data_9C87
#
_model_server_result.job_id            D8USvY_3HGjWi6rciJmTlA 
_model_server_result.datetime_utc      '2024-10-26 04:32:25' 
_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          9c87 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"FA","auth_seq_id":201}' 
#
_entry.id    9C87 
#
_exptl.entry_id    9C87 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              454.439 
_entity.id                          7 
_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            9C87 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9C87 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    21-meric 
_pdbx_struct_assembly.oligomeric_count      21 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      7 
_struct_asym.id                             FA 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
metalc ? metalc1 A OG1 THR 90 A THR 126 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc2 V O2B ATP . A ATP 500 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc3 V O1A ATP . A ATP 500 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc4 V O3A ATP . A ATP 500 1_555 W MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc5 B OG1 THR 90 B THR 126 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc6 X O2B ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc7 X O3B ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? 
metalc ? metalc8 X O1A ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc9 X O3A ATP . B ATP 500 1_555 Y MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc10 C OG1 THR 90 C THR 126 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? 
metalc ? metalc11 Z O2G ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc12 Z O2B ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc13 Z O3B ATP . C ATP 500 1_555 AA MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc14 D OG1 THR 90 D THR 126 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? 
metalc ? metalc15 BA O1B ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
metalc ? metalc16 BA O2B ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc17 BA O1A ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? 
metalc ? metalc18 BA O2A ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc19 BA O3A ADP . D ADP 500 1_555 CA MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? 
#
_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 328 n y 
N1 C8A MTX sing 329 n y 
C2 NA2 MTX sing 330 n n 
C2 N3 MTX sing 331 n y 
NA2 HN21 MTX sing 332 n n 
NA2 HN22 MTX sing 333 n n 
N3 C4 MTX doub 334 n y 
C4 NA4 MTX sing 335 n n 
C4 C4A MTX sing 336 n y 
NA4 HN41 MTX sing 337 n n 
NA4 HN42 MTX sing 338 n n 
C4A N5 MTX sing 339 n y 
C4A C8A MTX doub 340 n y 
N5 C6 MTX doub 341 n y 
C6 C7 MTX sing 342 n y 
C6 C9 MTX sing 343 n n 
C7 N8 MTX doub 344 n y 
C7 H7 MTX sing 345 n n 
N8 C8A MTX sing 346 n y 
C9 N10 MTX sing 347 n n 
C9 H91 MTX sing 348 n n 
C9 H92 MTX sing 349 n n 
N10 CM MTX sing 350 n n 
N10 C14 MTX sing 351 n n 
CM HM1 MTX sing 352 n n 
CM HM2 MTX sing 353 n n 
CM HM3 MTX sing 354 n n 
C11 C12 MTX doub 355 n y 
C11 C16 MTX sing 356 n y 
C11 C MTX sing 357 n n 
C12 C13 MTX sing 358 n y 
C12 H12 MTX sing 359 n n 
C13 C14 MTX doub 360 n y 
C13 H13 MTX sing 361 n n 
C14 C15 MTX sing 362 n y 
C15 C16 MTX doub 363 n y 
C15 H15 MTX sing 364 n n 
C16 H16 MTX sing 365 n n 
C O MTX doub 366 n n 
C N MTX sing 367 n n 
N CA MTX sing 368 n n 
N HN MTX sing 369 n n 
CA CT MTX sing 370 n n 
CA CB MTX sing 371 n n 
CA HA MTX sing 372 n n 
CT O1 MTX doub 373 n n 
CT O2 MTX sing 374 n n 
O2 HO2 MTX sing 375 n n 
CB CG MTX sing 376 n n 
CB HB1 MTX sing 377 n n 
CB HB2 MTX sing 378 n n 
CG CD MTX sing 379 n n 
CG HG1 MTX sing 380 n n 
CG HG2 MTX sing 381 n n 
CD OE1 MTX doub 382 n n 
CD OE2 MTX sing 383 n n 
OE2 HOE2 MTX sing 384 n n 
#
_atom_sites.entry_id                     9C87 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
V 4 ATP A 1 500 500 ATP ATP . 
W 5 MG A 1 501 501 MG MG . 
X 4 ATP B 1 500 500 ATP ATP . 
Y 5 MG B 1 501 501 MG MG . 
Z 4 ATP C 1 500 500 ATP ATP . 
AA 5 MG C 1 501 501 MG MG . 
BA 6 ADP D 1 500 500 ADP ADP . 
CA 5 MG D 1 501 501 MG MG . 
DA 6 ADP E 1 501 501 ADP ADP . 
EA 6 ADP F 1 500 500 ADP ADP . 
FA 7 MTX S 1 201 201 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 . . . FA 7 143.322 130.375 213.761 1 282.1 ? N1 MTX 201 S 1 
HETATM 2 C C2 MTX . . . FA 7 143.404 130.505 212.39 1 282.1 ? C2 MTX 201 S 1 
HETATM 3 N NA2 MTX . . . FA 7 143.382 129.422 211.618 1 282.1 ? NA2 MTX 201 S 1 
HETATM 4 N N3 MTX . . . FA 7 143.51 131.756 211.817 1 282.1 ? N3 MTX 201 S 1 
HETATM 5 C C4 MTX . . . FA 7 143.529 132.892 212.603 1 282.1 ? C4 MTX 201 S 1 
HETATM 6 N NA4 MTX . . . FA 7 143.207 134.053 212.034 1 282.1 ? NA4 MTX 201 S 1 
HETATM 7 C C4A MTX . . . FA 7 143.45 132.759 213.986 1 282.1 ? C4A MTX 201 S 1 
HETATM 8 N N5 MTX . . . FA 7 143.472 133.877 214.795 1 282.1 ? N5 MTX 201 S 1 
HETATM 9 C C6 MTX . . . FA 7 143.396 133.758 216.166 1 282.1 ? C6 MTX 201 S 1 
HETATM 10 C C7 MTX . . . FA 7 143.281 132.493 216.736 1 282.1 ? C7 MTX 201 S 1 
HETATM 11 N N8 MTX . . . FA 7 143.262 131.371 215.931 1 282.1 ? N8 MTX 201 S 1 
HETATM 12 C C8A MTX . . . FA 7 143.344 131.499 214.56 1 282.1 ? C8A MTX 201 S 1 
HETATM 13 C C9 MTX . . . FA 7 143.416 135.028 216.996 1 282.1 ? C9 MTX 201 S 1 
HETATM 14 N N10 MTX . . . FA 7 143.756 134.839 218.405 1 282.1 ? N10 MTX 201 S 1 
HETATM 15 C CM MTX . . . FA 7 142.891 135.544 219.379 1 282.1 ? CM MTX 201 S 1 
HETATM 16 C C11 MTX . . . FA 7 147.535 133.359 219.6 1 282.1 ? C11 MTX 201 S 1 
HETATM 17 C C12 MTX . . . FA 7 146.436 133.215 220.434 1 282.1 ? C12 MTX 201 S 1 
HETATM 18 C C13 MTX . . . FA 7 145.195 133.697 220.034 1 282.1 ? C13 MTX 201 S 1 
HETATM 19 C C14 MTX . . . FA 7 145.042 134.342 218.807 1 282.1 ? C14 MTX 201 S 1 
HETATM 20 C C15 MTX . . . FA 7 146.158 134.478 217.983 1 282.1 ? C15 MTX 201 S 1 
HETATM 21 C C16 MTX . . . FA 7 147.421 134.157 218.468 1 282.1 ? C16 MTX 201 S 1 
HETATM 22 C C MTX . . . FA 7 148.871 132.83 220.036 1 282.1 ? C MTX 201 S 1 
HETATM 23 O O MTX . . . FA 7 149.194 132.87 221.408 1 282.1 ? O MTX 201 S 1 
HETATM 24 N N MTX . . . FA 7 149.709 132.352 219.114 1 282.1 ? N MTX 201 S 1 
HETATM 25 C CA MTX . . . FA 7 150.86 131.529 219.446 1 282.1 ? CA MTX 201 S 1 
HETATM 26 C CT MTX . . . FA 7 152.15 132.257 219.212 1 282.1 ? CT MTX 201 S 1 
HETATM 27 O O1 MTX . . . FA 7 152.207 133.209 218.406 1 282.1 ? O1 MTX 201 S 1 
HETATM 28 O O2 MTX . . . FA 7 153.184 131.914 219.825 1 282.1 ? O2 MTX 201 S 1 
HETATM 29 C CB MTX . . . FA 7 150.842 130.254 218.609 1 282.1 ? CB MTX 201 S 1 
HETATM 30 C CG MTX . . . FA 7 150.494 129.023 219.44 1 282.1 ? CG MTX 201 S 1 
HETATM 31 C CD MTX . . . FA 7 151.69 128.595 220.259 1 282.1 ? CD MTX 201 S 1 
HETATM 32 O OE1 MTX . . . FA 7 152.637 127.979 219.723 1 282.1 ? OE1 MTX 201 S 1 
HETATM 33 O OE2 MTX . . . FA 7 151.746 128.85 221.481 1 282.1 ? OE2 MTX 201 S 1 
HETATM 34 H HN21 MTX . . . FA 7 143.448 129.518 210.61 1 282.1 ? HN21 MTX 201 S 1 
HETATM 35 H HN22 MTX . . . FA 7 143.19 128.513 212.027 1 282.1 ? HN22 MTX 201 S 1 
HETATM 36 H HN41 MTX . . . FA 7 143.043 134.873 212.609 1 282.1 ? HN41 MTX 201 S 1 
HETATM 37 H HN42 MTX . . . FA 7 142.878 134.056 211.075 1 282.1 ? HN42 MTX 201 S 1 
HETATM 38 H H7 MTX . . . FA 7 143.383 132.379 217.815 1 282.1 ? H7 MTX 201 S 1 
HETATM 39 H H91 MTX . . . FA 7 142.422 135.47 216.928 1 282.1 ? H91 MTX 201 S 1 
HETATM 40 H H92 MTX . . . FA 7 144.104 135.741 216.543 1 282.1 ? H92 MTX 201 S 1 
HETATM 41 H HM1 MTX . . . FA 7 143.415 135.765 220.307 1 282.1 ? HM1 MTX 201 S 1 
HETATM 42 H HM2 MTX . . . FA 7 142.024 134.922 219.6 1 282.1 ? HM2 MTX 201 S 1 
HETATM 43 H HM3 MTX . . . FA 7 142.552 136.488 218.953 1 282.1 ? HM3 MTX 201 S 1 
HETATM 44 H H12 MTX . . . FA 7 146.518 132.614 221.34 1 282.1 ? H12 MTX 201 S 1 
HETATM 45 H H13 MTX . . . FA 7 144.323 133.526 220.664 1 282.1 ? H13 MTX 201 S 1 
HETATM 46 H H15 MTX . . . FA 7 146.027 134.668 216.917 1 282.1 ? H15 MTX 201 S 1 
HETATM 47 H H16 MTX . . . FA 7 148.303 134.653 218.061 1 282.1 ? H16 MTX 201 S 1 
HETATM 48 H HN MTX . . . FA 7 149.502 132.491 218.135 1 282.1 ? HN MTX 201 S 1 
HETATM 49 H HA MTX . . . FA 7 150.807 131.248 220.497 1 282.1 ? HA MTX 201 S 1 
HETATM 50 H HB1 MTX . . . FA 7 151.82 130.113 218.15 1 282.1 ? HB1 MTX 201 S 1 
HETATM 51 H HB2 MTX . . . FA 7 150.113 130.363 217.806 1 282.1 ? HB2 MTX 201 S 1 
HETATM 52 H HG1 MTX . . . FA 7 150.194 128.21 218.779 1 282.1 ? HG1 MTX 201 S 1 
HETATM 53 H HG2 MTX . . . FA 7 149.657 129.246 220.101 1 282.1 ? HG2 MTX 201 S 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    343 
_model_server_stats.query_time_ms           207 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           53 
#