data_6PF9
#
_model_server_result.job_id            arFJMacTxCiEeYDGFQRXZg 
_model_server_result.datetime_utc      '2024-11-13 11:46:45' 
_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          6pf9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":604}' 
#
_entry.id    6PF9 
#
_exptl.entry_id    6PF9 
_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          94.87 
_cell.angle_gamma         90 
_cell.entry_id            6PF9 
_cell.length_a            214.201 
_cell.length_b            116.51 
_cell.length_c            221.439 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PF9 
_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,F,G,H,I,J 1 1,2 
B,C,K,L,M,N,O,P,Q,R,S,T,EA,FA 2 1 
D,U,V,W,X,Y,GA 3 1 
E,Z,AA,BA,CA,DA,HA 3 3 
#
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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
3 'crystal symmetry operation' 3_555 x+1/2,y+1/2,z 1 0 0 0 1 0 0 0 1 107.1005 58.255 0 
#
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 N N N 
? 5 S N N 
? 5 X N N 
? 5 CA 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 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                     6PF9 
_atom_sites.fract_transf_matrix[1][1]    0.004669 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000398 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008583 
_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]    0.004532 
_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 OF7 A 1 603 603 OF7 M80 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 6 SO4 A 1 605 5 SO4 SO4 . 
K 2 NDP B 1 601 601 NDP NDP . 
L 3 UFP B 1 602 602 UFP UFP . 
M 4 OF7 B 1 603 603 OF7 M80 . 
N 5 MTX B 1 604 604 MTX MTX . 
O 6 SO4 B 1 605 1 SO4 SO4 . 
P 2 NDP C 1 601 601 NDP NDP . 
Q 3 UFP C 1 602 602 UFP UFP . 
R 4 OF7 C 1 603 603 OF7 M80 . 
S 5 MTX C 1 604 604 MTX MTX . 
T 6 SO4 C 1 605 4 SO4 SO4 . 
U 2 NDP D 1 601 601 NDP NDP . 
V 3 UFP D 1 602 602 UFP UFP . 
W 4 OF7 D 1 603 603 OF7 M80 . 
X 5 MTX D 1 604 604 MTX MTX . 
Y 6 SO4 D 1 605 2 SO4 SO4 . 
Z 2 NDP E 1 601 601 NDP NDP . 
AA 3 UFP E 1 602 602 UFP UFP . 
BA 4 OF7 E 1 603 603 OF7 M80 . 
CA 5 MTX E 1 604 604 MTX MTX . 
DA 6 SO4 E 1 605 3 SO4 SO4 . 
EA 7 HOH B 1 701 3 HOH HOH . 
FA 7 HOH C 1 701 9 HOH HOH . 
FA 7 HOH C 2 702 7 HOH HOH . 
FA 7 HOH C 3 703 6 HOH HOH . 
FA 7 HOH C 4 704 12 HOH HOH . 
GA 7 HOH D 1 701 5 HOH HOH . 
GA 7 HOH D 2 702 10 HOH HOH . 
GA 7 HOH D 3 703 4 HOH HOH . 
GA 7 HOH D 4 704 1 HOH HOH . 
GA 7 HOH D 5 705 11 HOH HOH . 
HA 7 HOH E 1 701 8 HOH HOH . 
HA 7 HOH E 2 702 2 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 . . . N 5 46.756 27.928 66.602 1 82.73 ? N1 MTX 604 B 1 
HETATM 2 C C2 MTX . . . N 5 46.508 27.621 65.315 1 80.49 ? C2 MTX 604 B 1 
HETATM 3 N NA2 MTX . . . N 5 45.456 26.687 65.01 1 85.47 ? NA2 MTX 604 B 1 
HETATM 4 N N3 MTX . . . N 5 47.21 28.158 64.305 1 82.77 ? N3 MTX 604 B 1 
HETATM 5 C C4 MTX . . . N 5 48.204 29.037 64.553 1 78.14 ? C4 MTX 604 B 1 
HETATM 6 N NA4 MTX . . . N 5 48.964 29.62 63.496 1 79.33 ? NA4 MTX 604 B 1 
HETATM 7 C C4A MTX . . . N 5 48.5 29.39 65.887 1 77.6 ? C4A MTX 604 B 1 
HETATM 8 N N5 MTX . . . N 5 49.498 30.275 66.173 1 90.87 ? N5 MTX 604 B 1 
HETATM 9 C C6 MTX . . . N 5 49.746 30.583 67.462 1 83.24 ? C6 MTX 604 B 1 
HETATM 10 C C7 MTX . . . N 5 49.007 30.019 68.51 1 81.44 ? C7 MTX 604 B 1 
HETATM 11 N N8 MTX . . . N 5 48.023 29.143 68.207 1 74.32 ? N8 MTX 604 B 1 
HETATM 12 C C8A MTX . . . N 5 47.756 28.817 66.901 1 76.9 ? C8A MTX 604 B 1 
HETATM 13 C C9 MTX . . . N 5 50.853 31.563 67.767 1 66.11 ? C9 MTX 604 B 1 
HETATM 14 N N10 MTX . . . N 5 51.522 31.355 69.034 1 103.45 ? N10 MTX 604 B 1 
HETATM 15 C CM MTX . . . N 5 51.478 32.381 70.048 1 103.79 ? CM MTX 604 B 1 
HETATM 16 C C11 MTX . . . N 5 53.547 27.704 69.81 1 65.57 ? C11 MTX 604 B 1 
HETATM 17 C C12 MTX . . . N 5 52.959 28.429 70.842 1 80.83 ? C12 MTX 604 B 1 
HETATM 18 C C13 MTX . . . N 5 52.297 29.623 70.576 1 77.68 ? C13 MTX 604 B 1 
HETATM 19 C C14 MTX . . . N 5 52.224 30.102 69.277 1 82.99 ? C14 MTX 604 B 1 
HETATM 20 C C15 MTX . . . N 5 52.809 29.382 68.236 1 60.78 ? C15 MTX 604 B 1 
HETATM 21 C C16 MTX . . . N 5 53.472 28.183 68.507 1 66.15 ? C16 MTX 604 B 1 
HETATM 22 C C MTX . . . N 5 54.256 26.41 70.132 1 67.2 ? C MTX 604 B 1 
HETATM 23 O O MTX . . . N 5 54.822 26.303 71.207 1 67.94 ? O MTX 604 B 1 
HETATM 24 N N MTX . . . N 5 54.287 25.291 69.216 1 64.62 ? N MTX 604 B 1 
HETATM 25 C CA MTX . . . N 5 54.979 24.083 69.591 1 73.62 ? CA MTX 604 B 1 
HETATM 26 C CT MTX . . . N 5 55.616 23.51 68.386 1 79.41 ? CT MTX 604 B 1 
HETATM 27 O O1 MTX . . . N 5 55.533 24.126 67.292 1 75.83 ? O1 MTX 604 B 1 
HETATM 28 O O2 MTX . . . N 5 56.238 22.405 68.455 1 72.66 ? O2 MTX 604 B 1 
HETATM 29 C CB MTX . . . N 5 53.983 23.089 70.084 1 73.63 ? CB MTX 604 B 1 
HETATM 30 C CG MTX . . . N 5 53.865 22.801 71.551 1 79.13 ? CG MTX 604 B 1 
HETATM 31 C CD MTX . . . N 5 53.14 21.544 71.92 1 94.09 ? CD MTX 604 B 1 
HETATM 32 O OE1 MTX . . . N 5 53.289 20.518 71.215 1 78.93 ? OE1 MTX 604 B 1 
HETATM 33 O OE2 MTX . . . N 5 52.206 21.582 72.764 1 93.58 ? OE2 MTX 604 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           33 
#