638 40 HOH HOH . E 5 HOH A 39 639 48 HOH HOH . E 5 HOH A 40 640 31 HOH HOH . E 5 HOH A 41 641 49 HOH HOH . E 5 HOH A 42 642 16 HOH HOH . E 5 HOH A 43 643 42 HOH HOH . E 5 HOH A 44 644 63 HOH HOH . E 5 HOH A 45 645 39 HOH HOH . E 5 HOH A 46 646 53 HOH HOH . E 5 HOH A 47 647 50 HOH HOH . E 5 HOH A 48 648 29 HOH HOH . E 5 HOH A 49 649 45 HOH HOH . E 5 HOH A 50 650 46 HOH HOH . E 5 HOH A 51 651 57 HOH HOH . E 5 HOH A 52 652 33 HOH HOH . E 5 HOH A 53 653 60 HOH HOH . E 5 HOH A 54 654 51 HOH HOH . E 5 HOH A 55 655 22 HOH HOH . E 5 HOH A 56 656 28 HOH HOH . E 5 HOH A 57 657 36 HOH HOH . E 5 HOH A 58 658 54 HOH HOH . E 5 HOH A 59 659 61 HOH HOH . E 5 HOH A 60 660 24 HOH HOH . E 5 HOH A 61 661 62 HOH HOH . E 5 HOH A 62 662 47 HOH HOH . E 5 HOH A 63 663 52 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 . . . D 4 12.434 76.929 40.698 0.91 92.33 ? C1 GOL 502 A 1 HETATM 2 O O1 GOL . . . D 4 13.317 77.994 40.535 0.91 94.77 ? O1 GOL 502 A 1 HETATM 3 C C2 GOL . . . D 4 11.001 77.522 40.75 0.91 95.5 ? C2 GOL 502 A 1 HETATM 4 O O2 GOL . . . D 4 10.704 78.267 39.618 0.91 85.46 ? O2 GOL 502 A 1 HETATM 5 C C3 GOL . . . D 4 10.953 78.369 42.049 0.91 95.89 ? C3 GOL 502 A 1 HETATM 6 O O3 GOL . . . D 4 11.651 79.549 41.793 0.91 102.03 ? O3 GOL 502 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #