data_5OGL # _model_server_result.job_id iCrknrJ2nK_A6VOvAxe0wQ _model_server_result.datetime_utc '2025-08-31 14:21:39' _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 5ogl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":803}' # _entry.id 5OGL # _exptl.entry_id 5OGL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 651.663 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid' _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 90 _cell.entry_id 5OGL _cell.length_a 83.94 _cell.length_b 116.18 _cell.length_c 172.02 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OGL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F,G,H _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 E _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 covale ? covale1 B C THR 6 B THR 15 1_555 B N PPN 7 B PPN 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale2 B C PPN 7 B PPN 16 1_555 B N GLY 8 B GLY 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OE1 GLU 43 A GLU 43 1_555 F NA NA . A NA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? metalc ? metalc2 A OE2 GLU 43 A GLU 43 1_555 F NA NA . A NA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc3 A OD2 ASP 56 A ASP 56 1_555 C MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc4 A OE1 GLN 73 A GLN 73 1_555 D MN MN . A MN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc5 A OD2 ASP 76 A ASP 76 1_555 D MN MN . A MN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc6 A OD1 ASP 154 A ASP 154 1_555 C MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc7 A OD1 ASP 475 A ASP 475 1_555 D MN MN . A MN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc8 C MN MN . A MN 801 1_555 G O HOH . A HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc9 C MN MN . A MN 801 1_555 G O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc10 C MN MN . A MN 801 1_555 G O HOH . A HOH 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc11 D MN MN . A MN 802 1_555 G O HOH . A HOH 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? # _chem_comp.formula 'C29 H51 N O11 P2' _chem_comp.formula_weight 651.663 _chem_comp.id 9UB _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O43 C41 9UB doub 1 n n O34 C33 9UB sing 2 n n C41 C42 9UB sing 3 n n C41 N40 9UB sing 4 n n C39 N40 9UB sing 5 n n C39 C30 9UB sing 6 n n C39 C37 9UB sing 7 n n C33 C32 9UB sing 8 n n O31 C30 9UB sing 9 n n O31 C32 9UB sing 10 n n C30 C29 9UB sing 11 n n O38 C37 9UB sing 12 n n C35 C37 9UB sing 13 n n C35 C32 9UB sing 14 n n C35 O36 9UB sing 15 n n O28 P26 9UB doub 16 n n C29 P26 9UB sing 17 n n O23 P22 9UB doub 18 n n P26 O25 9UB sing 19 n n P26 O27 9UB sing 20 n n O25 P22 9UB sing 21 n n P22 O24 9UB sing 22 n n P22 O21 9UB sing 23 n n O21 C20 9UB sing 24 n n C20 C19 9UB sing 25 n n C19 C17 9UB doub 26 z n C13 C12 9UB sing 27 n n C14 C12 9UB doub 28 z n C14 C15 9UB sing 29 n n C17 C16 9UB sing 30 n n C17 C18 9UB sing 31 n n C16 C15 9UB sing 32 n n C12 C11 9UB sing 33 n n C11 C10 9UB sing 34 n n C10 C09 9UB sing 35 n n C09 C07 9UB doub 36 z n C07 C06 9UB sing 37 n n C07 C08 9UB sing 38 n n C03 C02 9UB sing 39 n n C06 C05 9UB sing 40 n n C04 C02 9UB doub 41 n n C04 C05 9UB sing 42 n n C02 C01 9UB sing 43 n n C30 H1 9UB sing 44 n n C29 H2 9UB sing 45 n n C29 H3 9UB sing 46 n n C20 H4 9UB sing 47 n n C20 H5 9UB sing 48 n n C16 H6 9UB sing 49 n n C16 H7 9UB sing 50 n n C15 H8 9UB sing 51 n n C15 H9 9UB sing 52 n n C14 H10 9UB sing 53 n n C13 H11 9UB sing 54 n n C13 H12 9UB sing 55 n n C13 H13 9UB sing 56 n n C18 H14 9UB sing 57 n n C18 H15 9UB sing 58 n n C18 H16 9UB sing 59 n n C11 H17 9UB sing 60 n n C11 H18 9UB sing 61 n n C09 H19 9UB sing 62 n n C08 H20 9UB sing 63 n n C08 H21 9UB sing 64 n n C08 H22 9UB sing 65 n n C06 H23 9UB sing 66 n n C06 H24 9UB sing 67 n n C05 H25 9UB sing 68 n n C05 H26 9UB sing 69 n n C04 H27 9UB sing 70 n n C03 H28 9UB sing 71 n n C03 H29 9UB sing 72 n n C03 H30 9UB sing 73 n n C01 H31 9UB sing 74 n n C01 H32 9UB sing 75 n n C01 H33 9UB sing 76 n n C10 H34 9UB sing 77 n n C10 H35 9UB sing 78 n n C19 H36 9UB sing 79 n n O24 H37 9UB sing 80 n n O27 H38 9UB sing 81 n n C32 H39 9UB sing 82 n n C33 H40 9UB sing 83 n n C33 H41 9UB sing 84 n n O34 H42 9UB sing 85 n n C35 H43 9UB sing 86 n n O36 H44 9UB sing 87 n n C37 H45 9UB sing 88 n n O38 H46 9UB sing 89 n n C39 H47 9UB sing 90 n n N40 H48 9UB sing 91 n n C42 H49 9UB sing 92 n n C42 H50 9UB sing 93 n n C42 H51 9UB sing 94 n n # _atom_sites.entry_id 5OGL _atom_sites.fract_transf_matrix[1][1] 0.011913 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008607 _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] 0.005813 _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 MN A 1 801 1 MN MN . D 3 MN A 1 802 2 MN MN . E 4 9UB A 1 803 1 9UB JB1 . F 5 NA A 1 804 1 NA NA . G 6 HOH A 1 901 70 HOH HOH . G 6 HOH A 2 902 76 HOH HOH . G 6 HOH A 3 903 69 HOH HOH . G 6 HOH A 4 904 49 HOH HOH . G 6 HOH A 5 905 1 HOH HOH . G 6 HOH A 6 906 16 HOH HOH . G 6 HOH A 7 907 42 HOH HOH . G 6 HOH A 8 908 55 HOH HOH . G 6 HOH A 9 909 2 HOH HOH . G 6 HOH A 10 910 77 HOH HOH . G 6 HOH A 11 911 32 HOH HOH . G 6 HOH A 12 912 71 HOH HOH . G 6 HOH A 13 913 5 HOH HOH . G 6 HOH A 14 914 3 HOH HOH . G 6 HOH A 15 915 75 HOH HOH . G 6 HOH A 16 916 74 HOH HOH . G 6 HOH A 17 917 50 HOH HOH . G 6 HOH A 18 918 72 HOH HOH . G 6 HOH A 19 919 73 HOH HOH . H 6 HOH B 1 101 57 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 C30 9UB . . . E 4 88.854 42.682 190.457 1 78.67 ? C30 9UB 803 A 1 HETATM 2 C C29 9UB . . . E 4 89.278 42.257 191.832 1 80.26 ? C29 9UB 803 A 1 HETATM 3 C C20 9UB . . . E 4 83.731 40.39 195.114 1 75.74 ? C20 9UB 803 A 1 HETATM 4 C C17 9UB . . . E 4 83.722 40.117 197.615 1 73.08 ? C17 9UB 803 A 1 HETATM 5 C C16 9UB . . . E 4 82.838 41.397 197.682 1 73.44 ? C16 9UB 803 A 1 HETATM 6 C C15 9UB . . . E 4 81.438 41.201 198.314 1 73 ? C15 9UB 803 A 1 HETATM 7 C C14 9UB . . . E 4 80.6 40.178 197.571 1 72.98 ? C14 9UB 803 A 1 HETATM 8 C C13 9UB . . . E 4 78.515 39.013 196.966 1 73.6 ? C13 9UB 803 A 1 HETATM 9 C C18 9UB . . . E 4 84.164 39.338 198.895 1 72.91 ? C18 9UB 803 A 1 HETATM 10 C C12 9UB . . . E 4 79.289 40.085 197.739 1 75.84 ? C12 9UB 803 A 1 HETATM 11 C C11 9UB . . . E 4 78.511 41.022 198.72 1 77.06 ? C11 9UB 803 A 1 HETATM 12 C C09 9UB . . . E 4 77.37 41.227 201.032 1 79.53 ? C09 9UB 803 A 1 HETATM 13 C C08 9UB . . . E 4 76.633 42.268 203.207 1 78.64 ? C08 9UB 803 A 1 HETATM 14 C C07 9UB . . . E 4 77.631 41.453 202.346 1 81.49 ? C07 9UB 803 A 1 HETATM 15 C C06 9UB . . . E 4 78.941 40.897 203.01 1 79.73 ? C06 9UB 803 A 1 HETATM 16 C C05 9UB . . . E 4 78.599 39.824 204.049 1 78.1 ? C05 9UB 803 A 1 HETATM 17 C C04 9UB . . . E 4 78.072 38.562 203.378 1 76.96 ? C04 9UB 803 A 1 HETATM 18 C C03 9UB . . . E 4 76.365 36.844 202.892 1 76.48 ? C03 9UB 803 A 1 HETATM 19 C C02 9UB . . . E 4 76.852 38.128 203.593 1 78.74 ? C02 9UB 803 A 1 HETATM 20 C C01 9UB . . . E 4 75.917 38.909 204.533 1 76.66 ? C01 9UB 803 A 1 HETATM 21 C C10 9UB . . . E 4 78.328 40.41 200.131 1 77.99 ? C10 9UB 803 A 1 HETATM 22 C C19 9UB . . . E 4 84.134 39.649 196.413 1 78.03 ? C19 9UB 803 A 1 HETATM 23 O O21 9UB . . . E 4 84.861 40.321 194.282 1 73.5 ? O21 9UB 803 A 1 HETATM 24 P P22 9UB . . . E 4 85.107 41.558 193.233 1 73.71 ? P22 9UB 803 A 1 HETATM 25 O O23 9UB . . . E 4 84.549 41.099 191.912 1 73.81 ? O23 9UB 803 A 1 HETATM 26 O O24 9UB . . . E 4 84.386 42.803 193.688 1 73.72 ? O24 9UB 803 A 1 HETATM 27 O O25 9UB . . . E 4 86.722 41.991 193.142 1 73.8 ? O25 9UB 803 A 1 HETATM 28 P P26 9UB . . . E 4 88.018 41.07 192.632 1 73.84 ? P26 9UB 803 A 1 HETATM 29 O O27 9UB . . . E 4 88.645 40.299 193.772 1 73.69 ? O27 9UB 803 A 1 HETATM 30 O O28 9UB . . . E 4 87.511 40.103 191.602 1 73.88 ? O28 9UB 803 A 1 HETATM 31 O O31 9UB . . . E 4 87.404 42.995 190.427 1 86.22 ? O31 9UB 803 A 1 HETATM 32 C C32 9UB . . . E 4 86.981 44.337 190.88 1 86.24 ? C32 9UB 803 A 1 HETATM 33 C C33 9UB . . . E 4 85.645 44.653 190.256 1 86.67 ? C33 9UB 803 A 1 HETATM 34 O O34 9UB . . . E 4 85.835 44.63 188.847 1 91.34 ? O34 9UB 803 A 1 HETATM 35 C C35 9UB . . . E 4 87.958 45.464 190.504 1 84.67 ? C35 9UB 803 A 1 HETATM 36 O O36 9UB . . . E 4 87.564 46.648 191.219 1 83.68 ? O36 9UB 803 A 1 HETATM 37 C C37 9UB . . . E 4 89.352 45.051 190.807 1 80.8 ? C37 9UB 803 A 1 HETATM 38 O O38 9UB . . . E 4 90.352 46.085 190.504 1 79.5 ? O38 9UB 803 A 1 HETATM 39 C C39 9UB . . . E 4 89.678 43.874 190.009 1 78.62 ? C39 9UB 803 A 1 HETATM 40 N N40 9UB . . . E 4 91.122 43.6 190.195 1 79.87 ? N40 9UB 803 A 1 HETATM 41 C C41 9UB . . . E 4 91.784 42.831 189.153 1 79.4 ? C41 9UB 803 A 1 HETATM 42 C C42 9UB . . . E 4 93.276 42.533 189.281 1 77.77 ? C42 9UB 803 A 1 HETATM 43 O O43 9UB . . . E 4 91.139 42.453 188.228 1 77.31 ? O43 9UB 803 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 61 _model_server_stats.query_time_ms 412 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #