data_3CL9 # _model_server_result.job_id hD2LBI0vpL10D8uCwFqUVw _model_server_result.datetime_utc '2024-11-27 04:02:56' _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 3cl9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":602}' # _entry.id 3CL9 # _exptl.entry_id 3CL9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 454.439 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description METHOTREXATE _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 3CL9 _cell.length_a 121.05 _cell.length_b 121.05 _cell.length_c 260.76 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CL9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # 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 1 1,2 A,B,C,D,E,F,G,H,I,J,K,L 2 1,3 A,B,C,D,E,F,G,H,I,J,K,L 3 1,2,4,3 # 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' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H22 N8 O5' _chem_comp.formula_weight 454.439 _chem_comp.id MTX _chem_comp.mon_nstd_flag . _chem_comp.name METHOTREXATE _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 N1 C2 MTX doub 246 n y N1 C8A MTX sing 247 n y C2 NA2 MTX sing 248 n n C2 N3 MTX sing 249 n y NA2 HN21 MTX sing 250 n n NA2 HN22 MTX sing 251 n n N3 C4 MTX doub 252 n y C4 NA4 MTX sing 253 n n C4 C4A MTX sing 254 n y NA4 HN41 MTX sing 255 n n NA4 HN42 MTX sing 256 n n C4A N5 MTX sing 257 n y C4A C8A MTX doub 258 n y N5 C6 MTX doub 259 n y C6 C7 MTX sing 260 n y C6 C9 MTX sing 261 n n C7 N8 MTX doub 262 n y C7 H7 MTX sing 263 n n N8 C8A MTX sing 264 n y C9 N10 MTX sing 265 n n C9 H91 MTX sing 266 n n C9 H92 MTX sing 267 n n N10 CM MTX sing 268 n n N10 C14 MTX sing 269 n n CM HM1 MTX sing 270 n n CM HM2 MTX sing 271 n n CM HM3 MTX sing 272 n n C11 C12 MTX doub 273 n y C11 C16 MTX sing 274 n y C11 C MTX sing 275 n n C12 C13 MTX sing 276 n y C12 H12 MTX sing 277 n n C13 C14 MTX doub 278 n y C13 H13 MTX sing 279 n n C14 C15 MTX sing 280 n y C15 C16 MTX doub 281 n y C15 H15 MTX sing 282 n n C16 H16 MTX sing 283 n n C O MTX doub 284 n n C N MTX sing 285 n n N CA MTX sing 286 n n N HN MTX sing 287 n n CA CT MTX sing 288 n n CA CB MTX sing 289 n n CA HA MTX sing 290 n n CT O1 MTX doub 291 n n CT O2 MTX sing 292 n n O2 HO2 MTX sing 293 n n CB CG MTX sing 294 n n CB HB1 MTX sing 295 n n CB HB2 MTX sing 296 n n CG CD MTX sing 297 n n CG HG1 MTX sing 298 n n CG HG2 MTX sing 299 n n CD OE1 MTX doub 300 n n CD OE2 MTX sing 301 n n OE2 HOE2 MTX sing 302 n n # _atom_sites.entry_id 3CL9 _atom_sites.fract_transf_matrix[1][1] 0.008261 _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] 0.008261 _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] 0.003835 _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 SO4 A 1 801 801 SO4 SO4 . C 2 SO4 A 1 802 802 SO4 SO4 . D 3 CL A 1 901 901 CL CL . E 3 CL A 1 902 902 CL CL . F 3 CL A 1 903 903 CL CL . G 4 NAP A 1 601 601 NAP NAP . H 5 MTX A 1 602 602 MTX MTX . I 6 UMP A 1 603 603 UMP UMP . J 7 EDO A 1 701 701 EDO EDO . K 7 EDO A 1 702 702 EDO EDO . L 8 HOH A 1 904 1 HOH HOH . L 8 HOH A 2 905 2 HOH HOH . L 8 HOH A 3 906 3 HOH HOH . L 8 HOH A 4 907 4 HOH HOH . L 8 HOH A 5 908 5 HOH HOH . L 8 HOH A 6 909 6 HOH HOH . L 8 HOH A 7 910 7 HOH HOH . L 8 HOH A 8 911 8 HOH HOH . L 8 HOH A 9 912 9 HOH HOH . L 8 HOH A 10 913 10 HOH HOH . L 8 HOH A 11 914 11 HOH HOH . L 8 HOH A 12 915 12 HOH HOH . L 8 HOH A 13 916 13 HOH HOH . L 8 HOH A 14 917 14 HOH HOH . L 8 HOH A 15 918 15 HOH HOH . L 8 HOH A 16 919 16 HOH HOH . L 8 HOH A 17 920 17 HOH HOH . L 8 HOH A 18 921 18 HOH HOH . L 8 HOH A 19 922 19 HOH HOH . L 8 HOH A 20 923 20 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 N N1 MTX . . . H 5 -38.518 5.566 -8.855 1 98.57 ? N1 MTX 602 A 1 HETATM 2 C C2 MTX . . . H 5 -37.338 5.328 -8.188 1 98.41 ? C2 MTX 602 A 1 HETATM 3 N NA2 MTX . . . H 5 -36.594 4.282 -8.517 1 98.5 ? NA2 MTX 602 A 1 HETATM 4 N N3 MTX . . . H 5 -36.928 6.17 -7.178 1 98.38 ? N3 MTX 602 A 1 HETATM 5 C C4 MTX . . . H 5 -37.679 7.269 -6.826 1 98.41 ? C4 MTX 602 A 1 HETATM 6 N NA4 MTX . . . H 5 -37.038 8.304 -6.294 1 98.79 ? NA4 MTX 602 A 1 HETATM 7 C C4A MTX . . . H 5 -38.873 7.51 -7.495 1 98.52 ? C4A MTX 602 A 1 HETATM 8 N N5 MTX . . . H 5 -39.649 8.602 -7.157 1 98.65 ? N5 MTX 602 A 1 HETATM 9 C C6 MTX . . . H 5 -40.843 8.859 -7.811 1 98.66 ? C6 MTX 602 A 1 HETATM 10 C C7 MTX . . . H 5 -41.256 8 -8.836 1 98.59 ? C7 MTX 602 A 1 HETATM 11 N N8 MTX . . . H 5 -40.481 6.905 -9.181 1 98.62 ? N8 MTX 602 A 1 HETATM 12 C C8A MTX . . . H 5 -39.291 6.657 -8.515 1 98.75 ? C8A MTX 602 A 1 HETATM 13 C C9 MTX . . . H 5 -41.645 10.082 -7.386 1 98.77 ? C9 MTX 602 A 1 HETATM 14 N N10 MTX . . . H 5 -43.036 10.108 -7.827 1 99.02 ? N10 MTX 602 A 1 HETATM 15 C CM MTX . . . H 5 -43.432 11.082 -8.857 1 99.4 ? CM MTX 602 A 1 HETATM 16 C C11 MTX . . . H 5 -45.713 7.078 -6.732 1 98.91 ? C11 MTX 602 A 1 HETATM 17 C C12 MTX . . . H 5 -45.742 7.603 -8.019 1 99.12 ? C12 MTX 602 A 1 HETATM 18 C C13 MTX . . . H 5 -44.853 8.607 -8.376 1 98.83 ? C13 MTX 602 A 1 HETATM 19 C C14 MTX . . . H 5 -43.944 9.088 -7.443 1 98.71 ? C14 MTX 602 A 1 HETATM 20 C C15 MTX . . . H 5 -43.916 8.562 -6.156 1 98.39 ? C15 MTX 602 A 1 HETATM 21 C C16 MTX . . . H 5 -44.875 7.635 -5.773 1 98.65 ? C16 MTX 602 A 1 HETATM 22 C C MTX . . . H 5 -46.676 5.993 -6.363 1 98.98 ? C MTX 602 A 1 HETATM 23 O O MTX . . . H 5 -47.592 5.53 -7.339 1 99.21 ? O MTX 602 A 1 HETATM 24 N N MTX . . . H 5 -46.623 5.513 -5.121 1 99.03 ? N MTX 602 A 1 HETATM 25 C CA MTX . . . H 5 -47.004 4.17 -4.731 1 99.04 ? CA MTX 602 A 1 HETATM 26 C CT MTX . . . H 5 -46.315 3.73 -3.48 1 99.13 ? CT MTX 602 A 1 HETATM 27 O O1 MTX . . . H 5 -45.156 4.119 -3.203 1 99.16 ? O1 MTX 602 A 1 HETATM 28 O O2 MTX . . . H 5 -46.907 2.943 -2.71 1 99.6 ? O2 MTX 602 A 1 HETATM 29 C CB MTX . . . H 5 -46.638 3.151 -5.791 1 98.97 ? CB MTX 602 A 1 HETATM 30 C CG MTX . . . H 5 -47.702 2.067 -5.87 1 98.9 ? CG MTX 602 A 1 HETATM 31 C CD MTX . . . H 5 -47.588 1.48 -7.247 1 98.89 ? CD MTX 602 A 1 HETATM 32 O OE1 MTX . . . H 5 -47.797 2.19 -8.261 1 99.14 ? OE1 MTX 602 A 1 HETATM 33 O OE2 MTX . . . H 5 -47.261 0.281 -7.377 1 98.94 ? OE2 MTX 602 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #