data_1VBD # _model_server_result.job_id JI9t5fna5glIeWx2RYBiVQ _model_server_result.datetime_utc '2024-12-25 16:46:57' _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 1vbd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1}' # _entry.id 1VBD # _exptl.entry_id 1VBD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.371 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MYRISTIC 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 1VBD _cell.length_a 322.94 _cell.length_b 358.04 _cell.length_c 380.15 _cell.Z_PDB 120 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 300-MERIC 300 'complete icosahedral assembly' 1 ? pentameric 5 'icosahedral asymmetric unit' 2 ? 25-meric 25 'icosahedral pentamer' 3 ? 30-meric 30 'icosahedral 23 hexamer' 4 ? pentameric 5 'icosahedral asymmetric unit, std point frame' 5 ? 150-meric 150 'crystal asymmetric unit, crystal frame' 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 (1-60) A,B,C,D,E,F,G 2 1 A,B,C,D,E,F,G 3 (1-5) A,B,C,D,E,F,G 4 (1,2,6,10,23,24) A,B,C,D,E,F,G 5 P A,B,C,D,E,F,G 6 (X0)(1-5,11-15,21-30,41-50) # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 P 'transform to point frame' ? ? 0.999288 0.037725 0 -0.037725 0.999288 0 0 0 1 0 0 94.92208 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.309289 -0.816217 0.487986 0.801817 0.499728 0.327659 -0.511302 0.289935 0.809017 46.32068 31.10212 -18.1285 3 'point symmetry operation' ? ? -0.808305 -0.518849 0.278277 0.481151 -0.309729 0.820099 -0.339317 0.796784 0.5 26.41461 77.84547 -47.46104 4 'point symmetry operation' ? ? -0.808305 0.481151 -0.339317 -0.518849 -0.309729 0.796783 0.278277 0.820099 0.5 -32.20869 75.63233 -47.46104 5 'point symmetry operation' ? ? 0.309289 0.801817 -0.511302 -0.816217 0.499728 0.289934 0.487986 0.32766 0.809017 -48.53382 27.52118 -18.1285 6 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 0 0 0 7 'point symmetry operation' ? ? -0.309289 0.816217 -0.487986 -0.801817 -0.499728 -0.327659 -0.511302 0.289935 0.809017 -46.32068 -31.10212 -18.1285 8 'point symmetry operation' ? ? 0.808305 0.518849 -0.278277 -0.481151 0.309729 -0.820099 -0.339317 0.796784 0.5 -26.41461 -77.84547 -47.46104 9 'point symmetry operation' ? ? 0.808305 -0.481151 0.339317 0.518849 0.309729 -0.796783 0.278277 0.820099 0.5 32.20869 -75.63233 -47.46104 10 'point symmetry operation' ? ? -0.309289 -0.801817 0.511302 0.816217 -0.499728 -0.289934 0.487986 0.32766 0.809017 48.53382 -27.52118 -18.1285 11 'point symmetry operation' ? ? -0.997154 -0.075396 0 -0.075396 0.997154 0 0 0 -1 0 0 -189.84416 12 'point symmetry operation' ? ? -0.368863 0.776216 -0.511302 0.776216 0.559846 0.289934 0.511302 -0.289935 -0.809017 -48.53382 27.52118 -171.71566 13 'point symmetry operation' ? ? 0.769728 0.540725 -0.339317 0.540725 -0.269728 0.796783 0.339317 -0.796784 -0.5 -32.20869 75.63233 -142.38312 14 'point symmetry operation' ? ? 0.845124 -0.456429 0.278277 -0.456429 -0.345124 0.820099 -0.278277 -0.820099 -0.5 26.41461 77.84547 -142.38312 15 'point symmetry operation' ? ? -0.246869 -0.837213 0.487986 -0.837213 0.437852 0.327659 -0.487986 -0.32766 -0.809017 46.32068 31.10212 -171.71566 16 'point symmetry operation' ? ? 0.997154 0.075396 0 0.075396 -0.997154 0 0 0 -1 0 0 -189.84416 17 'point symmetry operation' ? ? 0.368863 -0.776216 0.511302 -0.776216 -0.559846 -0.289934 0.511302 -0.289935 -0.809017 48.53382 -27.52118 -171.71566 18 'point symmetry operation' ? ? -0.769728 -0.540725 0.339317 -0.540725 0.269728 -0.796783 0.339317 -0.796784 -0.5 32.20869 -75.63233 -142.38312 19 'point symmetry operation' ? ? -0.845124 0.456429 -0.278277 0.456429 0.345124 -0.820099 -0.278277 -0.820099 -0.5 -26.41461 -77.84547 -142.38312 20 'point symmetry operation' ? ? 0.246869 0.837213 -0.487986 0.837213 -0.437852 -0.327659 -0.487986 -0.32766 -0.809017 -46.32068 -31.10212 -171.71566 21 'point symmetry operation' ? ? -0.037698 -0.001423 0.999288 0.998577 0.037698 0.037725 -0.037725 0.999288 0 94.8545 3.58094 -94.92208 22 'point symmetry operation' ? ? -0.523739 0.319787 0.789578 0.319787 -0.785278 0.530164 0.789579 0.530164 0.309017 74.94843 50.32429 -65.58954 23 'point symmetry operation' ? ? -0.309289 0.816217 0.487986 -0.801817 -0.499728 0.327659 0.511302 -0.289935 0.809017 46.32068 31.10212 -18.1285 24 'point symmetry operation' ? ? 0.309289 0.801817 0.511302 -0.816217 0.499728 -0.289934 -0.487986 -0.32766 0.809017 48.53382 -27.52118 -18.1285 25 'point symmetry operation' ? ? 0.477141 0.296488 0.827303 0.296488 0.831876 -0.469124 -0.827304 0.469124 0.309017 78.52937 -44.53021 -65.58954 26 'point symmetry operation' ? ? 0.037698 0.001423 0.999288 -0.998577 -0.037698 0.037725 0.037725 -0.999288 0 94.8545 3.58094 -94.92208 27 'point symmetry operation' ? ? -0.498137 0.259669 0.827303 -0.358365 0.807154 -0.469124 -0.789579 -0.530164 -0.309017 78.52937 -44.53021 -124.25462 28 'point symmetry operation' ? ? -0.368863 0.776216 0.511302 0.776216 0.559846 -0.289934 -0.511302 0.289935 -0.809017 48.53382 -27.52118 -171.71566 29 'point symmetry operation' ? ? 0.246869 0.837213 0.487986 0.837213 -0.437852 0.327659 0.487986 0.32766 -0.809017 46.32068 31.10212 -171.71566 30 'point symmetry operation' ? ? 0.498137 0.358365 0.789578 -0.259669 -0.807154 0.530164 0.827304 -0.469124 -0.309017 74.94843 50.32429 -124.25462 31 'point symmetry operation' ? ? 0.037698 0.001423 -0.999288 -0.998577 -0.037698 -0.037725 -0.037725 0.999288 0 -94.8545 -3.58094 -94.92208 32 'point symmetry operation' ? ? 0.523739 -0.319787 -0.789578 -0.319787 0.785278 -0.530164 0.789579 0.530164 0.309017 -74.94843 -50.32429 -65.58954 33 'point symmetry operation' ? ? 0.309289 -0.816217 -0.487986 0.801817 0.499728 -0.327659 0.511302 -0.289935 0.809017 -46.32068 -31.10212 -18.1285 34 'point symmetry operation' ? ? -0.309289 -0.801817 -0.511302 0.816217 -0.499728 0.289934 -0.487986 -0.32766 0.809017 -48.53382 27.52118 -18.1285 35 'point symmetry operation' ? ? -0.477141 -0.296488 -0.827303 -0.296488 -0.831876 0.469124 -0.827304 0.469124 0.309017 -78.52937 44.53021 -65.58954 36 'point symmetry operation' ? ? -0.037698 -0.001423 -0.999288 0.998577 0.037698 -0.037725 0.037725 -0.999288 0 -94.8545 -3.58094 -94.92208 37 'point symmetry operation' ? ? 0.498137 -0.259669 -0.827303 0.358365 -0.807154 0.469124 -0.789579 -0.530164 -0.309017 -78.52937 44.53021 -124.25462 38 'point symmetry operation' ? ? 0.368863 -0.776216 -0.511302 -0.776216 -0.559846 0.289934 -0.511302 0.289935 -0.809017 -48.53382 27.52118 -171.71566 39 'point symmetry operation' ? ? -0.246869 -0.837213 -0.487986 -0.837213 0.437852 -0.327659 0.487986 0.32766 -0.809017 -46.32068 -31.10212 -171.71566 40 'point symmetry operation' ? ? -0.498137 -0.358365 -0.789578 0.259669 0.807154 -0.530164 0.827304 -0.469124 -0.309017 -74.94843 -50.32429 -124.25462 41 'point symmetry operation' ? ? -0.037698 0.998577 -0.037725 -0.001423 0.037698 0.999288 0.999288 0.037725 0 -3.58094 94.8545 -94.92208 42 'point symmetry operation' ? ? 0.808305 0.518849 0.278277 -0.481151 0.309729 0.820099 0.339317 -0.796784 0.5 26.41461 77.84547 -47.46104 43 'point symmetry operation' ? ? 0.523739 -0.319787 0.789578 -0.319787 0.785278 0.530164 -0.789579 -0.530164 0.309017 74.94843 50.32429 -65.58954 44 'point symmetry operation' ? ? -0.498137 -0.358365 0.789578 0.259669 0.807154 0.530164 -0.827304 0.469124 -0.309017 74.94843 50.32429 -124.25462 45 'point symmetry operation' ? ? -0.845124 0.456429 0.278277 0.456429 0.345124 0.820099 0.278277 0.820099 -0.5 26.41461 77.84547 -142.38312 46 'point symmetry operation' ? ? 0.037698 -0.998577 -0.037725 0.001423 -0.037698 0.999288 -0.999288 -0.037725 0 -3.58094 94.8545 -94.92208 47 'point symmetry operation' ? ? -0.769728 -0.540725 -0.339317 -0.540725 0.269728 0.796783 -0.339317 0.796784 -0.5 -32.20869 75.63233 -142.38312 48 'point symmetry operation' ? ? -0.498137 0.259669 -0.827303 -0.358365 0.807154 0.469124 0.789579 0.530164 -0.309017 -78.52937 44.53021 -124.25462 49 'point symmetry operation' ? ? 0.477141 0.296488 -0.827303 0.296488 0.831876 0.469124 0.827304 -0.469124 0.309017 -78.52937 44.53021 -65.58954 50 'point symmetry operation' ? ? 0.808305 -0.481151 -0.339317 0.518849 0.309729 0.796783 -0.278277 -0.820099 0.5 -32.20869 75.63233 -47.46104 51 'point symmetry operation' ? ? -0.037698 0.998577 0.037725 -0.001423 0.037698 -0.999288 -0.999288 -0.037725 0 3.58094 -94.8545 -94.92208 52 'point symmetry operation' ? ? 0.769728 0.540725 0.339317 0.540725 -0.269728 -0.796783 -0.339317 0.796784 -0.5 32.20869 -75.63233 -142.38312 53 'point symmetry operation' ? ? 0.498137 -0.259669 0.827303 0.358365 -0.807154 -0.469124 0.789579 0.530164 -0.309017 78.52937 -44.53021 -124.25462 54 'point symmetry operation' ? ? -0.477141 -0.296488 0.827303 -0.296488 -0.831876 -0.469124 0.827304 -0.469124 0.309017 78.52937 -44.53021 -65.58954 55 'point symmetry operation' ? ? -0.808305 0.481151 0.339317 -0.518849 -0.309729 -0.796783 -0.278277 -0.820099 0.5 32.20869 -75.63233 -47.46104 56 'point symmetry operation' ? ? 0.037698 -0.998577 0.037725 0.001423 -0.037698 -0.999288 0.999288 0.037725 0 3.58094 -94.8545 -94.92208 57 'point symmetry operation' ? ? -0.808305 -0.518849 -0.278277 0.481151 -0.309729 -0.820099 0.339317 -0.796784 0.5 -26.41461 -77.84547 -47.46104 58 'point symmetry operation' ? ? -0.523739 0.319787 -0.789578 0.319787 -0.785278 -0.530164 -0.789579 -0.530164 0.309017 -74.94843 -50.32429 -65.58954 59 'point symmetry operation' ? ? 0.498137 0.358365 -0.789578 -0.259669 -0.807154 -0.530164 -0.827304 0.469124 -0.309017 -74.94843 -50.32429 -124.25462 60 'point symmetry operation' ? ? 0.845124 -0.456429 -0.278277 -0.456429 -0.345124 -0.820099 0.278277 0.820099 -0.5 -26.41461 -77.84547 -142.38312 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id G _struct_conn.ptnr1_label_atom_id C1 _struct_conn.ptnr1_label_comp_id MYR _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id 4 _struct_conn.ptnr1_auth_comp_id MYR _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id GLY _struct_conn.ptnr2_label_seq_id 1 _struct_conn.ptnr2_auth_asym_id 4 _struct_conn.ptnr2_auth_comp_id GLY _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _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 1.325 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C14 H28 O2' _chem_comp.formula_weight 228.371 _chem_comp.id MYR _chem_comp.mon_nstd_flag . _chem_comp.name 'MYRISTIC 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 C1 O1 MYR doub 294 n n C1 O2 MYR sing 295 n n C1 C2 MYR sing 296 n n O2 HO2 MYR sing 297 n n C2 C3 MYR sing 298 n n C2 H21 MYR sing 299 n n C2 H22 MYR sing 300 n n C3 C4 MYR sing 301 n n C3 H31 MYR sing 302 n n C3 H32 MYR sing 303 n n C4 C5 MYR sing 304 n n C4 H41 MYR sing 305 n n C4 H42 MYR sing 306 n n C5 C6 MYR sing 307 n n C5 H51 MYR sing 308 n n C5 H52 MYR sing 309 n n C6 C7 MYR sing 310 n n C6 H61 MYR sing 311 n n C6 H62 MYR sing 312 n n C7 C8 MYR sing 313 n n C7 H71 MYR sing 314 n n C7 H72 MYR sing 315 n n C8 C9 MYR sing 316 n n C8 H81 MYR sing 317 n n C8 H82 MYR sing 318 n n C9 C10 MYR sing 319 n n C9 H91 MYR sing 320 n n C9 H92 MYR sing 321 n n C10 C11 MYR sing 322 n n C10 H101 MYR sing 323 n n C10 H102 MYR sing 324 n n C11 C12 MYR sing 325 n n C11 H111 MYR sing 326 n n C11 H112 MYR sing 327 n n C12 C13 MYR sing 328 n n C12 H121 MYR sing 329 n n C12 H122 MYR sing 330 n n C13 C14 MYR sing 331 n n C13 H131 MYR sing 332 n n C13 H132 MYR sing 333 n n C14 H141 MYR sing 334 n n C14 H142 MYR sing 335 n n C14 H143 MYR sing 336 n n # _atom_sites.entry_id 1VBD _atom_sites.fract_transf_matrix[1][1] 0.003097 _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] 0.002793 _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] 0.002631 _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 F 6 J78 1 1 500 500 J78 J78 . G 7 MYR 4 1 1 1 MYR MYR . # 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 MYR . . . G 7 5.537 54.258 -5.553 1 44.66 ? C1 MYR 1 4 1 HETATM 2 O O1 MYR . . . G 7 5.645 54.649 -4.39 1 46.45 ? O1 MYR 1 4 1 HETATM 3 C C2 MYR . . . G 7 4.413 54.766 -6.425 1 46.75 ? C2 MYR 1 4 1 HETATM 4 C C3 MYR . . . G 7 3.062 54.851 -5.717 1 50.67 ? C3 MYR 1 4 1 HETATM 5 C C4 MYR . . . G 7 2.915 56.075 -4.805 1 54.81 ? C4 MYR 1 4 1 HETATM 6 C C5 MYR . . . G 7 1.624 55.973 -3.997 1 59.18 ? C5 MYR 1 4 1 HETATM 7 C C6 MYR . . . G 7 1.352 57.2 -3.115 1 63.68 ? C6 MYR 1 4 1 HETATM 8 C C7 MYR . . . G 7 2.453 57.448 -2.078 1 66.65 ? C7 MYR 1 4 1 HETATM 9 C C8 MYR . . . G 7 1.922 58.277 -0.9 1 68.91 ? C8 MYR 1 4 1 HETATM 10 C C9 MYR . . . G 7 2.562 59.647 -0.824 1 71.57 ? C9 MYR 1 4 1 HETATM 11 C C10 MYR . . . G 7 4.074 59.571 -0.574 1 73.92 ? C10 MYR 1 4 1 HETATM 12 C C11 MYR . . . G 7 4.658 60.966 -0.726 1 75.4 ? C11 MYR 1 4 1 HETATM 13 C C12 MYR . . . G 7 6.166 60.946 -0.752 1 76.23 ? C12 MYR 1 4 1 HETATM 14 C C13 MYR . . . G 7 6.812 60.815 0.618 1 76.6 ? C13 MYR 1 4 1 HETATM 15 C C14 MYR . . . G 7 7.785 61.987 0.853 1 77.43 ? C14 MYR 1 4 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 15 #