data_6PFI # _model_server_result.job_id A3EdndierTW0GnkQTOhaqg _model_server_result.datetime_utc '2024-11-28 22:55:23' _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 6pfi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":604}' # _entry.id 6PFI # _exptl.entry_id 6PFI _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 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.05 _cell.angle_gamma 90 _cell.entry_id 6PFI _cell.length_a 213.38 _cell.length_b 116.741 _cell.length_c 221.58 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PFI _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 dimeric 2 author_and_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,F,G,H,I,J,K,L,M,Z,AA 1 1 C,D,N,O,P,Q,R,S,T,U,BA,CA 2 1 E,V,W,X,Y,DA 3 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' 2_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -213.38 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 I N N ? 5 M N N ? 5 Q N N ? 5 U N N ? 5 Y N 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 237 n y N1 C8A MTX sing 238 n y C2 NA2 MTX sing 239 n n C2 N3 MTX sing 240 n y NA2 HN21 MTX sing 241 n n NA2 HN22 MTX sing 242 n n N3 C4 MTX doub 243 n y C4 NA4 MTX sing 244 n n C4 C4A MTX sing 245 n y NA4 HN41 MTX sing 246 n n NA4 HN42 MTX sing 247 n n C4A N5 MTX sing 248 n y C4A C8A MTX doub 249 n y N5 C6 MTX doub 250 n y C6 C7 MTX sing 251 n y C6 C9 MTX sing 252 n n C7 N8 MTX doub 253 n y C7 H7 MTX sing 254 n n N8 C8A MTX sing 255 n y C9 N10 MTX sing 256 n n C9 H91 MTX sing 257 n n C9 H92 MTX sing 258 n n N10 CM MTX sing 259 n n N10 C14 MTX sing 260 n n CM HM1 MTX sing 261 n n CM HM2 MTX sing 262 n n CM HM3 MTX sing 263 n n C11 C12 MTX doub 264 n y C11 C16 MTX sing 265 n y C11 C MTX sing 266 n n C12 C13 MTX sing 267 n y C12 H12 MTX sing 268 n n C13 C14 MTX doub 269 n y C13 H13 MTX sing 270 n n C14 C15 MTX sing 271 n y C15 C16 MTX doub 272 n y C15 H15 MTX sing 273 n n C16 H16 MTX sing 274 n n C O MTX doub 275 n n C N MTX sing 276 n n N CA MTX sing 277 n n N HN MTX sing 278 n n CA CT MTX sing 279 n n CA CB MTX sing 280 n n CA HA MTX sing 281 n n CT O1 MTX doub 282 n n CT O2 MTX sing 283 n n O2 HO2 MTX sing 284 n n CB CG MTX sing 285 n n CB HB1 MTX sing 286 n n CB HB2 MTX sing 287 n n CG CD MTX sing 288 n n CG HG1 MTX sing 289 n n CG HG2 MTX sing 290 n n CD OE1 MTX doub 291 n n CD OE2 MTX sing 292 n n OE2 HOE2 MTX sing 293 n n # _atom_sites.entry_id 6PFI _atom_sites.fract_transf_matrix[1][1] 0.004686 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000414 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008566 _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] 0.004531 _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 2 NDP A 1 601 601 NDP NDP . G 3 UFP A 1 602 602 UFP UFP . H 4 OEP A 1 603 603 OEP T26 . I 5 MTX A 1 604 604 MTX MTX . J 2 NDP B 1 601 601 NDP NDP . K 3 UFP B 1 602 602 UFP UFP . L 4 OEP B 1 603 603 OEP T26 . M 5 MTX B 1 604 604 MTX MTX . N 2 NDP C 1 601 601 NDP NDP . O 3 UFP C 1 602 602 UFP UFP . P 4 OEP C 1 603 603 OEP T26 . Q 5 MTX C 1 604 604 MTX MTX . R 2 NDP D 1 601 601 NDP NDP . S 3 UFP D 1 602 602 UFP UFP . T 4 OEP D 1 603 603 OEP T26 . U 5 MTX D 1 604 604 MTX MTX . V 2 NDP E 1 601 601 NDP NDP . W 3 UFP E 1 602 602 UFP UFP . X 4 OEP E 1 603 603 OEP T26 . Y 5 MTX E 1 604 604 MTX MTX . Z 6 HOH A 1 701 29 HOH HOH . Z 6 HOH A 2 702 9 HOH HOH . Z 6 HOH A 3 703 25 HOH HOH . Z 6 HOH A 4 704 21 HOH HOH . Z 6 HOH A 5 705 4 HOH HOH . Z 6 HOH A 6 706 1 HOH HOH . Z 6 HOH A 7 707 2 HOH HOH . Z 6 HOH A 8 708 7 HOH HOH . AA 6 HOH B 1 701 10 HOH HOH . AA 6 HOH B 2 702 13 HOH HOH . AA 6 HOH B 3 703 26 HOH HOH . AA 6 HOH B 4 704 18 HOH HOH . AA 6 HOH B 5 705 27 HOH HOH . AA 6 HOH B 6 706 17 HOH HOH . AA 6 HOH B 7 707 22 HOH HOH . AA 6 HOH B 8 708 14 HOH HOH . BA 6 HOH C 1 701 30 HOH HOH . BA 6 HOH C 2 702 20 HOH HOH . BA 6 HOH C 3 703 5 HOH HOH . BA 6 HOH C 4 704 3 HOH HOH . CA 6 HOH D 1 701 24 HOH HOH . CA 6 HOH D 2 702 8 HOH HOH . CA 6 HOH D 3 703 6 HOH HOH . CA 6 HOH D 4 704 15 HOH HOH . DA 6 HOH E 1 701 19 HOH HOH . DA 6 HOH E 2 702 12 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 . . . U 5 -80.117 -78.51 25.808 1 70.22 ? N1 MTX 604 D 1 HETATM 2 C C2 MTX . . . U 5 -79.075 -77.848 26.343 1 75.25 ? C2 MTX 604 D 1 HETATM 3 N NA2 MTX . . . U 5 -79.188 -77.348 27.69 1 88.58 ? NA2 MTX 604 D 1 HETATM 4 N N3 MTX . . . U 5 -77.934 -77.64 25.666 1 86.61 ? N3 MTX 604 D 1 HETATM 5 C C4 MTX . . . U 5 -77.798 -78.098 24.402 1 82.53 ? C4 MTX 604 D 1 HETATM 6 N NA4 MTX . . . U 5 -76.597 -77.891 23.655 1 69.8 ? NA4 MTX 604 D 1 HETATM 7 C C4A MTX . . . U 5 -78.867 -78.796 23.801 1 75.06 ? C4A MTX 604 D 1 HETATM 8 N N5 MTX . . . U 5 -78.762 -79.274 22.53 1 77.52 ? N5 MTX 604 D 1 HETATM 9 C C6 MTX . . . U 5 -79.806 -79.935 21.992 1 81.27 ? C6 MTX 604 D 1 HETATM 10 C C7 MTX . . . U 5 -80.993 -80.146 22.702 1 80.88 ? C7 MTX 604 D 1 HETATM 11 N N8 MTX . . . U 5 -81.078 -79.671 23.965 1 79.41 ? N8 MTX 604 D 1 HETATM 12 C C8A MTX . . . U 5 -80.025 -78.993 24.528 1 76.61 ? C8A MTX 604 D 1 HETATM 13 C C9 MTX . . . U 5 -79.649 -80.436 20.579 1 81.19 ? C9 MTX 604 D 1 HETATM 14 N N10 MTX . . . U 5 -79.429 -79.327 19.675 1 83.58 ? N10 MTX 604 D 1 HETATM 15 C CM MTX . . . U 5 -78.147 -79.157 19.044 1 73.67 ? CM MTX 604 D 1 HETATM 16 C C11 MTX . . . U 5 -82.478 -76.457 19.041 1 68.29 ? C11 MTX 604 D 1 HETATM 17 C C12 MTX . . . U 5 -82.818 -77.777 19.331 1 66.99 ? C12 MTX 604 D 1 HETATM 18 C C13 MTX . . . U 5 -81.818 -78.726 19.537 1 62.1 ? C13 MTX 604 D 1 HETATM 19 C C14 MTX . . . U 5 -80.482 -78.354 19.446 1 73.72 ? C14 MTX 604 D 1 HETATM 20 C C15 MTX . . . U 5 -80.142 -77.034 19.171 1 69.57 ? C15 MTX 604 D 1 HETATM 21 C C16 MTX . . . U 5 -81.141 -76.089 18.966 1 71.74 ? C16 MTX 604 D 1 HETATM 22 C C MTX . . . U 5 -83.532 -75.4 18.822 1 60.92 ? C MTX 604 D 1 HETATM 23 O O MTX . . . U 5 -84.63 -75.7 18.385 1 75.47 ? O MTX 604 D 1 HETATM 24 N N MTX . . . U 5 -83.229 -74.024 19.142 1 62.79 ? N MTX 604 D 1 HETATM 25 C CA MTX . . . U 5 -84.187 -72.969 18.962 1 79.36 ? CA MTX 604 D 1 HETATM 26 C CT MTX . . . U 5 -83.433 -71.701 19.047 1 83.15 ? CT MTX 604 D 1 HETATM 27 O O1 MTX . . . U 5 -82.175 -71.742 19.041 1 74.34 ? O1 MTX 604 D 1 HETATM 28 O O2 MTX . . . U 5 -84.037 -70.586 19.129 1 84.17 ? O2 MTX 604 D 1 HETATM 29 C CB MTX . . . U 5 -85.154 -73.007 20.096 1 72 ? CB MTX 604 D 1 HETATM 30 C CG MTX . . . U 5 -86.544 -72.476 19.915 1 70.5 ? CG MTX 604 D 1 HETATM 31 C CD MTX . . . U 5 -87.313 -72.196 21.168 1 85.89 ? CD MTX 604 D 1 HETATM 32 O OE1 MTX . . . U 5 -87.431 -71.011 21.558 1 90.51 ? OE1 MTX 604 D 1 HETATM 33 O OE2 MTX . . . U 5 -87.532 -73.131 21.981 1 80.2 ? OE2 MTX 604 D 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 33 #