data_6PFD # _model_server_result.job_id qqxHXLRpujS8KmjEs4uVfw _model_server_result.datetime_utc '2024-11-13 11:32:12' _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 6pfd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":604}' # _entry.id 6PFD # _exptl.entry_id 6PFD _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 6PFD _cell.length_a 213.033 _cell.length_b 115.887 _cell.length_c 220.808 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PFD _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 1 1 C,D,N,O,P,Q,R,S,T,U 2 1 E,V,W,X,Y 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_858 -x+3,y,-z+3 -1 0 0 0 1 0 0 0 -1 580.789092 0 659.852643 # 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 235 n y N1 C8A MTX sing 236 n y C2 NA2 MTX sing 237 n n C2 N3 MTX sing 238 n y NA2 HN21 MTX sing 239 n n NA2 HN22 MTX sing 240 n n N3 C4 MTX doub 241 n y C4 NA4 MTX sing 242 n n C4 C4A MTX sing 243 n y NA4 HN41 MTX sing 244 n n NA4 HN42 MTX sing 245 n n C4A N5 MTX sing 246 n y C4A C8A MTX doub 247 n y N5 C6 MTX doub 248 n y C6 C7 MTX sing 249 n y C6 C9 MTX sing 250 n n C7 N8 MTX doub 251 n y C7 H7 MTX sing 252 n n N8 C8A MTX sing 253 n y C9 N10 MTX sing 254 n n C9 H91 MTX sing 255 n n C9 H92 MTX sing 256 n n N10 CM MTX sing 257 n n N10 C14 MTX sing 258 n n CM HM1 MTX sing 259 n n CM HM2 MTX sing 260 n n CM HM3 MTX sing 261 n n C11 C12 MTX doub 262 n y C11 C16 MTX sing 263 n y C11 C MTX sing 264 n n C12 C13 MTX sing 265 n y C12 H12 MTX sing 266 n n C13 C14 MTX doub 267 n y C13 H13 MTX sing 268 n n C14 C15 MTX sing 269 n y C15 C16 MTX doub 270 n y C15 H15 MTX sing 271 n n C16 H16 MTX sing 272 n n C O MTX doub 273 n n C N MTX sing 274 n n N CA MTX sing 275 n n N HN MTX sing 276 n n CA CT MTX sing 277 n n CA CB MTX sing 278 n n CA HA MTX sing 279 n n CT O1 MTX doub 280 n n CT O2 MTX sing 281 n n O2 HO2 MTX sing 282 n n CB CG MTX sing 283 n n CB HB1 MTX sing 284 n n CB HB2 MTX sing 285 n n CG CD MTX sing 286 n n CG HG1 MTX sing 287 n n CG HG2 MTX sing 288 n n CD OE1 MTX doub 289 n n CD OE2 MTX sing 290 n n OE2 HOE2 MTX sing 291 n n # _atom_sites.entry_id 6PFD _atom_sites.fract_transf_matrix[1][1] 0.004694 _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] 0.008629 _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] 0.004546 _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 OEJ A 1 603 603 OEJ T11 . 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 OEJ B 1 603 603 OEJ T11 . 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 OEJ C 1 603 603 OEJ T11 . 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 OEJ D 1 603 603 OEJ T11 . 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 OEJ E 1 603 603 OEJ T11 . Y 5 MTX E 1 604 604 MTX MTX . # 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 . . . M 5 187.792 89.378 235.084 1 59.75 ? N1 MTX 604 B 1 HETATM 2 C C2 MTX . . . M 5 188.585 88.708 235.937 1 60.14 ? C2 MTX 604 B 1 HETATM 3 N NA2 MTX . . . M 5 190.001 88.974 235.929 1 67.04 ? NA2 MTX 604 B 1 HETATM 4 N N3 MTX . . . M 5 188.1 87.8 236.797 1 61.88 ? N3 MTX 604 B 1 HETATM 5 C C4 MTX . . . M 5 186.781 87.527 236.83 1 55.05 ? C4 MTX 604 B 1 HETATM 6 N NA4 MTX . . . M 5 186.261 86.561 237.742 1 65.27 ? NA4 MTX 604 B 1 HETATM 7 C C4A MTX . . . M 5 185.905 88.207 235.95 1 66.01 ? C4A MTX 604 B 1 HETATM 8 N N5 MTX . . . M 5 184.561 87.964 235.946 1 79.39 ? N5 MTX 604 B 1 HETATM 9 C C6 MTX . . . M 5 183.777 88.643 235.082 1 63.69 ? C6 MTX 604 B 1 HETATM 10 C C7 MTX . . . M 5 184.303 89.589 234.194 1 68.91 ? C7 MTX 604 B 1 HETATM 11 N N8 MTX . . . M 5 185.632 89.818 234.209 1 70.9 ? N8 MTX 604 B 1 HETATM 12 C C8A MTX . . . M 5 186.445 89.135 235.08 1 64.88 ? C8A MTX 604 B 1 HETATM 13 C C9 MTX . . . M 5 182.295 88.374 235.079 1 53.29 ? C9 MTX 604 B 1 HETATM 14 N N10 MTX . . . M 5 181.638 88.581 233.804 1 81.98 ? N10 MTX 604 B 1 HETATM 15 C CM MTX . . . M 5 180.552 89.528 233.714 1 79.1 ? CM MTX 604 B 1 HETATM 16 C C11 MTX . . . M 5 182.884 86.559 230.279 1 60.65 ? C11 MTX 604 B 1 HETATM 17 C C12 MTX . . . M 5 182.208 87.773 230.212 1 65.71 ? C12 MTX 604 B 1 HETATM 18 C C13 MTX . . . M 5 181.81 88.421 231.375 1 70.82 ? C13 MTX 604 B 1 HETATM 19 C C14 MTX . . . M 5 182.079 87.86 232.615 1 72.2 ? C14 MTX 604 B 1 HETATM 20 C C15 MTX . . . M 5 182.757 86.641 232.693 1 43.66 ? C15 MTX 604 B 1 HETATM 21 C C16 MTX . . . M 5 183.158 85.993 231.522 1 45.68 ? C16 MTX 604 B 1 HETATM 22 C C MTX . . . M 5 183.302 85.885 228.993 1 63.29 ? C MTX 604 B 1 HETATM 23 O O MTX . . . M 5 182.624 86.056 227.992 1 62.33 ? O MTX 604 B 1 HETATM 24 N N MTX . . . M 5 184.478 85.051 228.902 1 64.1 ? N MTX 604 B 1 HETATM 25 C CA MTX . . . M 5 184.817 84.443 227.641 1 70.59 ? CA MTX 604 B 1 HETATM 26 C CT MTX . . . M 5 185.194 83.04 227.902 1 72.18 ? CT MTX 604 B 1 HETATM 27 O O1 MTX . . . M 5 185.155 82.603 229.082 1 68.76 ? O1 MTX 604 B 1 HETATM 28 O O2 MTX . . . M 5 185.558 82.288 226.946 1 74.04 ? O2 MTX 604 B 1 HETATM 29 C CB MTX . . . M 5 186.003 85.138 227.06 1 67.58 ? CB MTX 604 B 1 HETATM 30 C CG MTX . . . M 5 186.056 85.419 225.587 1 84.5 ? CG MTX 604 B 1 HETATM 31 C CD MTX . . . M 5 187.124 86.36 225.118 1 96.38 ? CD MTX 604 B 1 HETATM 32 O OE1 MTX . . . M 5 188.1 85.907 224.474 1 98.39 ? OE1 MTX 604 B 1 HETATM 33 O OE2 MTX . . . M 5 186.9 87.599 225.104 1 90.82 ? OE2 MTX 604 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 33 #