data_6PF9
#
_model_server_result.job_id            tfWztEQCgboA0NBSUoYLGQ 
_model_server_result.datetime_utc      '2024-11-25 08:44:51' 
_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":"I","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 . . . I 5 -0.244 6.514 29.708 1 91.99 ? N1 MTX 604 A 1 
HETATM 2 C C2 MTX . . . I 5 -0.647 7.03 28.533 1 78.7 ? C2 MTX 604 A 1 
HETATM 3 N NA2 MTX . . . I 5 -0.709 6.176 27.375 1 84.19 ? NA2 MTX 604 A 1 
HETATM 4 N N3 MTX . . . I 5 -0.995 8.319 28.4 1 81.32 ? N3 MTX 604 A 1 
HETATM 5 C C4 MTX . . . I 5 -0.952 9.156 29.458 1 78.5 ? C4 MTX 604 A 1 
HETATM 6 N NA4 MTX . . . I 5 -1.322 10.53 29.326 1 81.55 ? NA4 MTX 604 A 1 
HETATM 7 C C4A MTX . . . I 5 -0.534 8.659 30.715 1 89.35 ? C4A MTX 604 A 1 
HETATM 8 N N5 MTX . . . I 5 -0.474 9.466 31.814 1 99.27 ? N5 MTX 604 A 1 
HETATM 9 C C6 MTX . . . I 5 -0.07 8.944 32.992 1 91.58 ? C6 MTX 604 A 1 
HETATM 10 C C7 MTX . . . I 5 0.292 7.596 33.115 1 95.63 ? C7 MTX 604 A 1 
HETATM 11 N N8 MTX . . . I 5 0.227 6.811 32.018 1 91.43 ? N8 MTX 604 A 1 
HETATM 12 C C8A MTX . . . I 5 -0.183 7.324 30.812 1 91.2 ? C8A MTX 604 A 1 
HETATM 13 C C9 MTX . . . I 5 -0.002 9.845 34.201 1 79.75 ? C9 MTX 604 A 1 
HETATM 14 N N10 MTX . . . I 5 1.021 9.478 35.16 1 113.93 ? N10 MTX 604 A 1 
HETATM 15 C CM MTX . . . I 5 0.647 9.114 36.507 1 108.51 ? CM MTX 604 A 1 
HETATM 16 C C11 MTX . . . I 5 5.12 9.394 34.051 1 81.54 ? C11 MTX 604 A 1 
HETATM 17 C C12 MTX . . . I 5 4.619 8.518 35.007 1 98.9 ? C12 MTX 604 A 1 
HETATM 18 C C13 MTX . . . I 5 3.275 8.561 35.362 1 105.5 ? C13 MTX 604 A 1 
HETATM 19 C C14 MTX . . . I 5 2.421 9.473 34.758 1 91.08 ? C14 MTX 604 A 1 
HETATM 20 C C15 MTX . . . I 5 2.915 10.353 33.795 1 66.3 ? C15 MTX 604 A 1 
HETATM 21 C C16 MTX . . . I 5 4.266 10.309 33.444 1 85.49 ? C16 MTX 604 A 1 
HETATM 22 C C MTX . . . I 5 6.583 9.328 33.681 1 77.85 ? C MTX 604 A 1 
HETATM 23 O O MTX . . . I 5 7.393 8.989 34.527 1 85.69 ? O MTX 604 A 1 
HETATM 24 N N MTX . . . I 5 7.051 9.64 32.348 1 85.82 ? N MTX 604 A 1 
HETATM 25 C CA MTX . . . I 5 8.455 9.558 32.041 1 83.49 ? CA MTX 604 A 1 
HETATM 26 C CT MTX . . . I 5 8.766 10.589 31.029 1 85.67 ? CT MTX 604 A 1 
HETATM 27 O O1 MTX . . . I 5 7.859 11.378 30.656 1 85.79 ? O1 MTX 604 A 1 
HETATM 28 O O2 MTX . . . I 5 9.935 10.677 30.541 1 89.44 ? O2 MTX 604 A 1 
HETATM 29 C CB MTX . . . I 5 8.735 8.222 31.44 1 81.73 ? CB MTX 604 A 1 
HETATM 30 C CG MTX . . . I 5 9.381 7.15 32.266 1 76.61 ? CG MTX 604 A 1 
HETATM 31 C CD MTX . . . I 5 9.967 6.001 31.508 1 89.66 ? CD MTX 604 A 1 
HETATM 32 O OE1 MTX . . . I 5 10.539 6.221 30.415 1 81.49 ? OE1 MTX 604 A 1 
HETATM 33 O OE2 MTX . . . I 5 9.606 4.827 31.786 1 87.83 ? OE2 MTX 604 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           33 
#