data_6PFA
#
_model_server_result.job_id            hG08AzfVzjg0RqyAaElWOw 
_model_server_result.datetime_utc      '2024-11-13 02:07:25' 
_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          6pfa 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":604}' 
#
_entry.id    6PFA 
#
_exptl.entry_id    6PFA 
_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          95.72 
_cell.angle_gamma         90 
_cell.entry_id            6PFA 
_cell.length_a            213.21 
_cell.length_b            117.294 
_cell.length_c            222.817 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFA 
_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,N,O,EA,FA 1 1 
C,D,P,Q,R,S,T,U,V,W,X,Y,GA,HA 2 1 
E,Z,AA,BA,CA,DA,IA 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 -213.21 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 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                     6PFA 
_atom_sites.fract_transf_matrix[1][1]    0.00469 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00047 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008526 
_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]    0.00451 
_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 OF4 A 1 603 603 OF4 M85 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 6 SO4 A 1 605 2 SO4 SO4 . 
K 2 NDP B 1 601 601 NDP NDP . 
L 3 UFP B 1 602 602 UFP UFP . 
M 4 OF4 B 1 603 603 OF4 M85 . 
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 OF4 C 1 603 603 OF4 M85 . 
S 5 MTX C 1 604 604 MTX MTX . 
T 6 SO4 C 1 605 3 SO4 SO4 . 
U 2 NDP D 1 601 601 NDP NDP . 
V 3 UFP D 1 602 602 UFP UFP . 
W 4 OF4 D 1 603 603 OF4 M85 . 
X 5 MTX D 1 604 604 MTX MTX . 
Y 6 SO4 D 1 605 4 SO4 SO4 . 
Z 2 NDP E 1 601 601 NDP NDP . 
AA 3 UFP E 1 602 602 UFP UFP . 
BA 4 OF4 E 1 603 603 OF4 M85 . 
CA 5 MTX E 1 604 604 MTX MTX . 
DA 6 SO4 E 1 605 5 SO4 SO4 . 
EA 7 HOH A 1 701 98 HOH HOH . 
EA 7 HOH A 2 702 59 HOH HOH . 
EA 7 HOH A 3 703 95 HOH HOH . 
EA 7 HOH A 4 704 63 HOH HOH . 
EA 7 HOH A 5 705 54 HOH HOH . 
EA 7 HOH A 6 706 4 HOH HOH . 
EA 7 HOH A 7 707 65 HOH HOH . 
EA 7 HOH A 8 708 100 HOH HOH . 
EA 7 HOH A 9 709 23 HOH HOH . 
EA 7 HOH A 10 710 6 HOH HOH . 
EA 7 HOH A 11 711 36 HOH HOH . 
EA 7 HOH A 12 712 45 HOH HOH . 
EA 7 HOH A 13 713 19 HOH HOH . 
EA 7 HOH A 14 714 72 HOH HOH . 
EA 7 HOH A 15 715 81 HOH HOH . 
EA 7 HOH A 16 716 62 HOH HOH . 
EA 7 HOH A 17 717 28 HOH HOH . 
EA 7 HOH A 18 718 70 HOH HOH . 
EA 7 HOH A 19 719 33 HOH HOH . 
EA 7 HOH A 20 720 110 HOH HOH . 
EA 7 HOH A 21 721 76 HOH HOH . 
EA 7 HOH A 22 722 96 HOH HOH . 
EA 7 HOH A 23 723 109 HOH HOH . 
EA 7 HOH A 24 724 69 HOH HOH . 
FA 7 HOH B 1 701 44 HOH HOH . 
FA 7 HOH B 2 702 1 HOH HOH . 
FA 7 HOH B 3 703 73 HOH HOH . 
FA 7 HOH B 4 704 3 HOH HOH . 
FA 7 HOH B 5 705 56 HOH HOH . 
FA 7 HOH B 6 706 67 HOH HOH . 
FA 7 HOH B 7 707 22 HOH HOH . 
FA 7 HOH B 8 708 13 HOH HOH . 
FA 7 HOH B 9 709 16 HOH HOH . 
FA 7 HOH B 10 710 55 HOH HOH . 
FA 7 HOH B 11 711 41 HOH HOH . 
FA 7 HOH B 12 712 99 HOH HOH . 
FA 7 HOH B 13 713 71 HOH HOH . 
FA 7 HOH B 14 714 27 HOH HOH . 
FA 7 HOH B 15 715 25 HOH HOH . 
FA 7 HOH B 16 716 2 HOH HOH . 
FA 7 HOH B 17 717 86 HOH HOH . 
FA 7 HOH B 18 718 50 HOH HOH . 
FA 7 HOH B 19 719 8 HOH HOH . 
FA 7 HOH B 20 720 12 HOH HOH . 
FA 7 HOH B 21 721 35 HOH HOH . 
FA 7 HOH B 22 722 11 HOH HOH . 
FA 7 HOH B 23 723 39 HOH HOH . 
FA 7 HOH B 24 724 32 HOH HOH . 
FA 7 HOH B 25 725 88 HOH HOH . 
FA 7 HOH B 26 726 40 HOH HOH . 
FA 7 HOH B 27 727 66 HOH HOH . 
FA 7 HOH B 28 728 101 HOH HOH . 
FA 7 HOH B 29 729 9 HOH HOH . 
FA 7 HOH B 30 730 43 HOH HOH . 
FA 7 HOH B 31 731 14 HOH HOH . 
FA 7 HOH B 32 732 105 HOH HOH . 
FA 7 HOH B 33 733 10 HOH HOH . 
FA 7 HOH B 34 734 18 HOH HOH . 
FA 7 HOH B 35 735 38 HOH HOH . 
FA 7 HOH B 36 736 57 HOH HOH . 
FA 7 HOH B 37 737 107 HOH HOH . 
GA 7 HOH C 1 701 15 HOH HOH . 
GA 7 HOH C 2 702 104 HOH HOH . 
GA 7 HOH C 3 703 48 HOH HOH . 
GA 7 HOH C 4 704 68 HOH HOH . 
GA 7 HOH C 5 705 29 HOH HOH . 
GA 7 HOH C 6 706 58 HOH HOH . 
GA 7 HOH C 7 707 30 HOH HOH . 
GA 7 HOH C 8 708 80 HOH HOH . 
GA 7 HOH C 9 709 78 HOH HOH . 
GA 7 HOH C 10 710 20 HOH HOH . 
GA 7 HOH C 11 711 90 HOH HOH . 
GA 7 HOH C 12 712 97 HOH HOH . 
GA 7 HOH C 13 713 24 HOH HOH . 
GA 7 HOH C 14 714 17 HOH HOH . 
GA 7 HOH C 15 715 64 HOH HOH . 
HA 7 HOH D 1 701 51 HOH HOH . 
HA 7 HOH D 2 702 77 HOH HOH . 
HA 7 HOH D 3 703 74 HOH HOH . 
HA 7 HOH D 4 704 42 HOH HOH . 
HA 7 HOH D 5 705 5 HOH HOH . 
HA 7 HOH D 6 706 83 HOH HOH . 
HA 7 HOH D 7 707 37 HOH HOH . 
HA 7 HOH D 8 708 92 HOH HOH . 
HA 7 HOH D 9 709 52 HOH HOH . 
HA 7 HOH D 10 710 61 HOH HOH . 
HA 7 HOH D 11 711 85 HOH HOH . 
HA 7 HOH D 12 712 94 HOH HOH . 
HA 7 HOH D 13 713 79 HOH HOH . 
HA 7 HOH D 14 714 26 HOH HOH . 
HA 7 HOH D 15 715 106 HOH HOH . 
HA 7 HOH D 16 716 102 HOH HOH . 
HA 7 HOH D 17 717 47 HOH HOH . 
HA 7 HOH D 18 718 82 HOH HOH . 
IA 7 HOH E 1 701 31 HOH HOH . 
IA 7 HOH E 2 702 7 HOH HOH . 
IA 7 HOH E 3 703 21 HOH HOH . 
IA 7 HOH E 4 704 84 HOH HOH . 
IA 7 HOH E 5 705 111 HOH HOH . 
IA 7 HOH E 6 706 46 HOH HOH . 
IA 7 HOH E 7 707 91 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 . . . X 5 -80.184 -79.388 26.095 1 80.26 ? N1 MTX 604 D 1 
HETATM 2 C C2 MTX . . . X 5 -79.187 -78.741 26.723 1 77.89 ? C2 MTX 604 D 1 
HETATM 3 N NA2 MTX . . . X 5 -79.379 -78.338 28.093 1 73.54 ? NA2 MTX 604 D 1 
HETATM 4 N N3 MTX . . . X 5 -78.021 -78.459 26.117 1 82.95 ? N3 MTX 604 D 1 
HETATM 5 C C4 MTX . . . X 5 -77.811 -78.824 24.833 1 81.59 ? C4 MTX 604 D 1 
HETATM 6 N NA4 MTX . . . X 5 -76.584 -78.541 24.155 1 74.74 ? NA4 MTX 604 D 1 
HETATM 7 C C4A MTX . . . X 5 -78.83 -79.504 24.133 1 82.91 ? C4A MTX 604 D 1 
HETATM 8 N N5 MTX . . . X 5 -78.65 -79.886 22.838 1 86.92 ? N5 MTX 604 D 1 
HETATM 9 C C6 MTX . . . X 5 -79.649 -80.534 22.207 1 83.64 ? C6 MTX 604 D 1 
HETATM 10 C C7 MTX . . . X 5 -80.861 -80.824 22.847 1 83.86 ? C7 MTX 604 D 1 
HETATM 11 N N8 MTX . . . X 5 -81.021 -80.436 24.131 1 87.66 ? N8 MTX 604 D 1 
HETATM 12 C C8A MTX . . . X 5 -80.015 -79.776 24.791 1 85.49 ? C8A MTX 604 D 1 
HETATM 13 C C9 MTX . . . X 5 -79.443 -80.951 20.772 1 83.9 ? C9 MTX 604 D 1 
HETATM 14 N N10 MTX . . . X 5 -80.652 -80.98 19.98 1 89.71 ? N10 MTX 604 D 1 
HETATM 15 C CM MTX . . . X 5 -81.09 -82.23 19.407 1 92.04 ? CM MTX 604 D 1 
HETATM 16 C C11 MTX . . . X 5 -82.981 -77.465 19.397 1 69.28 ? C11 MTX 604 D 1 
HETATM 17 C C12 MTX . . . X 5 -83.568 -78.726 19.387 1 77.58 ? C12 MTX 604 D 1 
HETATM 18 C C13 MTX . . . X 5 -82.795 -79.865 19.58 1 81.55 ? C13 MTX 604 D 1 
HETATM 19 C C14 MTX . . . X 5 -81.426 -79.758 19.782 1 82.96 ? C14 MTX 604 D 1 
HETATM 20 C C15 MTX . . . X 5 -80.83 -78.497 19.791 1 74.79 ? C15 MTX 604 D 1 
HETATM 21 C C16 MTX . . . X 5 -81.609 -77.353 19.597 1 72.01 ? C16 MTX 604 D 1 
HETATM 22 C C MTX . . . X 5 -83.851 -76.247 19.183 1 74.56 ? C MTX 604 D 1 
HETATM 23 O O MTX . . . X 5 -84.846 -76.355 18.484 1 80.81 ? O MTX 604 D 1 
HETATM 24 N N MTX . . . X 5 -83.556 -74.96 19.774 1 72.81 ? N MTX 604 D 1 
HETATM 25 C CA MTX . . . X 5 -84.435 -73.845 19.521 1 77.58 ? CA MTX 604 D 1 
HETATM 26 C CT MTX . . . X 5 -83.619 -72.615 19.429 1 83.15 ? CT MTX 604 D 1 
HETATM 27 O O1 MTX . . . X 5 -82.398 -72.661 19.728 1 82.22 ? O1 MTX 604 D 1 
HETATM 28 O O2 MTX . . . X 5 -84.15 -71.523 19.056 1 80.21 ? O2 MTX 604 D 1 
HETATM 29 C CB MTX . . . X 5 -85.371 -73.655 20.666 1 74.7 ? CB MTX 604 D 1 
HETATM 30 C CG MTX . . . X 5 -86.744 -74.258 20.633 1 80.16 ? CG MTX 604 D 1 
HETATM 31 C CD MTX . . . X 5 -87.747 -73.667 21.575 1 86.37 ? CD MTX 604 D 1 
HETATM 32 O OE1 MTX . . . X 5 -87.734 -72.429 21.768 1 83.31 ? OE1 MTX 604 D 1 
HETATM 33 O OE2 MTX . . . X 5 -88.32 -74.408 22.416 1 85.76 ? OE2 MTX 604 D 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           46 
_model_server_stats.create_model_time_ms    68 
_model_server_stats.query_time_ms           333 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           33 
#