data_6PF7 # _model_server_result.job_id slAH71waEqawMfjvbHCX9w _model_server_result.datetime_utc '2024-11-25 08:25:50' _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 6pf7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":604}' # _entry.id 6PF7 # _exptl.entry_id 6PF7 _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 94.68 _cell.angle_gamma 90 _cell.entry_id 6PF7 _cell.length_a 214.774 _cell.length_b 115.789 _cell.length_c 220.142 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PF7 _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,DA,EA 1 1 C,D,P,Q,R,S,T,U,V,W,X,Y,FA,GA 2 1 E,Z,AA,BA,CA,HA 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_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 196.81248 0 219.408031 # 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 6PF7 _atom_sites.fract_transf_matrix[1][1] 0.004656 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000381 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008636 _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] 0.004558 _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 OG7 A 1 603 603 OG7 TS1 . 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 OG7 B 1 603 603 OG7 TS1 . 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 OG7 C 1 603 603 OG7 TS1 . 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 OG7 D 1 603 603 OG7 TS1 . 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 OG7 E 1 603 603 OG7 TS1 . CA 5 MTX E 1 604 604 MTX MTX . DA 7 HOH A 1 701 74 HOH HOH . DA 7 HOH A 2 702 118 HOH HOH . DA 7 HOH A 3 703 51 HOH HOH . DA 7 HOH A 4 704 26 HOH HOH . DA 7 HOH A 5 705 56 HOH HOH . DA 7 HOH A 6 706 59 HOH HOH . DA 7 HOH A 7 707 64 HOH HOH . DA 7 HOH A 8 708 36 HOH HOH . DA 7 HOH A 9 709 32 HOH HOH . DA 7 HOH A 10 710 39 HOH HOH . DA 7 HOH A 11 711 58 HOH HOH . DA 7 HOH A 12 712 68 HOH HOH . DA 7 HOH A 13 713 114 HOH HOH . DA 7 HOH A 14 714 38 HOH HOH . DA 7 HOH A 15 715 53 HOH HOH . DA 7 HOH A 16 716 69 HOH HOH . DA 7 HOH A 17 717 37 HOH HOH . DA 7 HOH A 18 718 78 HOH HOH . DA 7 HOH A 19 719 107 HOH HOH . DA 7 HOH A 20 720 19 HOH HOH . DA 7 HOH A 21 721 132 HOH HOH . DA 7 HOH A 22 722 10 HOH HOH . DA 7 HOH A 23 723 17 HOH HOH . DA 7 HOH A 24 724 57 HOH HOH . DA 7 HOH A 25 725 12 HOH HOH . DA 7 HOH A 26 726 152 HOH HOH . DA 7 HOH A 27 727 3 HOH HOH . DA 7 HOH A 28 728 134 HOH HOH . DA 7 HOH A 29 729 7 HOH HOH . DA 7 HOH A 30 730 96 HOH HOH . DA 7 HOH A 31 731 135 HOH HOH . DA 7 HOH A 32 732 112 HOH HOH . DA 7 HOH A 33 733 133 HOH HOH . DA 7 HOH A 34 734 99 HOH HOH . DA 7 HOH A 35 735 111 HOH HOH . DA 7 HOH A 36 736 43 HOH HOH . DA 7 HOH A 37 737 4 HOH HOH . DA 7 HOH A 38 738 24 HOH HOH . DA 7 HOH A 39 739 66 HOH HOH . DA 7 HOH A 40 740 140 HOH HOH . DA 7 HOH A 41 741 23 HOH HOH . DA 7 HOH A 42 742 13 HOH HOH . DA 7 HOH A 43 743 5 HOH HOH . DA 7 HOH A 44 744 80 HOH HOH . DA 7 HOH A 45 745 142 HOH HOH . DA 7 HOH A 46 746 120 HOH HOH . DA 7 HOH A 47 747 82 HOH HOH . DA 7 HOH A 48 748 73 HOH HOH . DA 7 HOH A 49 749 93 HOH HOH . DA 7 HOH A 50 750 143 HOH HOH . DA 7 HOH A 51 751 117 HOH HOH . DA 7 HOH A 52 752 95 HOH HOH . DA 7 HOH A 53 753 122 HOH HOH . DA 7 HOH A 54 754 92 HOH HOH . DA 7 HOH A 55 755 75 HOH HOH . EA 7 HOH B 1 701 100 HOH HOH . EA 7 HOH B 2 702 89 HOH HOH . EA 7 HOH B 3 703 101 HOH HOH . EA 7 HOH B 4 704 54 HOH HOH . EA 7 HOH B 5 705 110 HOH HOH . EA 7 HOH B 6 706 18 HOH HOH . EA 7 HOH B 7 707 21 HOH HOH . EA 7 HOH B 8 708 87 HOH HOH . EA 7 HOH B 9 709 55 HOH HOH . EA 7 HOH B 10 710 50 HOH HOH . EA 7 HOH B 11 711 145 HOH HOH . EA 7 HOH B 12 712 81 HOH HOH . EA 7 HOH B 13 713 123 HOH HOH . EA 7 HOH B 14 714 14 HOH HOH . EA 7 HOH B 15 715 15 HOH HOH . EA 7 HOH B 16 716 45 HOH HOH . EA 7 HOH B 17 717 79 HOH HOH . EA 7 HOH B 18 718 131 HOH HOH . EA 7 HOH B 19 719 139 HOH HOH . EA 7 HOH B 20 720 128 HOH HOH . EA 7 HOH B 21 721 85 HOH HOH . EA 7 HOH B 22 722 130 HOH HOH . EA 7 HOH B 23 723 9 HOH HOH . EA 7 HOH B 24 724 47 HOH HOH . EA 7 HOH B 25 725 137 HOH HOH . EA 7 HOH B 26 726 91 HOH HOH . EA 7 HOH B 27 727 106 HOH HOH . FA 7 HOH C 1 701 121 HOH HOH . FA 7 HOH C 2 702 42 HOH HOH . FA 7 HOH C 3 703 102 HOH HOH . FA 7 HOH C 4 704 105 HOH HOH . FA 7 HOH C 5 705 94 HOH HOH . FA 7 HOH C 6 706 119 HOH HOH . FA 7 HOH C 7 707 70 HOH HOH . FA 7 HOH C 8 708 6 HOH HOH . FA 7 HOH C 9 709 49 HOH HOH . FA 7 HOH C 10 710 60 HOH HOH . FA 7 HOH C 11 711 46 HOH HOH . FA 7 HOH C 12 712 149 HOH HOH . FA 7 HOH C 13 713 71 HOH HOH . FA 7 HOH C 14 714 41 HOH HOH . FA 7 HOH C 15 715 84 HOH HOH . FA 7 HOH C 16 716 83 HOH HOH . FA 7 HOH C 17 717 76 HOH HOH . FA 7 HOH C 18 718 20 HOH HOH . FA 7 HOH C 19 719 8 HOH HOH . FA 7 HOH C 20 720 124 HOH HOH . FA 7 HOH C 21 721 2 HOH HOH . FA 7 HOH C 22 722 108 HOH HOH . FA 7 HOH C 23 723 138 HOH HOH . FA 7 HOH C 24 724 16 HOH HOH . FA 7 HOH C 25 725 126 HOH HOH . FA 7 HOH C 26 726 144 HOH HOH . FA 7 HOH C 27 727 104 HOH HOH . FA 7 HOH C 28 728 113 HOH HOH . GA 7 HOH D 1 701 125 HOH HOH . GA 7 HOH D 2 702 88 HOH HOH . GA 7 HOH D 3 703 67 HOH HOH . GA 7 HOH D 4 704 34 HOH HOH . GA 7 HOH D 5 705 44 HOH HOH . GA 7 HOH D 6 706 11 HOH HOH . GA 7 HOH D 7 707 115 HOH HOH . GA 7 HOH D 8 708 22 HOH HOH . GA 7 HOH D 9 709 25 HOH HOH . GA 7 HOH D 10 710 97 HOH HOH . GA 7 HOH D 11 711 109 HOH HOH . GA 7 HOH D 12 712 90 HOH HOH . GA 7 HOH D 13 713 147 HOH HOH . GA 7 HOH D 14 714 28 HOH HOH . GA 7 HOH D 15 715 63 HOH HOH . GA 7 HOH D 16 716 141 HOH HOH . GA 7 HOH D 17 717 77 HOH HOH . GA 7 HOH D 18 718 61 HOH HOH . GA 7 HOH D 19 719 86 HOH HOH . GA 7 HOH D 20 720 65 HOH HOH . GA 7 HOH D 21 721 1 HOH HOH . GA 7 HOH D 22 722 127 HOH HOH . GA 7 HOH D 23 723 148 HOH HOH . GA 7 HOH D 24 724 151 HOH HOH . GA 7 HOH D 25 725 72 HOH HOH . HA 7 HOH E 1 701 62 HOH HOH . HA 7 HOH E 2 702 52 HOH HOH . HA 7 HOH E 3 703 103 HOH HOH . HA 7 HOH E 4 704 150 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 . . . N 5 -5.485 -42.104 15.048 1 63.3 ? N1 MTX 604 B 1 HETATM 2 C C2 MTX . . . N 5 -4.742 -42.834 15.92 1 57.74 ? C2 MTX 604 B 1 HETATM 3 N NA2 MTX . . . N 5 -3.394 -42.645 15.947 1 65.15 ? NA2 MTX 604 B 1 HETATM 4 N N3 MTX . . . N 5 -5.346 -43.744 16.755 1 60.16 ? N3 MTX 604 B 1 HETATM 5 C C4 MTX . . . N 5 -6.672 -43.962 16.759 1 62.56 ? C4 MTX 604 B 1 HETATM 6 N NA4 MTX . . . N 5 -7.291 -44.87 17.588 1 51.16 ? NA4 MTX 604 B 1 HETATM 7 C C4A MTX . . . N 5 -7.49 -43.206 15.849 1 61.57 ? C4A MTX 604 B 1 HETATM 8 N N5 MTX . . . N 5 -8.846 -43.407 15.829 1 56.27 ? N5 MTX 604 B 1 HETATM 9 C C6 MTX . . . N 5 -9.55 -42.672 14.972 1 54.93 ? C6 MTX 604 B 1 HETATM 10 C C7 MTX . . . N 5 -8.89 -41.74 14.112 1 59.05 ? C7 MTX 604 B 1 HETATM 11 N N8 MTX . . . N 5 -7.575 -41.522 14.105 1 57.66 ? N8 MTX 604 B 1 HETATM 12 C C8A MTX . . . N 5 -6.843 -42.28 15.003 1 57.36 ? C8A MTX 604 B 1 HETATM 13 C C9 MTX . . . N 5 -11.015 -42.968 15.023 1 45.31 ? C9 MTX 604 B 1 HETATM 14 N N10 MTX . . . N 5 -11.276 -44.367 14.596 1 51.23 ? N10 MTX 604 B 1 HETATM 15 C CM MTX . . . N 5 -11.699 -45.44 15.498 1 58.96 ? CM MTX 604 B 1 HETATM 16 C C11 MTX . . . N 5 -10.6 -45.31 10.519 1 53.58 ? C11 MTX 604 B 1 HETATM 17 C C12 MTX . . . N 5 -10.975 -43.991 10.847 1 49.35 ? C12 MTX 604 B 1 HETATM 18 C C13 MTX . . . N 5 -11.192 -43.707 12.191 1 44.47 ? C13 MTX 604 B 1 HETATM 19 C C14 MTX . . . N 5 -11.059 -44.657 13.228 1 52.39 ? C14 MTX 604 B 1 HETATM 20 C C15 MTX . . . N 5 -10.68 -45.969 12.857 1 52.4 ? C15 MTX 604 B 1 HETATM 21 C C16 MTX . . . N 5 -10.461 -46.265 11.531 1 45.97 ? C16 MTX 604 B 1 HETATM 22 C C MTX . . . N 5 -10.326 -45.778 9.148 1 55.51 ? C MTX 604 B 1 HETATM 23 O O MTX . . . N 5 -10.938 -45.371 8.154 1 55.06 ? O MTX 604 B 1 HETATM 24 N N MTX . . . N 5 -9.324 -46.708 9.088 1 56.95 ? N MTX 604 B 1 HETATM 25 C CA MTX . . . N 5 -8.901 -47.269 7.813 1 53.46 ? CA MTX 604 B 1 HETATM 26 C CT MTX . . . N 5 -8.316 -48.646 8.053 1 61.55 ? CT MTX 604 B 1 HETATM 27 O O1 MTX . . . N 5 -7.924 -48.92 9.198 1 54.62 ? O1 MTX 604 B 1 HETATM 28 O O2 MTX . . . N 5 -8.263 -49.446 7.084 1 56.21 ? O2 MTX 604 B 1 HETATM 29 C CB MTX . . . N 5 -7.863 -46.336 7.175 1 63.55 ? CB MTX 604 B 1 HETATM 30 C CG MTX . . . N 5 -7.59 -46.708 5.724 1 79.28 ? CG MTX 604 B 1 HETATM 31 C CD MTX . . . N 5 -6.385 -45.972 5.167 1 80.58 ? CD MTX 604 B 1 HETATM 32 O OE1 MTX . . . N 5 -5.586 -46.57 4.403 1 87.22 ? OE1 MTX 604 B 1 HETATM 33 O OE2 MTX . . . N 5 -6.24 -44.782 5.504 1 78.28 ? OE2 MTX 604 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 66 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 33 #