data_9ONI
#
_model_server_result.job_id            CVuf_TzkYzfGrvR-1Wx2SQ 
_model_server_result.datetime_utc      '2025-08-28 00:15:14' 
_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          9oni 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":602}' 
#
_entry.id    9ONI 
#
_exptl.entry_id    9ONI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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         120 
_cell.entry_id            9ONI 
_cell.length_a            133.586 
_cell.length_b            133.586 
_cell.length_c            76.198 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9ONI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_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 
_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 
#
_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                     9ONI 
_atom_sites.fract_transf_matrix[1][1]    0.007486 
_atom_sites.fract_transf_matrix[1][2]    0.004322 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008644 
_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]    0.013124 
_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 NAP A 1 601 601 NAP NDP . 
C 3 MTX A 1 602 604 MTX MTX . 
D 4 HOH A 1 701 20 HOH HOH . 
D 4 HOH A 2 702 22 HOH HOH . 
D 4 HOH A 3 703 23 HOH HOH . 
D 4 HOH A 4 704 35 HOH HOH . 
D 4 HOH A 5 705 19 HOH HOH . 
D 4 HOH A 6 706 8 HOH HOH . 
D 4 HOH A 7 707 33 HOH HOH . 
D 4 HOH A 8 708 21 HOH HOH . 
D 4 HOH A 9 709 32 HOH HOH . 
D 4 HOH A 10 710 53 HOH HOH . 
D 4 HOH A 11 711 18 HOH HOH . 
D 4 HOH A 12 712 31 HOH HOH . 
D 4 HOH A 13 713 24 HOH HOH . 
D 4 HOH A 14 714 27 HOH HOH . 
D 4 HOH A 15 715 17 HOH HOH . 
D 4 HOH A 16 716 3 HOH HOH . 
D 4 HOH A 17 717 16 HOH HOH . 
D 4 HOH A 18 718 39 HOH HOH . 
D 4 HOH A 19 719 2 HOH HOH . 
D 4 HOH A 20 720 26 HOH HOH . 
D 4 HOH A 21 721 36 HOH HOH . 
D 4 HOH A 22 722 49 HOH HOH . 
D 4 HOH A 23 723 13 HOH HOH . 
D 4 HOH A 24 724 6 HOH HOH . 
D 4 HOH A 25 725 55 HOH HOH . 
D 4 HOH A 26 726 30 HOH HOH . 
D 4 HOH A 27 727 34 HOH HOH . 
D 4 HOH A 28 728 11 HOH HOH . 
D 4 HOH A 29 729 25 HOH HOH . 
D 4 HOH A 30 730 5 HOH HOH . 
D 4 HOH A 31 731 46 HOH HOH . 
D 4 HOH A 32 732 44 HOH HOH . 
D 4 HOH A 33 733 15 HOH HOH . 
D 4 HOH A 34 734 50 HOH HOH . 
D 4 HOH A 35 735 38 HOH HOH . 
D 4 HOH A 36 736 4 HOH HOH . 
D 4 HOH A 37 737 45 HOH HOH . 
D 4 HOH A 38 738 9 HOH HOH . 
D 4 HOH A 39 739 40 HOH HOH . 
D 4 HOH A 40 740 52 HOH HOH . 
D 4 HOH A 41 741 47 HOH HOH . 
D 4 HOH A 42 742 42 HOH HOH . 
D 4 HOH A 43 743 43 HOH HOH . 
D 4 HOH A 44 744 14 HOH HOH . 
D 4 HOH A 45 745 10 HOH HOH . 
D 4 HOH A 46 746 51 HOH HOH . 
D 4 HOH A 47 747 48 HOH HOH . 
D 4 HOH A 48 748 56 HOH HOH . 
D 4 HOH A 49 749 29 HOH HOH . 
D 4 HOH A 50 750 7 HOH HOH . 
D 4 HOH A 51 751 12 HOH HOH . 
D 4 HOH A 52 752 54 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 . . . C 3 -17.184 -57.374 3.361 1 53.18 ? N1 MTX 602 A 1 
HETATM 2 C C2 MTX . . . C 3 -17.428 -56.509 4.378 1 45.46 ? C2 MTX 602 A 1 
HETATM 3 N NA2 MTX . . . C 3 -18.786 -56.068 4.649 1 48.74 ? NA2 MTX 602 A 1 
HETATM 4 N N3 MTX . . . C 3 -16.409 -56.05 5.151 1 37.37 ? N3 MTX 602 A 1 
HETATM 5 C C4 MTX . . . C 3 -15.166 -56.447 4.913 1 43.6 ? C4 MTX 602 A 1 
HETATM 6 N NA4 MTX . . . C 3 -14.077 -55.957 5.736 1 23.03 ? NA4 MTX 602 A 1 
HETATM 7 C C4A MTX . . . C 3 -14.909 -57.32 3.881 1 46.99 ? C4A MTX 602 A 1 
HETATM 8 N N5 MTX . . . C 3 -13.64 -57.721 3.64 1 42.78 ? N5 MTX 602 A 1 
HETATM 9 C C6 MTX . . . C 3 -13.379 -58.559 2.651 1 43.62 ? C6 MTX 602 A 1 
HETATM 10 C C7 MTX . . . C 3 -14.419 -59.022 1.864 1 30.18 ? C7 MTX 602 A 1 
HETATM 11 N N8 MTX . . . C 3 -15.66 -58.63 2.099 1 33.79 ? N8 MTX 602 A 1 
HETATM 12 C C8A MTX . . . C 3 -15.922 -57.774 3.114 1 24.63 ? C8A MTX 602 A 1 
HETATM 13 C C9 MTX . . . C 3 -11.97 -59.082 2.287 1 19.43 ? C9 MTX 602 A 1 
HETATM 14 N N10 MTX . . . C 3 -11.812 -59.482 0.889 1 36.01 ? N10 MTX 602 A 1 
HETATM 15 C CM MTX . . . C 3 -11.541 -60.877 0.585 1 31.71 ? CM MTX 602 A 1 
HETATM 16 C C11 MTX . . . C 3 -12.059 -56.719 -2.338 1 41 ? C11 MTX 602 A 1 
HETATM 17 C C12 MTX . . . C 3 -11.944 -58.074 -2.585 1 28.67 ? C12 MTX 602 A 1 
HETATM 18 C C13 MTX . . . C 3 -11.861 -58.971 -1.526 1 32.19 ? C13 MTX 602 A 1 
HETATM 19 C C14 MTX . . . C 3 -11.899 -58.518 -0.213 1 51.02 ? C14 MTX 602 A 1 
HETATM 20 C C15 MTX . . . C 3 -12.014 -57.155 0.033 1 33.07 ? C15 MTX 602 A 1 
HETATM 21 C C16 MTX . . . C 3 -12.098 -56.26 -1.027 1 41.32 ? C16 MTX 602 A 1 
HETATM 22 C C MTX . . . C 3 -12.16 -55.721 -3.496 1 53.27 ? C MTX 602 A 1 
HETATM 23 O O MTX . . . C 3 -11.66 -55.943 -4.544 1 54.6 ? O MTX 602 A 1 
HETATM 24 N N MTX . . . C 3 -12.903 -54.486 -3.279 1 69.87 ? N MTX 602 A 1 
HETATM 25 C CA MTX . . . C 3 -13.056 -53.485 -4.317 1 35.45 ? CA MTX 602 A 1 
HETATM 26 C CT MTX . . . C 3 -12.556 -52.156 -3.78 1 48.18 ? CT MTX 602 A 1 
HETATM 27 O O1 MTX . . . C 3 -12.801 -51.812 -2.591 1 44.82 ? O1 MTX 602 A 1 
HETATM 28 O O2 MTX . . . C 3 -11.903 -51.39 -4.532 1 41.39 ? O2 MTX 602 A 1 
HETATM 29 C CB MTX . . . C 3 -14.538 -53.322 -4.616 1 51.6 ? CB MTX 602 A 1 
HETATM 30 C CG MTX . . . C 3 -15.131 -54.568 -5.279 1 65.63 ? CG MTX 602 A 1 
HETATM 31 C CD MTX . . . C 3 -16.464 -54.167 -5.919 1 65.58 ? CD MTX 602 A 1 
HETATM 32 O OE1 MTX . . . C 3 -16.671 -52.96 -6.218 1 56.07 ? OE1 MTX 602 A 1 
HETATM 33 O OE2 MTX . . . C 3 -17.354 -55.033 -6.143 1 63.89 ? OE2 MTX 602 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           33 
#