data_3NTT # _model_server_result.job_id BguxyRc7Rd7GJlZjyRZBBQ _model_server_result.datetime_utc '2024-11-25 00:57:06' _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 3ntt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":725}' # _entry.id 3NTT # _exptl.entry_id 3NTT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 3NTT _cell.length_a 264.7 _cell.length_b 447.9 _cell.length_c 629.7 _cell.Z_PDB 240 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NTT _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 60-MERIC 60 'complete icosahedral assembly' 1 ? monomeric 1 'icosahedral asymmetric unit' 2 ? pentameric 5 'icosahedral pentamer' 3 ? hexameric 6 'icosahedral 23 hexamer' 4 ? monomeric 1 'icosahedral asymmetric unit, std point frame' 5 ? 60-meric 60 '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 1 (1-60) A,B,C,D,E 2 1 A,B,C,D,E 3 (1-5) A,B,C,D,E 4 (1,2,6,10,23,24) A,B,C,D,E 5 P A,B,C,D,E 6 (X0)(1-60) # 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' ? ? 0.340567 0.822371 -0.455763 -0.925292 0.207115 -0.317707 -0.166878 0.529914 0.83147 -33.09363 119.73625 -217.29675 X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.581885 -0.756835 0.297674 0.270805 0.525445 0.806581 -0.76686 -0.388726 0.510703 64.23468 -131.69117 211.13416 3 'point symmetry operation' ? ? -0.094638 -0.95378 -0.285213 -0.318664 -0.242401 0.916349 -0.943131 0.177609 -0.280995 264.12958 -13.1959 320.89386 4 'point symmetry operation' ? ? -0.094638 -0.318664 -0.943131 -0.95378 -0.242401 0.177609 -0.285213 0.916349 -0.280995 323.43675 191.72937 177.59492 5 'point symmetry operation' ? ? 0.581885 0.270805 -0.76686 -0.756835 0.525445 -0.388726 0.297674 0.806581 0.510703 160.19569 199.88488 -20.72839 6 'point symmetry operation' ? ? -0.944303 -0.176862 -0.277508 -0.176862 -0.438381 0.881216 -0.277508 0.881216 0.382685 244.12326 4.83225 45.91641 7 'point symmetry operation' ? ? -0.384562 0.729625 -0.565473 -0.897398 -0.439041 0.043803 -0.216306 0.524299 0.823603 148.16597 237.25732 -7.15972 8 'point symmetry operation' ? ? 0.407453 0.894242 0.185239 -0.674668 0.431463 -0.598884 -0.615471 0.119043 0.779117 -92.01201 246.67935 83.79112 9 'point symmetry operation' ? ? 0.337204 0.089493 0.937168 0.183523 0.970125 -0.158674 -0.92337 0.225498 0.310706 -144.49287 20.07742 193.07797 10 'point symmetry operation' ? ? -0.498228 -0.572486 0.651175 0.491184 0.432531 0.756079 -0.714498 0.696546 0.065697 63.25015 -129.39231 169.67011 11 'point symmetry operation' ? ? 0.712332 -0.383283 0.587944 -0.383283 -0.914207 -0.131604 0.587944 -0.131604 -0.798124 -49.98288 284.72785 331.18579 12 'point symmetry operation' ? ? -0.14017 -0.969061 0.203159 -0.369677 -0.139126 -0.918685 0.918527 -0.203875 -0.338738 170.38351 352.71479 217.77185 13 'point symmetry operation' ? ? -0.499783 -0.482076 -0.719597 0.451718 0.563798 -0.691435 0.739032 -0.670622 -0.064015 331.89027 153.32448 232.10252 14 'point symmetry operation' ? ? 0.130465 0.404675 -0.905106 0.945761 0.223148 0.236095 0.297515 -0.886816 -0.353613 211.34054 -37.89244 354.3733 15 'point symmetry operation' ? ? 0.879593 0.465732 -0.097002 0.429702 -0.690309 0.58209 0.204137 -0.553684 -0.807318 -24.67004 43.31931 415.61013 16 'point symmetry operation' ? ? -0.768028 0.560145 -0.310436 0.560145 0.352589 -0.749612 -0.310436 -0.749612 -0.58456 149.05797 180.69911 437.43359 17 'point symmetry operation' ? ? -0.057154 0.996271 0.06464 0.996271 0.052722 0.068302 0.06464 0.068302 -0.995568 -39.5858 11.97827 392.7895 18 'point symmetry operation' ? ? 0.186968 0.541615 0.819571 0.541615 -0.752861 0.373971 0.819571 0.373971 -0.434107 -160.80949 83.45127 177.74829 19 'point symmetry operation' ? ? -0.37303 -0.175504 0.911069 -0.175504 -0.950872 -0.25503 0.911069 -0.25503 0.323903 -47.08606 296.34485 89.4896 20 'point symmetry operation' ? ? -0.963251 -0.164051 0.212687 -0.164051 -0.267667 -0.949443 0.212687 -0.949443 0.230917 144.42256 356.44733 249.98394 21 'point symmetry operation' ? ? -0.217546 -0.615025 0.757904 -0.557025 0.715864 0.421024 -0.801497 -0.330579 -0.498318 22.4354 -4.53798 412.74092 22 'point symmetry operation' ? ? -0.874345 -0.453132 -0.173761 -0.453132 0.63406 0.626609 -0.173761 0.626609 -0.759716 249.47407 -45.6987 299.5794 23 'point symmetry operation' ? ? -0.498228 0.491184 -0.714498 -0.572486 0.432531 0.696546 0.651175 0.756079 0.065697 216.29736 -26.0071 45.49705 24 'point symmetry operation' ? ? 0.391023 0.912911 -0.117026 -0.750143 0.389783 0.534186 0.533279 -0.121092 0.837228 -31.24565 27.32369 1.62704 25 'point symmetry operation' ? ? 0.564494 0.229236 0.792968 -0.740588 0.564893 0.363904 -0.364522 -0.792684 0.488648 -151.05893 40.59233 228.59624 26 'point symmetry operation' ? ? 0.10388 0.975968 -0.191561 0.282554 0.155708 0.94653 0.95361 -0.152452 -0.259588 1.15552 -117.72956 192.59854 27 'point symmetry operation' ? ? 0.471643 0.508662 0.720288 -0.519275 -0.499971 0.693096 0.712675 -0.700922 0.028328 -161.14315 79.75952 219.12197 28 'point symmetry operation' ? ? -0.14017 -0.369677 0.918527 -0.969061 -0.139126 -0.203875 0.203159 -0.918685 -0.338738 -45.75613 258.58206 363.18664 29 'point symmetry operation' ? ? -0.886054 -0.445215 0.129196 -0.445215 0.739568 -0.5048 0.129196 -0.5048 -0.853513 187.85565 171.61138 425.70007 30 'point symmetry operation' ? ? -0.735223 0.38644 -0.556876 0.328326 0.921785 0.206189 0.593 -0.031242 -0.804596 216.84865 -60.962 320.27083 31 'point symmetry operation' ? ? 0.526368 0.545899 -0.651867 -0.423626 -0.496358 -0.757739 -0.737209 0.674998 -0.03001 109.20109 366.56751 193.64119 32 'point symmetry operation' ? ? 0.954009 0.141864 0.264087 0.200162 0.354359 -0.913436 -0.223165 0.924286 0.309666 -66.50931 244.73734 51.05944 33 'point symmetry operation' ? ? 0.391023 -0.750143 0.533279 0.912911 0.389783 -0.121092 -0.117026 0.534186 0.837228 31.84678 18.0712 -19.61469 34 'point symmetry operation' ? ? -0.384562 -0.897398 -0.216306 0.729625 -0.439041 0.524299 -0.565473 0.043803 0.823603 268.3446 -0.186 79.28804 35 'point symmetry operation' ? ? -0.300914 -0.0964 -0.948767 -0.0964 -0.986707 0.13083 -0.948767 0.13083 0.287621 316.15219 215.19656 211.08743 36 'point symmetry operation' ? ? -0.412702 -0.906842 0.085524 0.698098 -0.375214 -0.609815 0.585095 -0.191967 0.787916 210.40634 225.95924 15.55513 37 'point symmetry operation' ? ? -0.551307 -0.197394 -0.810614 0.772246 -0.488449 -0.406269 -0.315748 -0.849973 0.421722 321.37675 191.46104 244.77497 38 'point symmetry operation' ? ? 0.247375 0.628636 -0.737308 0.628636 -0.683188 -0.371579 -0.737308 -0.371579 -0.564187 140.81035 219.61305 425.46679 39 'point symmetry operation' ? ? 0.879593 0.429702 0.204137 0.465732 -0.690309 -0.553684 -0.097002 0.58209 -0.807318 -81.75624 271.51014 307.92063 40 'point symmetry operation' ? ? 0.471643 -0.519275 0.712675 0.508662 -0.499971 -0.700922 0.720288 0.693096 0.028328 -38.74355 275.43231 54.5813 41 'point symmetry operation' ? ? -0.217546 -0.557025 -0.801497 -0.615025 0.715864 -0.330579 0.757904 0.421024 -0.498318 333.16342 153.49032 190.58296 42 'point symmetry operation' ? ? 0.337204 0.183523 -0.92337 0.089493 0.970125 0.225498 0.937168 -0.158674 0.310706 223.32134 -50.08511 78.60951 43 'point symmetry operation' ? ? 0.954009 0.200162 -0.223165 0.141864 0.354359 0.924286 0.264087 -0.913436 0.309666 25.85809 -124.48319 225.30472 44 'point symmetry operation' ? ? 0.780465 -0.530103 0.331459 -0.530287 -0.280465 0.800084 -0.331165 -0.800206 -0.5 13.66117 33.1117 427.94079 45 'point symmetry operation' ? ? 0.056404 -0.99807 -0.025969 -0.99807 -0.057043 0.024535 -0.025969 0.024535 -0.999362 203.58631 204.90878 406.48156 46 'point symmetry operation' ? ? 0.526368 -0.423626 -0.737209 0.545899 -0.496358 0.674998 -0.651867 -0.757739 -0.03001 240.56177 -8.37137 354.75835 47 'point symmetry operation' ? ? 0.756902 -0.334394 -0.561498 -0.334394 -0.936354 0.106871 -0.561498 0.106871 -0.820548 174.51071 234.57544 406.33738 48 'point symmetry operation' ? ? 0.780465 -0.530287 -0.331165 -0.530103 -0.280465 -0.800206 0.331459 0.800084 -0.5 148.61545 358.9694 182.95011 49 'point symmetry operation' ? ? 0.564494 -0.740588 -0.364522 0.229236 0.564893 -0.792684 0.792968 0.363904 0.488648 198.66236 192.90229 -6.68984 50 'point symmetry operation' ? ? 0.407453 -0.674668 -0.615471 0.894242 0.431463 0.119043 0.185239 -0.598884 0.779117 255.4883 -34.1268 99.49349 51 'point symmetry operation' ? ? -0.412702 0.698098 0.585095 -0.906842 -0.375214 -0.191967 0.085524 -0.609815 0.787916 -80.00778 278.57455 107.54227 52 'point symmetry operation' ? ? -0.499783 0.451718 0.739032 -0.482076 0.563798 -0.670622 -0.719597 -0.691435 -0.064015 -74.91722 229.20537 359.69909 53 'point symmetry operation' ? ? -0.735223 0.328326 0.593 0.38644 0.921785 -0.031242 -0.556876 0.206189 -0.804596 -10.47304 -17.59917 391.01623 54 'point symmetry operation' ? ? -0.793652 0.498446 0.348811 0.498446 0.204021 0.842572 0.348811 0.842572 -0.41037 24.26509 -120.76357 158.21446 55 'point symmetry operation' ? ? -0.594322 0.726977 0.343926 -0.300847 -0.597569 0.743238 0.745837 0.338254 0.573857 -18.70975 62.28186 -16.98208 56 'point symmetry operation' ? ? 0.10388 0.282554 0.95361 0.975968 0.155708 -0.152452 -0.191561 0.94653 -0.259588 -150.51905 46.5657 161.65221 57 'point symmetry operation' ? ? -0.594322 -0.300847 0.745837 0.726977 -0.597569 0.338254 0.343926 0.743238 0.573857 20.28352 56.56351 -30.11019 58 'point symmetry operation' ? ? -0.99925 0.0018 -0.03867 0.0018 -0.99568 -0.092838 -0.03867 -0.092838 0.99493 179.19785 253.37216 15.26473 59 'point symmetry operation' ? ? -0.551307 0.772246 -0.315748 -0.197394 -0.488449 -0.849973 -0.810614 -0.406269 0.421722 106.60974 365.00878 235.07038 60 'point symmetry operation' ? ? 0.130465 0.945761 0.297515 0.404675 0.223148 -0.886816 -0.905106 0.236095 -0.353613 -97.16651 237.19536 325.54281 # _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 '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 3NTT _atom_sites.fract_transf_matrix[1][1] 0.003779 _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] 0.002233 _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] 0.001588 _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 GOL A 1 725 725 GOL GOL . C 3 NA A 1 726 726 NA NA . D 3 NA A 1 727 727 NA NA . E 3 NA A 1 728 728 NA NA . # 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 . . . B 2 51.5 188.489 281.593 1 41.29 ? C1 GOL 725 A 1 HETATM 2 O O1 GOL . . . B 2 51.223 188.629 280.217 1 76.58 ? O1 GOL 725 A 1 HETATM 3 C C2 GOL . . . B 2 52.959 188.084 281.777 1 43.44 ? C2 GOL 725 A 1 HETATM 4 O O2 GOL . . . B 2 53.789 189.136 281.332 1 34.66 ? O2 GOL 725 A 1 HETATM 5 C C3 GOL . . . B 2 53.227 187.827 283.257 1 43.34 ? C3 GOL 725 A 1 HETATM 6 O O3 GOL . . . B 2 54.513 187.269 283.41 1 61.5 ? O3 GOL 725 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 6 #