data_8XOM
#
_model_server_result.job_id            Hv2r_vKpAjHro0kRPq36yw 
_model_server_result.datetime_utc      '2025-01-03 04:01:00' 
_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          8xom 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1402}' 
#
_entry.id    8XOM 
#
_exptl.entry_id    8XOM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              454.439 
_entity.id                          3 
_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            8XOM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XOM 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_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 
_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    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 B O2B ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? 
metalc ? metalc2 B O1A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc3 B O2A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc4 B O3A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? 
#
_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 379 n y 
N1 C8A MTX sing 380 n y 
C2 NA2 MTX sing 381 n n 
C2 N3 MTX sing 382 n y 
NA2 HN21 MTX sing 383 n n 
NA2 HN22 MTX sing 384 n n 
N3 C4 MTX doub 385 n y 
C4 NA4 MTX sing 386 n n 
C4 C4A MTX sing 387 n y 
NA4 HN41 MTX sing 388 n n 
NA4 HN42 MTX sing 389 n n 
C4A N5 MTX sing 390 n y 
C4A C8A MTX doub 391 n y 
N5 C6 MTX doub 392 n y 
C6 C7 MTX sing 393 n y 
C6 C9 MTX sing 394 n n 
C7 N8 MTX doub 395 n y 
C7 H7 MTX sing 396 n n 
N8 C8A MTX sing 397 n y 
C9 N10 MTX sing 398 n n 
C9 H91 MTX sing 399 n n 
C9 H92 MTX sing 400 n n 
N10 CM MTX sing 401 n n 
N10 C14 MTX sing 402 n n 
CM HM1 MTX sing 403 n n 
CM HM2 MTX sing 404 n n 
CM HM3 MTX sing 405 n n 
C11 C12 MTX doub 406 n y 
C11 C16 MTX sing 407 n y 
C11 C MTX sing 408 n n 
C12 C13 MTX sing 409 n y 
C12 H12 MTX sing 410 n n 
C13 C14 MTX doub 411 n y 
C13 H13 MTX sing 412 n n 
C14 C15 MTX sing 413 n y 
C15 C16 MTX doub 414 n y 
C15 H15 MTX sing 415 n n 
C16 H16 MTX sing 416 n n 
C O MTX doub 417 n n 
C N MTX sing 418 n n 
N CA MTX sing 419 n n 
N HN MTX sing 420 n n 
CA CT MTX sing 421 n n 
CA CB MTX sing 422 n n 
CA HA MTX sing 423 n n 
CT O1 MTX doub 424 n n 
CT O2 MTX sing 425 n n 
O2 HO2 MTX sing 426 n n 
CB CG MTX sing 427 n n 
CB HB1 MTX sing 428 n n 
CB HB2 MTX sing 429 n n 
CG CD MTX sing 430 n n 
CG HG1 MTX sing 431 n n 
CG HG2 MTX sing 432 n n 
CD OE1 MTX doub 433 n n 
CD OE2 MTX sing 434 n n 
OE2 HOE2 MTX sing 435 n n 
#
_atom_sites.entry_id                     8XOM 
_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
B 2 ANP A 1 1401 1401 ANP ANP . 
C 3 MTX A 1 1402 1501 MTX MTX . 
D 4 DU0 A 1 1403 1 DU0 DU0 . 
E 4 DU0 A 1 1404 2 DU0 DU0 . 
F 4 DU0 A 1 1405 3 DU0 DU0 . 
G 4 DU0 A 1 1406 4 DU0 DU0 . 
H 4 DU0 A 1 1407 5 DU0 DU0 . 
I 4 DU0 A 1 1408 6 DU0 DU0 . 
J 4 DU0 A 1 1409 7 DU0 DU0 . 
K 4 DU0 A 1 1410 8 DU0 DU0 . 
L 4 DU0 A 1 1411 9 DU0 DU0 . 
M 4 DU0 A 1 1412 10 DU0 DU0 . 
N 4 DU0 A 1 1413 11 DU0 DU0 . 
O 4 DU0 A 1 1414 12 DU0 DU0 . 
P 4 DU0 A 1 1415 13 DU0 DU0 . 
Q 4 DU0 A 1 1416 14 DU0 DU0 . 
R 5 PLM A 1 1417 16 PLM PLM . 
S 6 MG A 1 1418 1 MG MG . 
#
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 . . . C 3 102.849 109.145 109.495 1 165 ? N1 MTX 1402 A 1 
HETATM 2 C C2 MTX . . . C 3 101.761 108.428 109.704 1 161.32 ? C2 MTX 1402 A 1 
HETATM 3 N NA2 MTX . . . C 3 100.698 108.697 108.933 1 162.54 ? NA2 MTX 1402 A 1 
HETATM 4 N N3 MTX . . . C 3 101.592 107.443 110.614 1 155.9 ? N3 MTX 1402 A 1 
HETATM 5 C C4 MTX . . . C 3 102.605 107.146 111.393 1 152.27 ? C4 MTX 1402 A 1 
HETATM 6 N NA4 MTX . . . C 3 102.489 106.189 112.302 1 139 ? NA4 MTX 1402 A 1 
HETATM 7 C C4A MTX . . . C 3 103.854 107.856 111.266 1 160.32 ? C4A MTX 1402 A 1 
HETATM 8 N N5 MTX . . . C 3 104.901 107.572 112.035 1 159.08 ? N5 MTX 1402 A 1 
HETATM 9 C C6 MTX . . . C 3 105.989 108.283 111.837 1 160.01 ? C6 MTX 1402 A 1 
HETATM 10 C C7 MTX . . . C 3 106.025 109.287 110.851 1 162.27 ? C7 MTX 1402 A 1 
HETATM 11 N N8 MTX . . . C 3 105.01 109.568 110.089 1 165.58 ? N8 MTX 1402 A 1 
HETATM 12 C C8A MTX . . . C 3 103.888 108.855 110.278 1 166.98 ? C8A MTX 1402 A 1 
HETATM 13 C C9 MTX . . . C 3 107.206 108.012 112.68 1 154.04 ? C9 MTX 1402 A 1 
HETATM 14 N N10 MTX . . . C 3 107.51 106.654 113.053 1 147.24 ? N10 MTX 1402 A 1 
HETATM 15 C CM MTX . . . C 3 107.679 106.404 114.458 1 140.52 ? CM MTX 1402 A 1 
HETATM 16 C C11 MTX . . . C 3 108.072 103.399 110.356 1 156.87 ? C11 MTX 1402 A 1 
HETATM 17 C C12 MTX . . . C 3 108.129 103.244 111.74 1 149.85 ? C12 MTX 1402 A 1 
HETATM 18 C C13 MTX . . . C 3 107.958 104.306 112.61 1 146.13 ? C13 MTX 1402 A 1 
HETATM 19 C C14 MTX . . . C 3 107.677 105.616 112.165 1 147.44 ? C14 MTX 1402 A 1 
HETATM 20 C C15 MTX . . . C 3 107.572 105.765 110.771 1 148.89 ? C15 MTX 1402 A 1 
HETATM 21 C C16 MTX . . . C 3 107.743 104.686 109.922 1 152.4 ? C16 MTX 1402 A 1 
HETATM 22 C C MTX . . . C 3 108.208 102.224 109.418 1 162.96 ? C MTX 1402 A 1 
HETATM 23 O O MTX . . . C 3 107.137 101.858 108.945 1 160.07 ? O MTX 1402 A 1 
HETATM 24 N N MTX . . . C 3 109.307 101.534 109.028 1 173.04 ? N MTX 1402 A 1 
HETATM 25 C CA MTX . . . C 3 110.748 101.448 109.19 1 176.99 ? CA MTX 1402 A 1 
HETATM 26 C CT MTX . . . C 3 111.412 102.641 109.925 1 167.9 ? CT MTX 1402 A 1 
HETATM 27 O O1 MTX . . . C 3 111.071 102.803 111.106 1 157.09 ? O1 MTX 1402 A 1 
HETATM 28 O O2 MTX . . . C 3 112.242 103.328 109.296 1 166.18 ? O2 MTX 1402 A 1 
HETATM 29 C CB MTX . . . C 3 111.326 101.264 107.778 1 176.42 ? CB MTX 1402 A 1 
HETATM 30 C CG MTX . . . C 3 110.278 100.697 106.818 1 178.4 ? CG MTX 1402 A 1 
HETATM 31 C CD MTX . . . C 3 109.668 101.655 105.772 1 172.34 ? CD MTX 1402 A 1 
HETATM 32 O OE1 MTX . . . C 3 110.248 101.672 104.669 1 170.73 ? OE1 MTX 1402 A 1 
HETATM 33 O OE2 MTX . . . C 3 108.658 102.321 106.091 1 171.17 ? OE2 MTX 1402 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           33 
#