data_4FYG # _model_server_result.job_id rSpxYPKOhps_vtcGtWKEwA _model_server_result.datetime_utc '2024-12-02 04:10:18' _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 4fyg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 4FYG # _exptl.entry_id 4FYG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 634.354 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate' _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 4FYG _cell.length_a 71.23 _cell.length_b 114.833 _cell.length_c 124.366 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FYG _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 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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C17 H33 O19 P3' _chem_comp.formula_weight 634.354 _chem_comp.id 3PT _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate' _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 O0M C0L 3PT doub 1 n n C0L C0N 3PT sing 2 n n C0L O0F 3PT sing 3 n n C0N C0P 3PT sing 4 n n O0F C0E 3PT sing 5 n n C0P C0Q 3PT sing 6 n n C0K C0J 3PT sing 7 n n C0E C0C 3PT sing 8 n n C0I C0J 3PT sing 9 n n C0I C0G 3PT sing 10 n n C0C O0D 3PT sing 11 n n C0C C0B 3PT sing 12 n n O0D C0G 3PT sing 13 n n C0G O0H 3PT doub 14 n n O6 C6 3PT sing 15 n n C0B OP1 3PT sing 16 n n O5 C5 3PT sing 17 n n OP5 P4 3PT doub 18 n n C5 C6 3PT sing 19 n n C5 C4 3PT sing 20 n n C6 C1 3PT sing 21 n n OP1 P1 3PT sing 22 n n OP4 P4 3PT sing 23 n n P4 O4 3PT sing 24 n n P4 OP6 3PT sing 25 n n O4 C4 3PT sing 26 n n C4 C3 3PT sing 27 n n C1 O1 3PT sing 28 n n C1 C2 3PT sing 29 n n OP2 P1 3PT doub 30 n n O1 P1 3PT sing 31 n n P1 OP3 3PT sing 32 n n C3 C2 3PT sing 33 n n C3 O3 3PT sing 34 n n C2 O2 3PT sing 35 n n O3 P3 3PT sing 36 n n O10 P3 3PT doub 37 n n P3 O12 3PT sing 38 n n P3 O11 3PT sing 39 n n C0I H1 3PT sing 40 n n C0I H2 3PT sing 41 n n C0J H3 3PT sing 42 n n C0J H4 3PT sing 43 n n C0K H5 3PT sing 44 n n C0K H6 3PT sing 45 n n C0K H7 3PT sing 46 n n C0C H8 3PT sing 47 n n C0E H9 3PT sing 48 n n C0E H10 3PT sing 49 n n C0N H11 3PT sing 50 n n C0N H12 3PT sing 51 n n C0P H13 3PT sing 52 n n C0P H14 3PT sing 53 n n C0Q H15 3PT sing 54 n n C0Q H16 3PT sing 55 n n C0Q H17 3PT sing 56 n n C0B H18 3PT sing 57 n n C0B H19 3PT sing 58 n n OP3 H20 3PT sing 59 n n C1 H21 3PT sing 60 n n C2 H22 3PT sing 61 n n O2 H23 3PT sing 62 n n C3 H24 3PT sing 63 n n O12 H25 3PT sing 64 n n O11 H26 3PT sing 65 n n C4 H27 3PT sing 66 n n OP4 H28 3PT sing 67 n n OP6 H29 3PT sing 68 n n C5 H30 3PT sing 69 n n O5 H31 3PT sing 70 n n C6 H32 3PT sing 71 n n O6 H33 3PT sing 72 n n # _atom_sites.entry_id 4FYG _atom_sites.fract_transf_matrix[1][1] 0.014039 _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] 0.008708 _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] 0.008041 _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 3PT A 1 801 1 3PT 3PT . C 3 HOH A 1 901 1 HOH HOH . C 3 HOH A 2 902 2 HOH HOH . C 3 HOH A 3 903 3 HOH HOH . C 3 HOH A 4 904 4 HOH HOH . C 3 HOH A 5 905 5 HOH HOH . C 3 HOH A 6 906 6 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 O O0H 3PT . . . B 2 8.487 34.356 6.383 1 95.43 ? O0H 3PT 801 A 1 HETATM 2 C C0G 3PT . . . B 2 8.048 34.935 5.385 1 94.44 ? C0G 3PT 801 A 1 HETATM 3 C C0I 3PT . . . B 2 8.991 35.235 4.229 1 87.7 ? C0I 3PT 801 A 1 HETATM 4 C C0J 3PT . . . B 2 10.43 34.908 4.628 1 84.87 ? C0J 3PT 801 A 1 HETATM 5 C C0K 3PT . . . B 2 11.154 34.224 3.497 1 80.88 ? C0K 3PT 801 A 1 HETATM 6 O O0D 3PT . . . B 2 6.6 35.239 5.339 1 92.74 ? O0D 3PT 801 A 1 HETATM 7 C C0C 3PT . . . B 2 6.002 36.551 5.17 1 82.62 ? C0C 3PT 801 A 1 HETATM 8 C C0E 3PT . . . B 2 6.084 37.066 3.723 1 88.69 ? C0E 3PT 801 A 1 HETATM 9 O O0F 3PT . . . B 2 6.356 36.007 2.781 1 99.53 ? O0F 3PT 801 A 1 HETATM 10 C C0L 3PT . . . B 2 5.585 34.755 2.677 1 113.05 ? C0L 3PT 801 A 1 HETATM 11 C C0N 3PT . . . B 2 6.258 33.371 2.737 1 115.56 ? C0N 3PT 801 A 1 HETATM 12 C C0P 3PT . . . B 2 5.452 32.262 3.45 1 109.08 ? C0P 3PT 801 A 1 HETATM 13 C C0Q 3PT . . . B 2 6.28 31.256 4.25 1 89.51 ? C0Q 3PT 801 A 1 HETATM 14 O O0M 3PT . . . B 2 4.375 34.856 2.529 1 123.47 ? O0M 3PT 801 A 1 HETATM 15 C C0B 3PT . . . B 2 6.484 37.525 6.24 1 74.54 ? C0B 3PT 801 A 1 HETATM 16 O OP1 3PT . . . B 2 5.977 37.045 7.487 1 67.74 ? OP1 3PT 801 A 1 HETATM 17 P P1 3PT . . . B 2 5.343 37.897 8.728 1 68.22 ? P1 3PT 801 A 1 HETATM 18 O OP3 3PT . . . B 2 5.728 37.273 10.067 1 74.32 ? OP3 3PT 801 A 1 HETATM 19 O OP2 3PT . . . B 2 5.558 39.378 8.527 1 72.2 ? OP2 3PT 801 A 1 HETATM 20 O O1 3PT . . . B 2 3.795 37.458 8.552 1 72.36 ? O1 3PT 801 A 1 HETATM 21 C C1 3PT . . . B 2 2.686 38.325 8.35 1 69.07 ? C1 3PT 801 A 1 HETATM 22 C C2 3PT . . . B 2 1.881 38.427 9.642 1 64.35 ? C2 3PT 801 A 1 HETATM 23 O O2 3PT . . . B 2 1.596 37.092 10.09 1 57.85 ? O2 3PT 801 A 1 HETATM 24 C C3 3PT . . . B 2 0.557 39.181 9.446 1 64.44 ? C3 3PT 801 A 1 HETATM 25 O O3 3PT . . . B 2 -0.244 39.085 10.64 1 61.47 ? O3 3PT 801 A 1 HETATM 26 P P3 3PT . . . B 2 -0.087 40.007 11.96 1 51.61 ? P3 3PT 801 A 1 HETATM 27 O O12 3PT . . . B 2 1.35 39.959 12.463 1 51.57 ? O12 3PT 801 A 1 HETATM 28 O O10 3PT . . . B 2 -0.527 41.298 11.379 1 56.49 ? O10 3PT 801 A 1 HETATM 29 O O11 3PT . . . B 2 -1.089 39.402 12.896 1 60.99 ? O11 3PT 801 A 1 HETATM 30 C C4 3PT . . . B 2 -0.261 38.509 8.342 1 64.36 ? C4 3PT 801 A 1 HETATM 31 O O4 3PT . . . B 2 -1.477 39.204 8.079 1 67.38 ? O4 3PT 801 A 1 HETATM 32 P P4 3PT . . . B 2 -2.881 38.412 8.065 1 63.56 ? P4 3PT 801 A 1 HETATM 33 O OP4 3PT . . . B 2 -2.538 37.001 7.66 1 68.65 ? OP4 3PT 801 A 1 HETATM 34 O OP6 3PT . . . B 2 -3.398 38.531 9.475 1 66.46 ? OP6 3PT 801 A 1 HETATM 35 O OP5 3PT . . . B 2 -3.682 39.143 7.026 1 63.04 ? OP5 3PT 801 A 1 HETATM 36 C C5 3PT . . . B 2 0.476 38.181 7.039 1 61.5 ? C5 3PT 801 A 1 HETATM 37 O O5 3PT . . . B 2 -0.264 37.101 6.491 1 59.86 ? O5 3PT 801 A 1 HETATM 38 C C6 3PT . . . B 2 1.879 37.628 7.256 1 66.85 ? C6 3PT 801 A 1 HETATM 39 O O6 3PT . . . B 2 2.619 37.621 6.035 1 71.41 ? O6 3PT 801 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #