data_4PDW # _model_server_result.job_id nh5ZO00Qvq1XycLsoEvVYg _model_server_result.datetime_utc '2024-12-22 06:01:54' _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 4pdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":301}' # _entry.id 4PDW # _exptl.entry_id 4PDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 4 _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 4PDW _cell.length_a 439.411 _cell.length_b 439.411 _cell.length_c 439.411 _cell.Z_PDB 240 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 240-meric 240 'complete icosahedral assembly' 1 ? tetrameric 4 'icosahedral asymmetric unit' 2 ? eicosameric 20 'icosahedral pentamer' 3 ? 24-meric 24 'icosahedral 23 hexamer' 4 ? tetrameric 4 'icosahedral asymmetric unit, std point frame' 5 # 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,H,I,J,K,L,M 1 (1-60) A,B,C,D,E,F,G,H,I,J,K,L,M 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M 3 (1-5) A,B,C,D,E,F,G,H,I,J,K,L,M 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H,I,J,K,L,M 5 P # 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] P 'transform to point frame' ? ? 0.467091 -0.231855 0.85327 0.384056 -0.816028 -0.431972 0.796447 0.529473 -0.292114 -17.07935 179.28579 61.74823 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.843395 0.465306 -0.268655 -0.439316 0.309333 -0.843395 -0.309333 0.829339 0.465306 -38.68813 120.20219 -66.13295 3 'point symmetry operation' ? ? 0.590002 0.313565 -0.744026 -0.245522 -0.80819 -0.535302 -0.769166 0.498504 -0.399846 2.3803 230.1572 14.75084 4 'point symmetry operation' ? ? 0.590002 -0.245522 -0.769166 0.313565 -0.80819 0.498504 -0.744026 -0.535302 -0.399846 66.45011 177.91093 130.87273 5 'point symmetry operation' ? ? 0.843395 -0.439316 -0.309333 0.465306 0.309333 0.829339 -0.268655 -0.843395 0.465306 64.97901 35.66596 121.75621 6 'point symmetry operation' ? ? 0.268655 0.843395 -0.465306 0.843395 -0.439316 -0.309333 -0.465306 -0.309333 -0.829339 -121.75621 284.68451 184.03954 7 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 0 219.7055 219.7055 8 'point symmetry operation' ? ? 0.309333 -0.829339 -0.465306 0.843395 0.465306 -0.268655 0.439316 -0.309333 0.843395 66.13296 181.01737 99.50331 9 'point symmetry operation' ? ? 0.769166 -0.498504 0.399846 0.590002 0.313565 -0.744026 0.245522 0.80819 0.535302 -14.75084 222.08579 -10.4517 10 'point symmetry operation' ? ? 0.744026 0.535302 0.399846 0.590002 -0.245522 -0.769166 -0.313565 0.80819 -0.498504 -130.87273 286.15561 41.79457 11 'point symmetry operation' ? ? -0.705003 -0.6268 -0.331803 -0.6268 0.331803 0.705003 -0.331803 0.705003 -0.6268 -82.40315 -73.30794 65.22162 12 'point symmetry operation' ? ? -0.216595 -0.797109 0.563652 -0.892487 0.39567 0.216595 -0.39567 -0.456139 -0.797109 -108.52757 -55.79871 204.25345 13 'point symmetry operation' ? ? -0.006848 0.120104 0.992738 -0.993542 -0.113256 0.006848 0.113256 -0.98628 0.120104 -233.23818 11.96624 217.44743 14 'point symmetry operation' ? ? -0.365626 0.857282 0.362472 -0.790312 -0.491656 0.365626 0.491656 -0.152783 0.857282 -284.18915 36.33806 86.56993 15 'point symmetry operation' ? ? -0.797109 0.39567 -0.456139 -0.563652 -0.216595 0.797109 0.216595 0.892487 0.39567 -190.96798 -16.36428 -7.51079 16 'point symmetry operation' ? ? -0.563652 -0.216595 0.797109 -0.216595 -0.892487 -0.39567 0.797109 -0.39567 0.456139 -236.06978 227.21629 190.96798 17 'point symmetry operation' ? ? -0.6268 0.331803 0.705003 0.331803 -0.705003 0.6268 0.705003 0.6268 0.331803 -293.01344 154.48388 82.40315 18 'point symmetry operation' ? ? -0.892487 0.39567 0.216595 0.39567 0.456139 0.797109 0.216595 0.797109 -0.563652 -275.50421 15.45205 108.52757 19 'point symmetry operation' ? ? -0.993542 -0.113256 0.006848 -0.113256 0.98628 -0.120104 0.006848 -0.120104 -0.992738 -207.73926 2.25807 233.23818 20 'point symmetry operation' ? ? -0.790312 -0.491656 0.365626 -0.491656 0.152784 -0.857282 0.365626 -0.857282 -0.362472 -183.36744 133.13557 284.18916 21 'point symmetry operation' ? ? 0.857282 -0.491656 -0.152783 -0.362472 -0.365626 -0.857282 0.365626 0.790312 -0.491656 55.01692 204.19585 117.75113 22 'point symmetry operation' ? ? 0.98628 0.120104 0.113256 0.120104 -0.992738 0.006848 0.113256 0.006848 -0.993542 -27.14379 230.96475 231.11757 23 'point symmetry operation' ? ? 0.744026 0.590002 -0.313565 0.535302 -0.245522 0.80819 0.399846 -0.769166 -0.498504 -58.3543 106.53601 293.26498 24 'point symmetry operation' ? ? 0.465306 0.268655 -0.843395 0.309333 0.843395 0.439316 0.829339 -0.465306 0.309333 4.51725 2.86592 218.30774 25 'point symmetry operation' ? ? 0.535302 -0.399846 -0.744026 -0.245522 0.769166 -0.590002 0.80819 0.498504 0.313565 74.58452 63.22302 109.83421 26 'point symmetry operation' ? ? -0.113256 0.98628 -0.120104 -0.006848 0.120104 0.992738 0.993542 0.113256 -0.006848 -217.44743 -13.53268 207.73926 27 'point symmetry operation' ? ? -0.491656 0.152784 -0.857282 -0.365626 0.857282 0.362472 0.790312 0.491656 -0.365626 -86.56993 -64.48365 183.36744 28 'point symmetry operation' ? ? -0.216595 -0.892487 -0.39567 -0.797109 0.39567 -0.456139 0.563652 0.216595 -0.797109 7.51079 28.73752 236.06978 29 'point symmetry operation' ? ? 0.331803 -0.705003 0.6268 -0.705003 -0.6268 -0.331803 0.6268 -0.331803 -0.705003 -65.22162 137.30235 293.01344 30 'point symmetry operation' ? ? 0.39567 0.456139 0.797109 -0.216595 -0.797109 0.563652 0.892487 -0.39567 -0.216595 -204.25345 111.17793 275.50421 31 'point symmetry operation' ? ? -0.245522 -0.80819 -0.535302 0.769166 -0.498504 0.399846 -0.590002 -0.313565 0.744026 10.4517 204.95466 -2.38029 32 'point symmetry operation' ? ? 0.313565 -0.80819 0.498504 0.744026 0.535302 0.399846 -0.590002 0.245522 0.769166 -41.79457 88.83277 -66.45011 33 'point symmetry operation' ? ? 0.465306 0.309333 0.829339 0.268655 0.843395 -0.465306 -0.843395 0.439316 0.309333 -184.03954 97.94929 -64.97901 34 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 -219.7055 219.7055 0 35 'point symmetry operation' ? ? -0.439316 0.309333 -0.843395 0.309333 -0.829339 -0.465306 -0.843395 -0.465306 0.268655 -99.5033 285.83845 38.68814 36 'point symmetry operation' ? ? -0.498504 0.313565 0.80819 -0.399846 0.744026 -0.535302 -0.769166 -0.590002 -0.245522 -288.25033 42.97503 117.11906 37 'point symmetry operation' ? ? -0.80819 0.535302 0.245522 -0.498504 -0.399846 -0.769166 -0.313565 -0.744026 0.590002 -284.72085 183.279 92.19424 38 'point symmetry operation' ? ? -0.992738 -0.006848 -0.120104 -0.006848 -0.993542 0.113256 -0.120104 0.113256 0.98628 -205.34609 205.37004 -24.12661 39 'point symmetry operation' ? ? -0.797109 -0.563652 0.216595 0.39567 -0.216595 0.892487 -0.456139 0.797109 0.39567 -159.81927 78.71909 -71.09204 40 'point symmetry operation' ? ? -0.491656 -0.365626 0.790312 0.152783 0.857282 0.491656 -0.857282 0.362472 -0.365626 -211.0569 -21.64655 16.20259 41 'point symmetry operation' ? ? 0.857282 -0.362472 0.365626 -0.491656 -0.365626 0.790312 -0.152783 -0.857282 -0.491656 -16.20258 8.6486 241.35205 42 'point symmetry operation' ? ? 0.769166 0.590002 0.245522 -0.498504 0.313565 0.80819 0.399846 -0.744026 0.535302 -117.11905 -68.54483 176.73047 43 'point symmetry operation' ? ? 0.313565 0.744026 -0.590002 -0.80819 0.535302 0.245522 0.498504 0.399846 0.769166 -92.19424 -65.01535 36.4265 44 'point symmetry operation' ? ? 0.120104 -0.113256 -0.98628 -0.992738 -0.006848 -0.120104 0.006848 0.993542 -0.113256 24.12661 14.35941 14.33546 45 'point symmetry operation' ? ? 0.456139 -0.797109 -0.39567 -0.797109 -0.563652 0.216595 -0.39567 0.216595 -0.892487 71.09204 59.88623 140.98641 46 'point symmetry operation' ? ? -0.245522 0.769166 -0.590002 -0.80819 -0.498504 -0.313565 -0.535302 0.399846 0.744026 -156.48248 109.87129 -74.58451 47 'point symmetry operation' ? ? -0.362472 -0.365626 -0.857282 -0.365626 -0.790312 0.491656 -0.857282 0.491656 0.152784 -15.50965 101.95437 -55.01692 48 'point symmetry operation' ? ? 0.120104 -0.992738 0.006848 -0.113256 -0.006848 0.993542 -0.98628 -0.120104 -0.113256 11.25925 -11.41207 27.14379 49 'point symmetry operation' ? ? 0.535302 -0.245522 0.80819 -0.399846 0.769166 0.498504 -0.744026 -0.590002 0.313565 -113.16949 -73.55948 58.3543 50 'point symmetry operation' ? ? 0.309333 0.843395 0.439316 -0.829339 0.465306 -0.309333 -0.465306 -0.268655 0.843395 -216.83958 1.39776 -4.51725 51 'point symmetry operation' ? ? -0.498504 -0.399846 -0.769166 0.313565 0.744026 -0.590002 0.80819 -0.535302 -0.245522 -36.4265 127.51126 284.72086 52 'point symmetry operation' ? ? -0.006848 -0.993542 0.113256 0.120104 -0.113256 -0.98628 0.992738 0.006848 0.120104 -14.33546 243.83211 205.3461 53 'point symmetry operation' ? ? 0.39567 -0.216595 0.892487 0.456139 -0.797109 -0.39567 0.797109 0.563652 -0.216595 -140.98641 290.79754 159.81927 54 'point symmetry operation' ? ? 0.152784 0.857282 0.491656 0.857282 -0.362472 0.365626 0.491656 0.365626 -0.790312 -241.35205 203.50292 211.0569 55 'point symmetry operation' ? ? -0.399846 0.744026 -0.535302 0.769166 0.590002 0.245522 0.498504 -0.313565 -0.80819 -176.73047 102.58645 288.25033 56 'point symmetry operation' ? ? -0.113256 -0.006848 0.993542 0.98628 0.120104 0.113256 -0.120104 0.992738 -0.006848 -231.11757 192.56171 -11.25925 57 'point symmetry operation' ? ? -0.399846 0.769166 0.498504 0.744026 0.590002 -0.313565 -0.535302 0.245522 -0.80819 -293.26497 161.3512 113.16949 58 'point symmetry operation' ? ? -0.829339 0.465306 -0.309333 0.465306 0.268655 -0.843395 -0.309333 -0.843395 -0.439316 -218.30773 224.22275 216.83958 59 'point symmetry operation' ? ? -0.80819 -0.498504 -0.313565 0.535302 -0.399846 -0.744026 0.245522 -0.769166 0.590002 -109.83421 294.29001 156.48248 60 'point symmetry operation' ? ? -0.365626 -0.790312 0.491656 0.857282 -0.491656 -0.152783 0.362472 0.365626 0.857282 -117.75112 274.72242 15.50965 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 H N N ? 5 I 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 168 n n C1 C2 GOL sing 169 n n C1 H11 GOL sing 170 n n C1 H12 GOL sing 171 n n O1 HO1 GOL sing 172 n n C2 O2 GOL sing 173 n n C2 C3 GOL sing 174 n n C2 H2 GOL sing 175 n n O2 HO2 GOL sing 176 n n C3 O3 GOL sing 177 n n C3 H31 GOL sing 178 n n C3 H32 GOL sing 179 n n O3 HO3 GOL sing 180 n n # _atom_sites.entry_id 4PDW _atom_sites.fract_transf_matrix[1][1] 0.002276 _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] 0.002276 _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] 0.002276 _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 5 GOL A 1 301 1 GOL GOL . F 5 GOL A 1 302 4 GOL GOL . G 6 2XK A 1 303 1 2XK LIG . H 5 GOL B 1 301 2 GOL GOL . I 5 GOL C 1 301 3 GOL GOL . J 7 HOH A 1 401 3 HOH HOH . J 7 HOH A 2 402 4 HOH HOH . J 7 HOH A 3 403 14 HOH HOH . J 7 HOH A 4 404 18 HOH HOH . J 7 HOH A 5 405 19 HOH HOH . J 7 HOH A 6 406 20 HOH HOH . J 7 HOH A 7 407 22 HOH HOH . J 7 HOH A 8 408 27 HOH HOH . J 7 HOH A 9 409 28 HOH HOH . J 7 HOH A 10 410 29 HOH HOH . J 7 HOH A 11 411 30 HOH HOH . J 7 HOH A 12 412 46 HOH HOH . J 7 HOH A 13 413 47 HOH HOH . J 7 HOH A 14 414 48 HOH HOH . J 7 HOH A 15 415 49 HOH HOH . J 7 HOH A 16 416 53 HOH HOH . J 7 HOH A 17 417 55 HOH HOH . J 7 HOH A 18 418 56 HOH HOH . J 7 HOH A 19 419 61 HOH HOH . J 7 HOH A 20 420 124 HOH HOH . J 7 HOH A 21 421 128 HOH HOH . K 7 HOH B 1 401 16 HOH HOH . K 7 HOH B 2 402 17 HOH HOH . K 7 HOH B 3 403 21 HOH HOH . K 7 HOH B 4 404 25 HOH HOH . K 7 HOH B 5 405 34 HOH HOH . K 7 HOH B 6 406 37 HOH HOH . K 7 HOH B 7 407 40 HOH HOH . K 7 HOH B 8 408 58 HOH HOH . K 7 HOH B 9 409 62 HOH HOH . K 7 HOH B 10 410 65 HOH HOH . K 7 HOH B 11 411 67 HOH HOH . K 7 HOH B 12 412 69 HOH HOH . K 7 HOH B 13 413 70 HOH HOH . K 7 HOH B 14 414 72 HOH HOH . K 7 HOH B 15 415 73 HOH HOH . K 7 HOH B 16 416 74 HOH HOH . K 7 HOH B 17 417 75 HOH HOH . K 7 HOH B 18 418 76 HOH HOH . K 7 HOH B 19 419 78 HOH HOH . K 7 HOH B 20 420 79 HOH HOH . K 7 HOH B 21 421 86 HOH HOH . K 7 HOH B 22 422 87 HOH HOH . K 7 HOH B 23 423 88 HOH HOH . K 7 HOH B 24 424 91 HOH HOH . K 7 HOH B 25 425 93 HOH HOH . K 7 HOH B 26 426 94 HOH HOH . L 7 HOH C 1 401 10 HOH HOH . L 7 HOH C 2 402 13 HOH HOH . L 7 HOH C 3 403 15 HOH HOH . L 7 HOH C 4 404 26 HOH HOH . L 7 HOH C 5 405 89 HOH HOH . L 7 HOH C 6 406 96 HOH HOH . L 7 HOH C 7 407 99 HOH HOH . L 7 HOH C 8 408 101 HOH HOH . L 7 HOH C 9 409 102 HOH HOH . L 7 HOH C 10 410 105 HOH HOH . L 7 HOH C 11 411 106 HOH HOH . L 7 HOH C 12 412 109 HOH HOH . L 7 HOH C 13 413 110 HOH HOH . L 7 HOH C 14 414 111 HOH HOH . L 7 HOH C 15 415 112 HOH HOH . L 7 HOH C 16 416 114 HOH HOH . L 7 HOH C 17 417 115 HOH HOH . L 7 HOH C 18 418 116 HOH HOH . L 7 HOH C 19 419 117 HOH HOH . L 7 HOH C 20 420 120 HOH HOH . L 7 HOH C 21 421 127 HOH HOH . M 7 HOH D 1 101 98 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 . . . H 5 28.923 121.731 110.589 1 63.65 ? C1 GOL 301 B 1 HETATM 2 O O1 GOL . . . H 5 29.53 122.186 109.394 1 60.7 ? O1 GOL 301 B 1 HETATM 3 C C2 GOL . . . H 5 28.608 120.231 110.571 1 65.41 ? C2 GOL 301 B 1 HETATM 4 O O2 GOL . . . H 5 28.147 119.848 111.867 1 65.27 ? O2 GOL 301 B 1 HETATM 5 C C3 GOL . . . H 5 29.803 119.35 110.213 1 66.01 ? C3 GOL 301 B 1 HETATM 6 O O3 GOL . . . H 5 29.414 118.045 109.796 1 65.3 ? O3 GOL 301 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 23 _model_server_stats.element_count 6 #