data_4QI9 # _model_server_result.job_id xjknXBDJsiKexS2plDNH_Q _model_server_result.datetime_utc '2024-12-26 11:32:09' _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 4qi9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 4QI9 # _exptl.entry_id 4QI9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 454.439 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description METHOTREXATE _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93 _cell.angle_gamma 90 _cell.entry_id 4QI9 _cell.length_a 178.196 _cell.length_b 103.641 _cell.length_c 34.288 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QI9 _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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 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,D,G 1 1 B,E,H 2 1 C,F,I 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C MSE 1 A MSE 1 1_555 A N ILE 2 A ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C ILE 42 A ILE 42 1_555 A N MSE 43 A MSE 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C MSE 43 A MSE 43 1_555 A N GLY 44 A GLY 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 A C VAL 92 A VAL 92 1_555 A N MSE 93 A MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C MSE 93 A MSE 93 1_555 A N VAL 94 A VAL 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C VAL 94 A VAL 94 1_555 A N MSE 95 A MSE 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale7 A C MSE 95 A MSE 95 1_555 A N GLY 96 A GLY 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C ARG 110 A ARG 110 1_555 A N MSE 111 A MSE 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale9 A C MSE 111 A MSE 111 1_555 A N TYR 112 A TYR 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 B C MSE 1 B MSE 1 1_555 B N ILE 2 B ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 B C ILE 42 B ILE 42 1_555 B N MSE 43 B MSE 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale12 B C MSE 43 B MSE 43 1_555 B N GLY 44 B GLY 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale13 B C VAL 92 B VAL 92 1_555 B N MSE 93 B MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale14 B C MSE 93 B MSE 93 1_555 B N VAL 94 B VAL 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 B C VAL 94 B VAL 94 1_555 B N MSE 95 B MSE 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale16 B C MSE 95 B MSE 95 1_555 B N GLY 96 B GLY 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale17 B C ARG 110 B ARG 110 1_555 B N MSE 111 B MSE 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale18 B C MSE 111 B MSE 111 1_555 B N TYR 112 B TYR 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale19 C C MSE 1 C MSE 1 1_555 C N ILE 2 C ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale20 C C ILE 42 C ILE 42 1_555 C N MSE 43 C MSE 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale21 C C MSE 43 C MSE 43 1_555 C N GLY 44 C GLY 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale22 C C VAL 92 C VAL 92 1_555 C N MSE 93 C MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale23 C C MSE 93 C MSE 93 1_555 C N VAL 94 C VAL 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale24 C C VAL 94 C VAL 94 1_555 C N MSE 95 C MSE 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale25 C C MSE 95 C MSE 95 1_555 C N GLY 96 C GLY 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale26 C C ARG 110 C ARG 110 1_555 C N MSE 111 C MSE 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale27 C C MSE 111 C MSE 111 1_555 C N TYR 112 C TYR 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _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 4QI9 _atom_sites.fract_transf_matrix[1][1] 0.005612 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000294 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009649 _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] 0.029205 _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 D 2 MTX A 1 201 180 MTX MTX . E 2 MTX B 1 201 180 MTX MTX . F 2 MTX C 1 201 180 MTX MTX . G 3 HOH A 1 301 1 HOH HOH . G 3 HOH A 2 302 7 HOH HOH . G 3 HOH A 3 303 9 HOH HOH . G 3 HOH A 4 304 10 HOH HOH . G 3 HOH A 5 305 11 HOH HOH . G 3 HOH A 6 306 16 HOH HOH . G 3 HOH A 7 307 17 HOH HOH . G 3 HOH A 8 308 18 HOH HOH . G 3 HOH A 9 309 23 HOH HOH . G 3 HOH A 10 310 24 HOH HOH . G 3 HOH A 11 311 27 HOH HOH . G 3 HOH A 12 312 30 HOH HOH . G 3 HOH A 13 313 31 HOH HOH . G 3 HOH A 14 314 33 HOH HOH . G 3 HOH A 15 315 36 HOH HOH . G 3 HOH A 16 316 38 HOH HOH . G 3 HOH A 17 317 39 HOH HOH . G 3 HOH A 18 318 40 HOH HOH . G 3 HOH A 19 319 42 HOH HOH . G 3 HOH A 20 320 44 HOH HOH . G 3 HOH A 21 321 47 HOH HOH . G 3 HOH A 22 322 48 HOH HOH . G 3 HOH A 23 323 49 HOH HOH . G 3 HOH A 24 324 52 HOH HOH . G 3 HOH A 25 325 53 HOH HOH . G 3 HOH A 26 326 70 HOH HOH . G 3 HOH A 27 327 78 HOH HOH . G 3 HOH A 28 328 79 HOH HOH . H 3 HOH B 1 301 2 HOH HOH . H 3 HOH B 2 302 3 HOH HOH . H 3 HOH B 3 303 4 HOH HOH . H 3 HOH B 4 304 5 HOH HOH . H 3 HOH B 5 305 6 HOH HOH . H 3 HOH B 6 306 8 HOH HOH . H 3 HOH B 7 307 12 HOH HOH . H 3 HOH B 8 308 13 HOH HOH . H 3 HOH B 9 309 14 HOH HOH . H 3 HOH B 10 310 19 HOH HOH . H 3 HOH B 11 311 20 HOH HOH . H 3 HOH B 12 312 21 HOH HOH . H 3 HOH B 13 313 26 HOH HOH . H 3 HOH B 14 314 28 HOH HOH . H 3 HOH B 15 315 29 HOH HOH . H 3 HOH B 16 316 32 HOH HOH . H 3 HOH B 17 317 34 HOH HOH . H 3 HOH B 18 318 35 HOH HOH . H 3 HOH B 19 319 41 HOH HOH . H 3 HOH B 20 320 43 HOH HOH . H 3 HOH B 21 321 45 HOH HOH . H 3 HOH B 22 322 46 HOH HOH . H 3 HOH B 23 323 51 HOH HOH . H 3 HOH B 24 324 55 HOH HOH . H 3 HOH B 25 325 57 HOH HOH . H 3 HOH B 26 326 60 HOH HOH . H 3 HOH B 27 327 61 HOH HOH . H 3 HOH B 28 328 67 HOH HOH . H 3 HOH B 29 329 68 HOH HOH . I 3 HOH C 1 301 15 HOH HOH . I 3 HOH C 2 302 22 HOH HOH . I 3 HOH C 3 303 25 HOH HOH . I 3 HOH C 4 304 37 HOH HOH . I 3 HOH C 5 305 50 HOH HOH . I 3 HOH C 6 306 54 HOH HOH . I 3 HOH C 7 307 56 HOH HOH . I 3 HOH C 8 308 58 HOH HOH . I 3 HOH C 9 309 59 HOH HOH . I 3 HOH C 10 310 62 HOH HOH . I 3 HOH C 11 311 63 HOH HOH . I 3 HOH C 12 312 64 HOH HOH . I 3 HOH C 13 313 65 HOH HOH . I 3 HOH C 14 314 66 HOH HOH . I 3 HOH C 15 315 69 HOH HOH . I 3 HOH C 16 316 71 HOH HOH . I 3 HOH C 17 317 72 HOH HOH . I 3 HOH C 18 318 73 HOH HOH . I 3 HOH C 19 319 74 HOH HOH . I 3 HOH C 20 320 75 HOH HOH . I 3 HOH C 21 321 76 HOH HOH . I 3 HOH C 22 322 77 HOH HOH . I 3 HOH C 23 323 80 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 . . . E 2 -38.256 -83.848 6.52 1 16.03 ? N1 MTX 201 B 1 HETATM 2 C C2 MTX . . . E 2 -37.952 -85.127 6.1 1 18.56 ? C2 MTX 201 B 1 HETATM 3 N NA2 MTX . . . E 2 -37.374 -85.316 4.918 1 15.58 ? NA2 MTX 201 B 1 HETATM 4 N N3 MTX . . . E 2 -38.251 -86.226 6.891 1 17.6 ? N3 MTX 201 B 1 HETATM 5 C C4 MTX . . . E 2 -38.855 -86.063 8.107 1 18.01 ? C4 MTX 201 B 1 HETATM 6 N NA4 MTX . . . E 2 -39.023 -87.13 8.883 1 18.92 ? NA4 MTX 201 B 1 HETATM 7 C C4A MTX . . . E 2 -39.151 -84.772 8.546 1 22.05 ? C4A MTX 201 B 1 HETATM 8 N N5 MTX . . . E 2 -39.761 -84.567 9.761 1 21.35 ? N5 MTX 201 B 1 HETATM 9 C C6 MTX . . . E 2 -40.071 -83.288 10.194 1 23.97 ? C6 MTX 201 B 1 HETATM 10 C C7 MTX . . . E 2 -39.766 -82.191 9.394 1 20.16 ? C7 MTX 201 B 1 HETATM 11 N N8 MTX . . . E 2 -39.162 -82.397 8.171 1 25.19 ? N8 MTX 201 B 1 HETATM 12 C C8A MTX . . . E 2 -38.854 -83.671 7.744 1 20.62 ? C8A MTX 201 B 1 HETATM 13 C C9 MTX . . . E 2 -40.749 -83.1 11.537 1 23.38 ? C9 MTX 201 B 1 HETATM 14 N N10 MTX . . . E 2 -41.395 -81.8 11.678 1 28.85 ? N10 MTX 201 B 1 HETATM 15 C CM MTX . . . E 2 -40.978 -80.923 12.782 1 24.63 ? CM MTX 201 B 1 HETATM 16 C C11 MTX . . . E 2 -44.618 -80.496 9.288 1 27.84 ? C11 MTX 201 B 1 HETATM 17 C C12 MTX . . . E 2 -44.173 -79.711 10.354 1 21.61 ? C12 MTX 201 B 1 HETATM 18 C C13 MTX . . . E 2 -43.076 -80.12 11.109 1 25.24 ? C13 MTX 201 B 1 HETATM 19 C C14 MTX . . . E 2 -42.491 -81.367 10.872 1 23.94 ? C14 MTX 201 B 1 HETATM 20 C C15 MTX . . . E 2 -42.982 -82.156 9.846 1 26.89 ? C15 MTX 201 B 1 HETATM 21 C C16 MTX . . . E 2 -44.037 -81.728 9.057 1 23.52 ? C16 MTX 201 B 1 HETATM 22 C C MTX . . . E 2 -45.78 -80.058 8.445 1 28.43 ? C MTX 201 B 1 HETATM 23 O O MTX . . . E 2 -46.696 -79.156 9.021 1 33.89 ? O MTX 201 B 1 HETATM 24 N N MTX . . . E 2 -45.968 -80.522 7.21 1 29.19 ? N MTX 201 B 1 HETATM 25 C CA MTX . . . E 2 -47.326 -80.513 6.672 1 31.76 ? CA MTX 201 B 1 HETATM 26 C CT MTX . . . E 2 -47.67 -81.576 5.663 1 29.41 ? CT MTX 201 B 1 HETATM 27 O O1 MTX . . . E 2 -46.878 -82.505 5.376 1 30.82 ? O1 MTX 201 B 1 HETATM 28 O O2 MTX . . . E 2 -48.78 -81.543 5.09 1 25.47 ? O2 MTX 201 B 1 HETATM 29 C CB MTX . . . E 2 -47.641 -79.176 6.032 1 36.49 ? CB MTX 201 B 1 HETATM 30 C CG MTX . . . E 2 -46.476 -78.634 5.22 1 33.83 ? CG MTX 201 B 1 HETATM 31 C CD MTX . . . E 2 -46.896 -77.227 4.872 1 56.02 ? CD MTX 201 B 1 HETATM 32 O OE1 MTX . . . E 2 -47.837 -76.698 5.515 1 51.52 ? OE1 MTX 201 B 1 HETATM 33 O OE2 MTX . . . E 2 -46.329 -76.59 3.956 1 54.17 ? OE2 MTX 201 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #