data_6PFI
#
_model_server_result.job_id            HTsnmwYMfuaUXGf87AYW1Q 
_model_server_result.datetime_utc      '2024-11-14 05:16:11' 
_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          6pfi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Y","auth_seq_id":604}' 
#
_entry.id    6PFI 
#
_exptl.entry_id    6PFI 
_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          95.05 
_cell.angle_gamma         90 
_cell.entry_id            6PFI 
_cell.length_a            213.38 
_cell.length_b            116.741 
_cell.length_c            221.58 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFI 
_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,Z,AA 1 1 
C,D,N,O,P,Q,R,S,T,U,BA,CA 2 1 
E,V,W,X,Y,DA 3 1,2 
#
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_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -213.38 0 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 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 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                     6PFI 
_atom_sites.fract_transf_matrix[1][1]    0.004686 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000414 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008566 
_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]    0.004531 
_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 OEP A 1 603 603 OEP T26 . 
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 OEP B 1 603 603 OEP T26 . 
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 OEP C 1 603 603 OEP T26 . 
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 OEP D 1 603 603 OEP T26 . 
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 OEP E 1 603 603 OEP T26 . 
Y 5 MTX E 1 604 604 MTX MTX . 
Z 6 HOH A 1 701 29 HOH HOH . 
Z 6 HOH A 2 702 9 HOH HOH . 
Z 6 HOH A 3 703 25 HOH HOH . 
Z 6 HOH A 4 704 21 HOH HOH . 
Z 6 HOH A 5 705 4 HOH HOH . 
Z 6 HOH A 6 706 1 HOH HOH . 
Z 6 HOH A 7 707 2 HOH HOH . 
Z 6 HOH A 8 708 7 HOH HOH . 
AA 6 HOH B 1 701 10 HOH HOH . 
AA 6 HOH B 2 702 13 HOH HOH . 
AA 6 HOH B 3 703 26 HOH HOH . 
AA 6 HOH B 4 704 18 HOH HOH . 
AA 6 HOH B 5 705 27 HOH HOH . 
AA 6 HOH B 6 706 17 HOH HOH . 
AA 6 HOH B 7 707 22 HOH HOH . 
AA 6 HOH B 8 708 14 HOH HOH . 
BA 6 HOH C 1 701 30 HOH HOH . 
BA 6 HOH C 2 702 20 HOH HOH . 
BA 6 HOH C 3 703 5 HOH HOH . 
BA 6 HOH C 4 704 3 HOH HOH . 
CA 6 HOH D 1 701 24 HOH HOH . 
CA 6 HOH D 2 702 8 HOH HOH . 
CA 6 HOH D 3 703 6 HOH HOH . 
CA 6 HOH D 4 704 15 HOH HOH . 
DA 6 HOH E 1 701 19 HOH HOH . 
DA 6 HOH E 2 702 12 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 . . . Y 5 -107.219 -62.055 29.475 1 91.08 ? N1 MTX 604 E 1 
HETATM 2 C C2 MTX . . . Y 5 -107.627 -61.445 28.347 1 84.58 ? C2 MTX 604 E 1 
HETATM 3 N NA2 MTX . . . Y 5 -107.687 -62.209 27.128 1 89.67 ? NA2 MTX 604 E 1 
HETATM 4 N N3 MTX . . . Y 5 -107.978 -60.149 28.322 1 85.44 ? N3 MTX 604 E 1 
HETATM 5 C C4 MTX . . . Y 5 -107.93 -59.407 29.45 1 82.32 ? C4 MTX 604 E 1 
HETATM 6 N NA4 MTX . . . Y 5 -108.298 -58.028 29.458 1 82.22 ? NA4 MTX 604 E 1 
HETATM 7 C C4A MTX . . . Y 5 -107.508 -60.004 30.656 1 77.74 ? C4A MTX 604 E 1 
HETATM 8 N N5 MTX . . . Y 5 -107.449 -59.285 31.812 1 81.35 ? N5 MTX 604 E 1 
HETATM 9 C C6 MTX . . . Y 5 -107.046 -59.898 32.942 1 86.24 ? C6 MTX 604 E 1 
HETATM 10 C C7 MTX . . . Y 5 -106.676 -61.248 32.957 1 92.34 ? C7 MTX 604 E 1 
HETATM 11 N N8 MTX . . . Y 5 -106.742 -61.947 31.802 1 88.09 ? N8 MTX 604 E 1 
HETATM 12 C C8A MTX . . . Y 5 -107.155 -61.34 30.642 1 85.48 ? C8A MTX 604 E 1 
HETATM 13 C C9 MTX . . . Y 5 -106.978 -59.083 34.209 1 85.7 ? C9 MTX 604 E 1 
HETATM 14 N N10 MTX . . . Y 5 -106.023 -58.001 34.109 1 87.6 ? N10 MTX 604 E 1 
HETATM 15 C CM MTX . . . Y 5 -106.47 -56.632 34.086 1 85.2 ? CM MTX 604 E 1 
HETATM 16 C C11 MTX . . . Y 5 -101.909 -58.929 33.73 1 65.36 ? C11 MTX 604 E 1 
HETATM 17 C C12 MTX . . . Y 5 -102.753 -59.788 34.429 1 56.81 ? C12 MTX 604 E 1 
HETATM 18 C C13 MTX . . . Y 5 -104.105 -59.481 34.556 1 67.13 ? C13 MTX 604 E 1 
HETATM 19 C C14 MTX . . . Y 5 -104.609 -58.315 33.989 1 82.7 ? C14 MTX 604 E 1 
HETATM 20 C C15 MTX . . . Y 5 -103.768 -57.46 33.284 1 75.87 ? C15 MTX 604 E 1 
HETATM 21 C C16 MTX . . . Y 5 -102.417 -57.77 33.158 1 73.91 ? C16 MTX 604 E 1 
HETATM 22 C C MTX . . . Y 5 -100.442 -59.235 33.566 1 76.78 ? C MTX 604 E 1 
HETATM 23 O O MTX . . . Y 5 -99.851 -59.883 34.414 1 87.56 ? O MTX 604 E 1 
HETATM 24 N N MTX . . . Y 5 -99.746 -58.752 32.392 1 78.26 ? N MTX 604 E 1 
HETATM 25 C CA MTX . . . Y 5 -98.35 -59.011 32.168 1 85.55 ? CA MTX 604 E 1 
HETATM 26 C CT MTX . . . Y 5 -97.929 -58.151 31.042 1 83.74 ? CT MTX 604 E 1 
HETATM 27 O O1 MTX . . . Y 5 -98.771 -57.376 30.518 1 82.36 ? O1 MTX 604 E 1 
HETATM 28 O O2 MTX . . . Y 5 -96.737 -58.191 30.606 1 79.73 ? O2 MTX 604 E 1 
HETATM 29 C CB MTX . . . Y 5 -98.202 -60.431 31.74 1 82.39 ? CB MTX 604 E 1 
HETATM 30 C CG MTX . . . Y 5 -96.901 -61.146 31.944 1 76.74 ? CG MTX 604 E 1 
HETATM 31 C CD MTX . . . Y 5 -96.719 -62.408 31.162 1 87.61 ? CD MTX 604 E 1 
HETATM 32 O OE1 MTX . . . Y 5 -96.002 -62.402 30.135 1 88.63 ? OE1 MTX 604 E 1 
HETATM 33 O OE2 MTX . . . Y 5 -97.441 -63.408 31.414 1 93.73 ? OE2 MTX 604 E 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           359 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           33 
#