data_6PFD
#
_model_server_result.job_id            6rA-njhbuBVR2maaYKuCGA 
_model_server_result.datetime_utc      '2024-11-13 11:37:13' 
_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          6pfd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":604}' 
#
_entry.id    6PFD 
#
_exptl.entry_id    6PFD 
_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            6PFD 
_cell.length_a            213.033 
_cell.length_b            115.887 
_cell.length_c            220.808 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFD 
_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,D,N,O,P,Q,R,S,T,U 2 1 
E,V,W,X,Y 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_858 -x+3,y,-z+3 -1 0 0 0 1 0 0 0 -1 580.789092 0 659.852643 
#
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                     6PFD 
_atom_sites.fract_transf_matrix[1][1]    0.004694 
_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]    0.008629 
_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]    0.004546 
_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 OEJ A 1 603 603 OEJ T11 . 
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 OEJ B 1 603 603 OEJ T11 . 
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 OEJ C 1 603 603 OEJ T11 . 
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 OEJ D 1 603 603 OEJ T11 . 
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 OEJ E 1 603 603 OEJ T11 . 
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 . . . U 5 243.946 93.751 263.657 1 73.48 ? N1 MTX 604 D 1 
HETATM 2 C C2 MTX . . . U 5 244.172 93.581 264.971 1 81.53 ? C2 MTX 604 D 1 
HETATM 3 N NA2 MTX . . . U 5 245.153 92.611 265.39 1 83.38 ? NA2 MTX 604 D 1 
HETATM 4 N N3 MTX . . . U 5 243.514 94.285 265.906 1 89.49 ? N3 MTX 604 D 1 
HETATM 5 C C4 MTX . . . U 5 242.588 95.201 265.547 1 85.19 ? C4 MTX 604 D 1 
HETATM 6 N NA4 MTX . . . U 5 241.88 95.959 266.528 1 82.75 ? NA4 MTX 604 D 1 
HETATM 7 C C4A MTX . . . U 5 242.316 95.414 264.175 1 88.94 ? C4A MTX 604 D 1 
HETATM 8 N N5 MTX . . . U 5 241.39 96.332 263.768 1 85.49 ? N5 MTX 604 D 1 
HETATM 9 C C6 MTX . . . U 5 241.165 96.498 262.448 1 72.55 ? C6 MTX 604 D 1 
HETATM 10 C C7 MTX . . . U 5 241.861 95.757 261.486 1 77.3 ? C7 MTX 604 D 1 
HETATM 11 N N8 MTX . . . U 5 242.776 94.854 261.904 1 80.45 ? N8 MTX 604 D 1 
HETATM 12 C C8A MTX . . . U 5 243.016 94.67 263.244 1 83.65 ? C8A MTX 604 D 1 
HETATM 13 C C9 MTX . . . U 5 240.136 97.515 262.018 1 76.79 ? C9 MTX 604 D 1 
HETATM 14 N N10 MTX . . . U 5 239.445 97.255 260.769 1 89.08 ? N10 MTX 604 D 1 
HETATM 15 C CM MTX . . . U 5 239.492 98.235 259.712 1 72.94 ? CM MTX 604 D 1 
HETATM 16 C C11 MTX . . . U 5 237.351 93.61 260.142 1 63.94 ? C11 MTX 604 D 1 
HETATM 17 C C12 MTX . . . U 5 237.815 94.365 259.068 1 70.94 ? C12 MTX 604 D 1 
HETATM 18 C C13 MTX . . . U 5 238.502 95.554 259.286 1 69.75 ? C13 MTX 604 D 1 
HETATM 19 C C14 MTX . . . U 5 238.718 96.004 260.581 1 77.84 ? C14 MTX 604 D 1 
HETATM 20 C C15 MTX . . . U 5 238.258 95.248 261.662 1 56.36 ? C15 MTX 604 D 1 
HETATM 21 C C16 MTX . . . U 5 237.574 94.051 261.441 1 46.42 ? C16 MTX 604 D 1 
HETATM 22 C C MTX . . . U 5 236.619 92.319 259.87 1 65.11 ? C MTX 604 D 1 
HETATM 23 O O MTX . . . U 5 235.959 92.205 258.852 1 72.46 ? O MTX 604 D 1 
HETATM 24 N N MTX . . . U 5 236.679 91.205 260.786 1 66.41 ? N MTX 604 D 1 
HETATM 25 C CA MTX . . . U 5 235.975 89.992 260.471 1 68.97 ? CA MTX 604 D 1 
HETATM 26 C CT MTX . . . U 5 235.427 89.449 261.729 1 70.69 ? CT MTX 604 D 1 
HETATM 27 O O1 MTX . . . U 5 234.805 88.356 261.72 1 89.92 ? O1 MTX 604 D 1 
HETATM 28 O O2 MTX . . . U 5 235.591 90.087 262.813 1 61.12 ? O2 MTX 604 D 1 
HETATM 29 C CB MTX . . . U 5 236.975 89.019 259.948 1 74.98 ? CB MTX 604 D 1 
HETATM 30 C CG MTX . . . U 5 236.865 88.48 258.552 1 83.49 ? CG MTX 604 D 1 
HETATM 31 C CD MTX . . . U 5 238.068 87.754 258.029 1 96.8 ? CD MTX 604 D 1 
HETATM 32 O OE1 MTX . . . U 5 238.013 86.508 257.91 1 108.44 ? OE1 MTX 604 D 1 
HETATM 33 O OE2 MTX . . . U 5 238.894 88.384 257.316 1 85.85 ? OE2 MTX 604 D 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    59 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           33 
#