data_6PFB
#
_model_server_result.job_id            AWCP52lhKGWDYPkyNJpgkA 
_model_server_result.datetime_utc      '2024-11-29 00:15:36' 
_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          6pfb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":604}' 
#
_entry.id    6PFB 
#
_exptl.entry_id    6PFB 
_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          94.75 
_cell.angle_gamma         90 
_cell.entry_id            6PFB 
_cell.length_a            213.994 
_cell.length_b            116.238 
_cell.length_c            221.672 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFB 
_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_658 -x+1,y,-z+3 -1 0 0 0 1 0 0 0 -1 158.925217 0 662.732004 
#
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                     6PFB 
_atom_sites.fract_transf_matrix[1][1]    0.004673 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000389 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008603 
_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]    0.004527 
_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 OG4 A 1 603 603 OG4 TS7 . 
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 OG4 B 1 603 603 OG4 TS7 . 
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 OG4 C 1 603 603 OG4 TS7 . 
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 OG4 D 1 603 603 OG4 TS7 . 
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 OG4 E 1 603 603 OG4 TS7 . 
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 52.353 56.939 305.932 1 96.44 ? N1 MTX 604 D 1 
HETATM 2 C C2 MTX . . . U 5 51.307 57.558 305.359 1 91.84 ? C2 MTX 604 D 1 
HETATM 3 N NA2 MTX . . . U 5 51.452 58.069 304.02 1 105.87 ? NA2 MTX 604 D 1 
HETATM 4 N N3 MTX . . . U 5 50.134 57.715 305.993 1 97.64 ? N3 MTX 604 D 1 
HETATM 5 C C4 MTX . . . U 5 49.965 57.247 307.248 1 96.2 ? C4 MTX 604 D 1 
HETATM 6 N NA4 MTX . . . U 5 48.725 57.404 307.938 1 101.93 ? NA4 MTX 604 D 1 
HETATM 7 C C4A MTX . . . U 5 51.037 56.59 307.893 1 102.57 ? C4A MTX 604 D 1 
HETATM 8 N N5 MTX . . . U 5 50.91 56.101 309.161 1 103.92 ? N5 MTX 604 D 1 
HETATM 9 C C6 MTX . . . U 5 51.965 55.477 309.727 1 104.55 ? C6 MTX 604 D 1 
HETATM 10 C C7 MTX . . . U 5 53.183 55.325 309.057 1 105.88 ? C7 MTX 604 D 1 
HETATM 11 N N8 MTX . . . U 5 53.289 55.815 307.803 1 98.27 ? N8 MTX 604 D 1 
HETATM 12 C C8A MTX . . . U 5 52.228 56.449 307.206 1 104.06 ? C8A MTX 604 D 1 
HETATM 13 C C9 MTX . . . U 5 51.82 54.949 311.131 1 98.84 ? C9 MTX 604 D 1 
HETATM 14 N N10 MTX . . . U 5 51.655 56.005 312.105 1 103.67 ? N10 MTX 604 D 1 
HETATM 15 C CM MTX . . . U 5 50.431 56.127 312.85 1 118.33 ? CM MTX 604 D 1 
HETATM 16 C C11 MTX . . . U 5 54.787 58.798 312.688 1 92.56 ? C11 MTX 604 D 1 
HETATM 17 C C12 MTX . . . U 5 55.077 57.457 312.449 1 78.28 ? C12 MTX 604 D 1 
HETATM 18 C C13 MTX . . . U 5 54.047 56.541 312.26 1 82.25 ? C13 MTX 604 D 1 
HETATM 19 C C14 MTX . . . U 5 52.727 56.965 312.308 1 99.48 ? C14 MTX 604 D 1 
HETATM 20 C C15 MTX . . . U 5 52.431 58.304 312.541 1 111.12 ? C15 MTX 604 D 1 
HETATM 21 C C16 MTX . . . U 5 53.464 59.219 312.732 1 107.79 ? C16 MTX 604 D 1 
HETATM 22 C C MTX . . . U 5 55.901 59.795 312.892 1 94.9 ? C MTX 604 D 1 
HETATM 23 O O MTX . . . U 5 56.973 59.411 313.33 1 105.68 ? O MTX 604 D 1 
HETATM 24 N N MTX . . . U 5 55.727 61.196 312.576 1 102.47 ? N MTX 604 D 1 
HETATM 25 C CA MTX . . . U 5 56.812 62.119 312.782 1 120.86 ? CA MTX 604 D 1 
HETATM 26 C CT MTX . . . U 5 56.254 63.484 312.907 1 119.02 ? CT MTX 604 D 1 
HETATM 27 O O1 MTX . . . U 5 55.358 63.866 312.111 1 97.63 ? O1 MTX 604 D 1 
HETATM 28 O O2 MTX . . . U 5 56.675 64.266 313.814 1 121.85 ? O2 MTX 604 D 1 
HETATM 29 C CB MTX . . . U 5 57.692 62.085 311.58 1 110.02 ? CB MTX 604 D 1 
HETATM 30 C CG MTX . . . U 5 59.17 62.292 311.722 1 108.2 ? CG MTX 604 D 1 
HETATM 31 C CD MTX . . . U 5 59.912 62.627 310.465 1 103.58 ? CD MTX 604 D 1 
HETATM 32 O OE1 MTX . . . U 5 59.863 63.8 310.03 1 100.7 ? OE1 MTX 604 D 1 
HETATM 33 O OE2 MTX . . . U 5 60.24 61.702 309.678 1 102.43 ? OE2 MTX 604 D 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           422 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           33 
#