data_6PFH
#
_model_server_result.job_id            TkDFGZ8zC7CH5bpdJDBt0Q 
_model_server_result.datetime_utc      '2024-11-25 08:24:59' 
_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          6pfh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Y","auth_seq_id":604}' 
#
_entry.id    6PFH 
#
_exptl.entry_id    6PFH 
_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          95.43 
_cell.angle_gamma         90 
_cell.entry_id            6PFH 
_cell.length_a            214.11 
_cell.length_b            116.936 
_cell.length_c            221.376 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFH 
_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,B,F,G,H,I,J,K,L,M 1 1 
C,N,O,P,Q 2 1,2 
D,E,R,S,T,U,V,W,X,Y 3 1 
#
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_558 -x,y,-z+3 -1 0 0 0 1 0 0 0 -1 -62.846151 0 661.147761 
#
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 M N N 
? 5 Q N N 
? 5 U N N 
? 5 Y 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 235 n y 
N1 C8A MTX sing 236 n y 
C2 NA2 MTX sing 237 n n 
C2 N3 MTX sing 238 n y 
NA2 HN21 MTX sing 239 n n 
NA2 HN22 MTX sing 240 n n 
N3 C4 MTX doub 241 n y 
C4 NA4 MTX sing 242 n n 
C4 C4A MTX sing 243 n y 
NA4 HN41 MTX sing 244 n n 
NA4 HN42 MTX sing 245 n n 
C4A N5 MTX sing 246 n y 
C4A C8A MTX doub 247 n y 
N5 C6 MTX doub 248 n y 
C6 C7 MTX sing 249 n y 
C6 C9 MTX sing 250 n n 
C7 N8 MTX doub 251 n y 
C7 H7 MTX sing 252 n n 
N8 C8A MTX sing 253 n y 
C9 N10 MTX sing 254 n n 
C9 H91 MTX sing 255 n n 
C9 H92 MTX sing 256 n n 
N10 CM MTX sing 257 n n 
N10 C14 MTX sing 258 n n 
CM HM1 MTX sing 259 n n 
CM HM2 MTX sing 260 n n 
CM HM3 MTX sing 261 n n 
C11 C12 MTX doub 262 n y 
C11 C16 MTX sing 263 n y 
C11 C MTX sing 264 n n 
C12 C13 MTX sing 265 n y 
C12 H12 MTX sing 266 n n 
C13 C14 MTX doub 267 n y 
C13 H13 MTX sing 268 n n 
C14 C15 MTX sing 269 n y 
C15 C16 MTX doub 270 n y 
C15 H15 MTX sing 271 n n 
C16 H16 MTX sing 272 n n 
C O MTX doub 273 n n 
C N MTX sing 274 n n 
N CA MTX sing 275 n n 
N HN MTX sing 276 n n 
CA CT MTX sing 277 n n 
CA CB MTX sing 278 n n 
CA HA MTX sing 279 n n 
CT O1 MTX doub 280 n n 
CT O2 MTX sing 281 n n 
O2 HO2 MTX sing 282 n n 
CB CG MTX sing 283 n n 
CB HB1 MTX sing 284 n n 
CB HB2 MTX sing 285 n n 
CG CD MTX sing 286 n n 
CG HG1 MTX sing 287 n n 
CG HG2 MTX sing 288 n n 
CD OE1 MTX doub 289 n n 
CD OE2 MTX sing 290 n n 
OE2 HOE2 MTX sing 291 n n 
#
_atom_sites.entry_id                     6PFH 
_atom_sites.fract_transf_matrix[1][1]    0.00467 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000444 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008552 
_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]    0.004538 
_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 OFD A 1 603 603 OFD T25 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 2 NDP B 1 601 601 NDP NDP . 
K 3 UFP B 1 602 602 UFP UFP . 
L 4 OFD B 1 603 603 OFD T25 . 
M 5 MTX B 1 604 604 MTX MTX . 
N 2 NDP C 1 601 601 NDP NDP . 
O 3 UFP C 1 602 602 UFP UFP . 
P 4 OFD C 1 603 603 OFD T25 . 
Q 5 MTX C 1 604 604 MTX MTX . 
R 2 NDP D 1 601 601 NDP NDP . 
S 3 UFP D 1 602 602 UFP UFP . 
T 4 OFD D 1 603 603 OFD T25 . 
U 5 MTX D 1 604 604 MTX MTX . 
V 2 NDP E 1 601 601 NDP NDP . 
W 3 UFP E 1 602 602 UFP UFP . 
X 4 OFD E 1 603 603 OFD T25 . 
Y 5 MTX E 1 604 604 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 . . . Y 5 -77.063 150.523 264.099 1 71.23 ? N1 MTX 604 E 1 
HETATM 2 C C2 MTX . . . Y 5 -76.9 150.273 265.411 1 68.59 ? C2 MTX 604 E 1 
HETATM 3 N NA2 MTX . . . Y 5 -75.891 149.33 265.823 1 82.71 ? NA2 MTX 604 E 1 
HETATM 4 N N3 MTX . . . Y 5 -77.645 150.873 266.352 1 77.93 ? N3 MTX 604 E 1 
HETATM 5 C C4 MTX . . . Y 5 -78.597 151.762 266.001 1 70.08 ? C4 MTX 604 E 1 
HETATM 6 N NA4 MTX . . . Y 5 -79.402 152.414 266.983 1 65.41 ? NA4 MTX 604 E 1 
HETATM 7 C C4A MTX . . . Y 5 -78.806 152.056 264.636 1 70.7 ? C4A MTX 604 E 1 
HETATM 8 N N5 MTX . . . Y 5 -79.758 152.949 264.247 1 69.53 ? N5 MTX 604 E 1 
HETATM 9 C C6 MTX . . . Y 5 -79.919 153.205 262.934 1 65.52 ? C6 MTX 604 E 1 
HETATM 10 C C7 MTX . . . Y 5 -79.143 152.571 261.956 1 65.31 ? C7 MTX 604 E 1 
HETATM 11 N N8 MTX . . . Y 5 -78.201 151.689 262.36 1 71.5 ? N8 MTX 604 E 1 
HETATM 12 C C8A MTX . . . Y 5 -78.02 151.419 263.695 1 74.28 ? C8A MTX 604 E 1 
HETATM 13 C C9 MTX . . . Y 5 -80.993 154.188 262.543 1 69.79 ? C9 MTX 604 E 1 
HETATM 14 N N10 MTX . . . Y 5 -82.301 153.741 262.975 1 67.64 ? N10 MTX 604 E 1 
HETATM 15 C CM MTX . . . Y 5 -82.977 154.401 264.062 1 64.09 ? CM MTX 604 E 1 
HETATM 16 C C11 MTX . . . Y 5 -84.062 150.337 261.168 1 60.04 ? C11 MTX 604 E 1 
HETATM 17 C C12 MTX . . . Y 5 -83.193 151.141 260.434 1 56.64 ? C12 MTX 604 E 1 
HETATM 18 C C13 MTX . . . Y 5 -82.616 152.264 261.025 1 59.03 ? C13 MTX 604 E 1 
HETATM 19 C C14 MTX . . . Y 5 -82.907 152.579 262.347 1 66.9 ? C14 MTX 604 E 1 
HETATM 20 C C15 MTX . . . Y 5 -83.768 151.771 263.083 1 72.55 ? C15 MTX 604 E 1 
HETATM 21 C C16 MTX . . . Y 5 -84.344 150.65 262.491 1 68.29 ? C16 MTX 604 E 1 
HETATM 22 C C MTX . . . Y 5 -84.69 149.109 260.562 1 54.18 ? C MTX 604 E 1 
HETATM 23 O O MTX . . . Y 5 -85.024 149.1 259.39 1 69.68 ? O MTX 604 E 1 
HETATM 24 N N MTX . . . Y 5 -84.888 147.938 261.389 1 57.67 ? N MTX 604 E 1 
HETATM 25 C CA MTX . . . Y 5 -85.472 146.727 260.883 1 72.99 ? CA MTX 604 E 1 
HETATM 26 C CT MTX . . . Y 5 -86.131 146.065 262.028 1 71.71 ? CT MTX 604 E 1 
HETATM 27 O O1 MTX . . . Y 5 -86.036 146.589 263.169 1 61.67 ? O1 MTX 604 E 1 
HETATM 28 O O2 MTX . . . Y 5 -86.779 144.985 261.868 1 79.04 ? O2 MTX 604 E 1 
HETATM 29 C CB MTX . . . Y 5 -84.367 145.839 260.425 1 61.58 ? CB MTX 604 E 1 
HETATM 30 C CG MTX . . . Y 5 -84.449 145.149 259.096 1 62.48 ? CG MTX 604 E 1 
HETATM 31 C CD MTX . . . Y 5 -83.491 144.018 258.895 1 80.62 ? CD MTX 604 E 1 
HETATM 32 O OE1 MTX . . . Y 5 -83.728 142.906 259.422 1 77.9 ? OE1 MTX 604 E 1 
HETATM 33 O OE2 MTX . . . Y 5 -82.534 144.135 258.084 1 85.85 ? OE2 MTX 604 E 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    64 
_model_server_stats.query_time_ms           392 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           33 
#