data_3CL9
#
_model_server_result.job_id            lmV8MNjHoxcGCLOSgRUvuQ 
_model_server_result.datetime_utc      '2024-11-13 03:34:20' 
_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          3cl9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":602}' 
#
_entry.id    3CL9 
#
_exptl.entry_id    3CL9 
_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    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            3CL9 
_cell.length_a            121.05 
_cell.length_b            121.05 
_cell.length_c            260.76 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3CL9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        98 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41 2 2' 
#
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 tetrameric 4 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,C,D,E,F,G,H,I,J,K,L 1 1,2 
A,B,C,D,E,F,G,H,I,J,K,L 2 1,3 
A,B,C,D,E,F,G,H,I,J,K,L 3 1,2,4,3 
#
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' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
4 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             H 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 246 n y 
N1 C8A MTX sing 247 n y 
C2 NA2 MTX sing 248 n n 
C2 N3 MTX sing 249 n y 
NA2 HN21 MTX sing 250 n n 
NA2 HN22 MTX sing 251 n n 
N3 C4 MTX doub 252 n y 
C4 NA4 MTX sing 253 n n 
C4 C4A MTX sing 254 n y 
NA4 HN41 MTX sing 255 n n 
NA4 HN42 MTX sing 256 n n 
C4A N5 MTX sing 257 n y 
C4A C8A MTX doub 258 n y 
N5 C6 MTX doub 259 n y 
C6 C7 MTX sing 260 n y 
C6 C9 MTX sing 261 n n 
C7 N8 MTX doub 262 n y 
C7 H7 MTX sing 263 n n 
N8 C8A MTX sing 264 n y 
C9 N10 MTX sing 265 n n 
C9 H91 MTX sing 266 n n 
C9 H92 MTX sing 267 n n 
N10 CM MTX sing 268 n n 
N10 C14 MTX sing 269 n n 
CM HM1 MTX sing 270 n n 
CM HM2 MTX sing 271 n n 
CM HM3 MTX sing 272 n n 
C11 C12 MTX doub 273 n y 
C11 C16 MTX sing 274 n y 
C11 C MTX sing 275 n n 
C12 C13 MTX sing 276 n y 
C12 H12 MTX sing 277 n n 
C13 C14 MTX doub 278 n y 
C13 H13 MTX sing 279 n n 
C14 C15 MTX sing 280 n y 
C15 C16 MTX doub 281 n y 
C15 H15 MTX sing 282 n n 
C16 H16 MTX sing 283 n n 
C O MTX doub 284 n n 
C N MTX sing 285 n n 
N CA MTX sing 286 n n 
N HN MTX sing 287 n n 
CA CT MTX sing 288 n n 
CA CB MTX sing 289 n n 
CA HA MTX sing 290 n n 
CT O1 MTX doub 291 n n 
CT O2 MTX sing 292 n n 
O2 HO2 MTX sing 293 n n 
CB CG MTX sing 294 n n 
CB HB1 MTX sing 295 n n 
CB HB2 MTX sing 296 n n 
CG CD MTX sing 297 n n 
CG HG1 MTX sing 298 n n 
CG HG2 MTX sing 299 n n 
CD OE1 MTX doub 300 n n 
CD OE2 MTX sing 301 n n 
OE2 HOE2 MTX sing 302 n n 
#
_atom_sites.entry_id                     3CL9 
_atom_sites.fract_transf_matrix[1][1]    0.008261 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008261 
_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]    0.003835 
_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
B 2 SO4 A 1 801 801 SO4 SO4 . 
C 2 SO4 A 1 802 802 SO4 SO4 . 
D 3 CL A 1 901 901 CL CL . 
E 3 CL A 1 902 902 CL CL . 
F 3 CL A 1 903 903 CL CL . 
G 4 NAP A 1 601 601 NAP NAP . 
H 5 MTX A 1 602 602 MTX MTX . 
I 6 UMP A 1 603 603 UMP UMP . 
J 7 EDO A 1 701 701 EDO EDO . 
K 7 EDO A 1 702 702 EDO EDO . 
L 8 HOH A 1 904 1 HOH HOH . 
L 8 HOH A 2 905 2 HOH HOH . 
L 8 HOH A 3 906 3 HOH HOH . 
L 8 HOH A 4 907 4 HOH HOH . 
L 8 HOH A 5 908 5 HOH HOH . 
L 8 HOH A 6 909 6 HOH HOH . 
L 8 HOH A 7 910 7 HOH HOH . 
L 8 HOH A 8 911 8 HOH HOH . 
L 8 HOH A 9 912 9 HOH HOH . 
L 8 HOH A 10 913 10 HOH HOH . 
L 8 HOH A 11 914 11 HOH HOH . 
L 8 HOH A 12 915 12 HOH HOH . 
L 8 HOH A 13 916 13 HOH HOH . 
L 8 HOH A 14 917 14 HOH HOH . 
L 8 HOH A 15 918 15 HOH HOH . 
L 8 HOH A 16 919 16 HOH HOH . 
L 8 HOH A 17 920 17 HOH HOH . 
L 8 HOH A 18 921 18 HOH HOH . 
L 8 HOH A 19 922 19 HOH HOH . 
L 8 HOH A 20 923 20 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 . . . H 5 -38.518 5.566 -8.855 1 98.57 ? N1 MTX 602 A 1 
HETATM 2 C C2 MTX . . . H 5 -37.338 5.328 -8.188 1 98.41 ? C2 MTX 602 A 1 
HETATM 3 N NA2 MTX . . . H 5 -36.594 4.282 -8.517 1 98.5 ? NA2 MTX 602 A 1 
HETATM 4 N N3 MTX . . . H 5 -36.928 6.17 -7.178 1 98.38 ? N3 MTX 602 A 1 
HETATM 5 C C4 MTX . . . H 5 -37.679 7.269 -6.826 1 98.41 ? C4 MTX 602 A 1 
HETATM 6 N NA4 MTX . . . H 5 -37.038 8.304 -6.294 1 98.79 ? NA4 MTX 602 A 1 
HETATM 7 C C4A MTX . . . H 5 -38.873 7.51 -7.495 1 98.52 ? C4A MTX 602 A 1 
HETATM 8 N N5 MTX . . . H 5 -39.649 8.602 -7.157 1 98.65 ? N5 MTX 602 A 1 
HETATM 9 C C6 MTX . . . H 5 -40.843 8.859 -7.811 1 98.66 ? C6 MTX 602 A 1 
HETATM 10 C C7 MTX . . . H 5 -41.256 8 -8.836 1 98.59 ? C7 MTX 602 A 1 
HETATM 11 N N8 MTX . . . H 5 -40.481 6.905 -9.181 1 98.62 ? N8 MTX 602 A 1 
HETATM 12 C C8A MTX . . . H 5 -39.291 6.657 -8.515 1 98.75 ? C8A MTX 602 A 1 
HETATM 13 C C9 MTX . . . H 5 -41.645 10.082 -7.386 1 98.77 ? C9 MTX 602 A 1 
HETATM 14 N N10 MTX . . . H 5 -43.036 10.108 -7.827 1 99.02 ? N10 MTX 602 A 1 
HETATM 15 C CM MTX . . . H 5 -43.432 11.082 -8.857 1 99.4 ? CM MTX 602 A 1 
HETATM 16 C C11 MTX . . . H 5 -45.713 7.078 -6.732 1 98.91 ? C11 MTX 602 A 1 
HETATM 17 C C12 MTX . . . H 5 -45.742 7.603 -8.019 1 99.12 ? C12 MTX 602 A 1 
HETATM 18 C C13 MTX . . . H 5 -44.853 8.607 -8.376 1 98.83 ? C13 MTX 602 A 1 
HETATM 19 C C14 MTX . . . H 5 -43.944 9.088 -7.443 1 98.71 ? C14 MTX 602 A 1 
HETATM 20 C C15 MTX . . . H 5 -43.916 8.562 -6.156 1 98.39 ? C15 MTX 602 A 1 
HETATM 21 C C16 MTX . . . H 5 -44.875 7.635 -5.773 1 98.65 ? C16 MTX 602 A 1 
HETATM 22 C C MTX . . . H 5 -46.676 5.993 -6.363 1 98.98 ? C MTX 602 A 1 
HETATM 23 O O MTX . . . H 5 -47.592 5.53 -7.339 1 99.21 ? O MTX 602 A 1 
HETATM 24 N N MTX . . . H 5 -46.623 5.513 -5.121 1 99.03 ? N MTX 602 A 1 
HETATM 25 C CA MTX . . . H 5 -47.004 4.17 -4.731 1 99.04 ? CA MTX 602 A 1 
HETATM 26 C CT MTX . . . H 5 -46.315 3.73 -3.48 1 99.13 ? CT MTX 602 A 1 
HETATM 27 O O1 MTX . . . H 5 -45.156 4.119 -3.203 1 99.16 ? O1 MTX 602 A 1 
HETATM 28 O O2 MTX . . . H 5 -46.907 2.943 -2.71 1 99.6 ? O2 MTX 602 A 1 
HETATM 29 C CB MTX . . . H 5 -46.638 3.151 -5.791 1 98.97 ? CB MTX 602 A 1 
HETATM 30 C CG MTX . . . H 5 -47.702 2.067 -5.87 1 98.9 ? CG MTX 602 A 1 
HETATM 31 C CD MTX . . . H 5 -47.588 1.48 -7.247 1 98.89 ? CD MTX 602 A 1 
HETATM 32 O OE1 MTX . . . H 5 -47.797 2.19 -8.261 1 99.14 ? OE1 MTX 602 A 1 
HETATM 33 O OE2 MTX . . . H 5 -47.261 0.281 -7.377 1 98.94 ? OE2 MTX 602 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           221 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           33 
#