data_5YI7 # _model_server_result.job_id '_JK8eG45BVibSy1UgIWlyw' _model_server_result.datetime_utc '2024-10-19 11:32:02' _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 5yi7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5YI7 # _exptl.entry_id 5YI7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 2 _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 5YI7 _cell.length_a 65.593 _cell.length_b 65.593 _cell.length_c 143.879 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YI7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 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 PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H 1 1,3 C,D,F,I,J 2 1,2 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_775 -y+2,-x+2,-z+2/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 65.593 113.610409 95.919333 3 'crystal symmetry operation' 5_655 -x+y+1,y,-z+1/3 -1 0 0 0 1 0 0 0 -1 65.593 0 47.959667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N # _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 5YI7 _atom_sites.fract_transf_matrix[1][1] 0.015246 _atom_sites.fract_transf_matrix[1][2] 0.008802 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017604 _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] 0.00695 _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 E 3 GOL A 1 301 1 GOL GOL . F 3 GOL C 1 301 2 GOL GOL . G 4 HOH A 1 401 148 HOH HOH . G 4 HOH A 2 402 22 HOH HOH . G 4 HOH A 3 403 143 HOH HOH . G 4 HOH A 4 404 98 HOH HOH . G 4 HOH A 5 405 41 HOH HOH . G 4 HOH A 6 406 28 HOH HOH . G 4 HOH A 7 407 20 HOH HOH . G 4 HOH A 8 408 130 HOH HOH . G 4 HOH A 9 409 60 HOH HOH . G 4 HOH A 10 410 92 HOH HOH . G 4 HOH A 11 411 122 HOH HOH . G 4 HOH A 12 412 107 HOH HOH . G 4 HOH A 13 413 35 HOH HOH . G 4 HOH A 14 414 103 HOH HOH . G 4 HOH A 15 415 144 HOH HOH . G 4 HOH A 16 416 38 HOH HOH . G 4 HOH A 17 417 154 HOH HOH . G 4 HOH A 18 418 15 HOH HOH . G 4 HOH A 19 419 52 HOH HOH . G 4 HOH A 20 420 109 HOH HOH . G 4 HOH A 21 421 108 HOH HOH . G 4 HOH A 22 422 77 HOH HOH . G 4 HOH A 23 423 54 HOH HOH . G 4 HOH A 24 424 23 HOH HOH . G 4 HOH A 25 425 7 HOH HOH . G 4 HOH A 26 426 31 HOH HOH . G 4 HOH A 27 427 9 HOH HOH . G 4 HOH A 28 428 40 HOH HOH . G 4 HOH A 29 429 129 HOH HOH . G 4 HOH A 30 430 101 HOH HOH . G 4 HOH A 31 431 26 HOH HOH . G 4 HOH A 32 432 25 HOH HOH . G 4 HOH A 33 433 3 HOH HOH . G 4 HOH A 34 434 51 HOH HOH . G 4 HOH A 35 435 142 HOH HOH . G 4 HOH A 36 436 113 HOH HOH . G 4 HOH A 37 437 11 HOH HOH . G 4 HOH A 38 438 73 HOH HOH . G 4 HOH A 39 439 37 HOH HOH . G 4 HOH A 40 440 74 HOH HOH . G 4 HOH A 41 441 53 HOH HOH . G 4 HOH A 42 442 111 HOH HOH . G 4 HOH A 43 443 47 HOH HOH . G 4 HOH A 44 444 4 HOH HOH . G 4 HOH A 45 445 69 HOH HOH . G 4 HOH A 46 446 127 HOH HOH . G 4 HOH A 47 447 43 HOH HOH . G 4 HOH A 48 448 6 HOH HOH . G 4 HOH A 49 449 72 HOH HOH . G 4 HOH A 50 450 81 HOH HOH . G 4 HOH A 51 451 49 HOH HOH . G 4 HOH A 52 452 57 HOH HOH . G 4 HOH A 53 453 131 HOH HOH . G 4 HOH A 54 454 132 HOH HOH . G 4 HOH A 55 455 16 HOH HOH . G 4 HOH A 56 456 119 HOH HOH . G 4 HOH A 57 457 137 HOH HOH . G 4 HOH A 58 458 63 HOH HOH . G 4 HOH A 59 459 34 HOH HOH . G 4 HOH A 60 460 87 HOH HOH . G 4 HOH A 61 461 99 HOH HOH . G 4 HOH A 62 462 46 HOH HOH . G 4 HOH A 63 463 114 HOH HOH . G 4 HOH A 64 464 68 HOH HOH . G 4 HOH A 65 465 124 HOH HOH . G 4 HOH A 66 466 93 HOH HOH . G 4 HOH A 67 467 96 HOH HOH . H 4 HOH B 1 201 141 HOH HOH . H 4 HOH B 2 202 18 HOH HOH . H 4 HOH B 3 203 133 HOH HOH . H 4 HOH B 4 204 82 HOH HOH . H 4 HOH B 5 205 91 HOH HOH . H 4 HOH B 6 206 97 HOH HOH . H 4 HOH B 7 207 128 HOH HOH . H 4 HOH B 8 208 84 HOH HOH . H 4 HOH B 9 209 78 HOH HOH . H 4 HOH B 10 210 94 HOH HOH . I 4 HOH C 1 401 21 HOH HOH . I 4 HOH C 2 402 67 HOH HOH . I 4 HOH C 3 403 135 HOH HOH . I 4 HOH C 4 404 42 HOH HOH . I 4 HOH C 5 405 90 HOH HOH . I 4 HOH C 6 406 27 HOH HOH . I 4 HOH C 7 407 147 HOH HOH . I 4 HOH C 8 408 19 HOH HOH . I 4 HOH C 9 409 89 HOH HOH . I 4 HOH C 10 410 83 HOH HOH . I 4 HOH C 11 411 88 HOH HOH . I 4 HOH C 12 412 29 HOH HOH . I 4 HOH C 13 413 39 HOH HOH . I 4 HOH C 14 414 145 HOH HOH . I 4 HOH C 15 415 17 HOH HOH . I 4 HOH C 16 416 32 HOH HOH . I 4 HOH C 17 417 140 HOH HOH . I 4 HOH C 18 418 115 HOH HOH . I 4 HOH C 19 419 24 HOH HOH . I 4 HOH C 20 420 104 HOH HOH . I 4 HOH C 21 421 36 HOH HOH . I 4 HOH C 22 422 10 HOH HOH . I 4 HOH C 23 423 45 HOH HOH . I 4 HOH C 24 424 62 HOH HOH . I 4 HOH C 25 425 125 HOH HOH . I 4 HOH C 26 426 86 HOH HOH . I 4 HOH C 27 427 123 HOH HOH . I 4 HOH C 28 428 79 HOH HOH . I 4 HOH C 29 429 12 HOH HOH . I 4 HOH C 30 430 152 HOH HOH . I 4 HOH C 31 431 76 HOH HOH . I 4 HOH C 32 432 33 HOH HOH . I 4 HOH C 33 433 1 HOH HOH . I 4 HOH C 34 434 14 HOH HOH . I 4 HOH C 35 435 8 HOH HOH . I 4 HOH C 36 436 70 HOH HOH . I 4 HOH C 37 437 106 HOH HOH . I 4 HOH C 38 438 110 HOH HOH . I 4 HOH C 39 439 112 HOH HOH . I 4 HOH C 40 440 153 HOH HOH . I 4 HOH C 41 441 30 HOH HOH . I 4 HOH C 42 442 55 HOH HOH . I 4 HOH C 43 443 59 HOH HOH . I 4 HOH C 44 444 134 HOH HOH . I 4 HOH C 45 445 71 HOH HOH . I 4 HOH C 46 446 44 HOH HOH . I 4 HOH C 47 447 105 HOH HOH . I 4 HOH C 48 448 56 HOH HOH . I 4 HOH C 49 449 64 HOH HOH . I 4 HOH C 50 450 5 HOH HOH . I 4 HOH C 51 451 2 HOH HOH . I 4 HOH C 52 452 58 HOH HOH . I 4 HOH C 53 453 102 HOH HOH . I 4 HOH C 54 454 75 HOH HOH . I 4 HOH C 55 455 13 HOH HOH . I 4 HOH C 56 456 118 HOH HOH . I 4 HOH C 57 457 50 HOH HOH . I 4 HOH C 58 458 85 HOH HOH . I 4 HOH C 59 459 95 HOH HOH . I 4 HOH C 60 460 120 HOH HOH . I 4 HOH C 61 461 48 HOH HOH . I 4 HOH C 62 462 121 HOH HOH . I 4 HOH C 63 463 66 HOH HOH . I 4 HOH C 64 464 61 HOH HOH . I 4 HOH C 65 465 100 HOH HOH . I 4 HOH C 66 466 146 HOH HOH . I 4 HOH C 67 467 138 HOH HOH . I 4 HOH C 68 468 136 HOH HOH . I 4 HOH C 69 469 150 HOH HOH . I 4 HOH C 70 470 117 HOH HOH . I 4 HOH C 71 471 116 HOH HOH . J 4 HOH D 1 201 149 HOH HOH . J 4 HOH D 2 202 65 HOH HOH . J 4 HOH D 3 203 151 HOH HOH . J 4 HOH D 4 204 126 HOH HOH . J 4 HOH D 5 205 155 HOH HOH . J 4 HOH D 6 206 80 HOH HOH . J 4 HOH D 7 207 139 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 . . . E 3 1.829 49.671 43.835 1 40.84 ? C1 GOL 301 A 1 HETATM 2 O O1 GOL . . . E 3 3.049 49.721 44.52 1 30.81 ? O1 GOL 301 A 1 HETATM 3 C C2 GOL . . . E 3 2.042 50.073 42.401 1 39.25 ? C2 GOL 301 A 1 HETATM 4 O O2 GOL . . . E 3 2.454 51.443 42.254 1 41.38 ? O2 GOL 301 A 1 HETATM 5 C C3 GOL . . . E 3 3.021 49.08 41.79 1 42.65 ? C3 GOL 301 A 1 HETATM 6 O O3 GOL . . . E 3 4.339 49.541 41.953 1 34.3 ? O3 GOL 301 A 1 # _model_server_stats.io_time_ms 123 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #