data_5YFY # _model_server_result.job_id i7tQpVw6JaCPc6c4A66TxQ _model_server_result.datetime_utc '2025-02-28 19:43:37' _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 5yfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 5YFY # _exptl.entry_id 5YFY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.209 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.01 _cell.angle_gamma 90 _cell.entry_id 5YFY _cell.length_a 101.647 _cell.length_b 58.804 _cell.length_c 235.489 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YFY _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,F,G,H,L,M 1 1 C,I,J,K,N 2 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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 G N N ? 2 I N N # _chem_comp.formula 'C10 H15 N2 O7 P' _chem_comp.formula_weight 306.209 _chem_comp.id PLG _chem_comp.mon_nstd_flag . _chem_comp.name N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE # 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 PLG doub 321 n y N1 C6 PLG sing 322 n y C2 C2A PLG sing 323 n n C2 C3 PLG sing 324 n y C2A H2A1 PLG sing 325 n n C2A H2A2 PLG sing 326 n n C2A H2A3 PLG sing 327 n n C3 O3 PLG sing 328 n n C3 C4 PLG doub 329 n y O3 HO3 PLG sing 330 n n C4 C4A PLG sing 331 n n C4 C5 PLG sing 332 n y C4A N PLG sing 333 n n C4A H4A1 PLG sing 334 n n C4A H4A2 PLG sing 335 n n C5 C6 PLG doub 336 n y C5 C5A PLG sing 337 n n C6 H6 PLG sing 338 n n C5A OP4 PLG sing 339 n n C5A H5A1 PLG sing 340 n n C5A H5A2 PLG sing 341 n n OP4 P PLG sing 342 n n P OP1 PLG doub 343 n n P OP2 PLG sing 344 n n P OP3 PLG sing 345 n n OP2 HOP2 PLG sing 346 n n OP3 HOP3 PLG sing 347 n n C O PLG doub 348 n n C OXT PLG sing 349 n n C CA PLG sing 350 n n OXT HXT PLG sing 351 n n CA N PLG sing 352 n n CA HA2 PLG sing 353 n n CA HA1 PLG sing 354 n n N H PLG sing 355 n n # _atom_sites.entry_id 5YFY _atom_sites.fract_transf_matrix[1][1] 0.009838 _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] 0.017006 _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] 0.004246 _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 D 2 PLG A 1 501 1 PLG PLG . E 3 8UL A 1 502 4 8UL S25 . F 4 CL A 1 503 7 CL CL . G 2 PLG B 1 501 2 PLG PLG . H 3 8UL B 1 502 5 8UL S25 . I 2 PLG C 1 501 3 PLG PLG . J 3 8UL C 1 502 6 8UL S25 . K 4 CL C 1 503 8 CL CL . L 5 HOH A 1 601 49 HOH HOH . L 5 HOH A 2 602 218 HOH HOH . L 5 HOH A 3 603 132 HOH HOH . L 5 HOH A 4 604 15 HOH HOH . L 5 HOH A 5 605 242 HOH HOH . L 5 HOH A 6 606 112 HOH HOH . L 5 HOH A 7 607 145 HOH HOH . L 5 HOH A 8 608 195 HOH HOH . L 5 HOH A 9 609 110 HOH HOH . L 5 HOH A 10 610 75 HOH HOH . L 5 HOH A 11 611 90 HOH HOH . L 5 HOH A 12 612 238 HOH HOH . L 5 HOH A 13 613 41 HOH HOH . L 5 HOH A 14 614 140 HOH HOH . L 5 HOH A 15 615 73 HOH HOH . L 5 HOH A 16 616 23 HOH HOH . L 5 HOH A 17 617 213 HOH HOH . L 5 HOH A 18 618 168 HOH HOH . L 5 HOH A 19 619 62 HOH HOH . L 5 HOH A 20 620 93 HOH HOH . L 5 HOH A 21 621 22 HOH HOH . L 5 HOH A 22 622 108 HOH HOH . L 5 HOH A 23 623 66 HOH HOH . L 5 HOH A 24 624 106 HOH HOH . L 5 HOH A 25 625 101 HOH HOH . L 5 HOH A 26 626 36 HOH HOH . L 5 HOH A 27 627 109 HOH HOH . L 5 HOH A 28 628 95 HOH HOH . L 5 HOH A 29 629 211 HOH HOH . L 5 HOH A 30 630 204 HOH HOH . L 5 HOH A 31 631 165 HOH HOH . L 5 HOH A 32 632 215 HOH HOH . L 5 HOH A 33 633 61 HOH HOH . L 5 HOH A 34 634 176 HOH HOH . L 5 HOH A 35 635 142 HOH HOH . L 5 HOH A 36 636 177 HOH HOH . L 5 HOH A 37 637 255 HOH HOH . L 5 HOH A 38 638 24 HOH HOH . L 5 HOH A 39 639 251 HOH HOH . L 5 HOH A 40 640 51 HOH HOH . L 5 HOH A 41 641 31 HOH HOH . L 5 HOH A 42 642 17 HOH HOH . L 5 HOH A 43 643 236 HOH HOH . L 5 HOH A 44 644 81 HOH HOH . L 5 HOH A 45 645 258 HOH HOH . L 5 HOH A 46 646 220 HOH HOH . L 5 HOH A 47 647 58 HOH HOH . L 5 HOH A 48 648 39 HOH HOH . L 5 HOH A 49 649 37 HOH HOH . L 5 HOH A 50 650 230 HOH HOH . L 5 HOH A 51 651 146 HOH HOH . L 5 HOH A 52 652 18 HOH HOH . L 5 HOH A 53 653 192 HOH HOH . L 5 HOH A 54 654 139 HOH HOH . L 5 HOH A 55 655 116 HOH HOH . L 5 HOH A 56 656 86 HOH HOH . L 5 HOH A 57 657 158 HOH HOH . L 5 HOH A 58 658 65 HOH HOH . L 5 HOH A 59 659 21 HOH HOH . L 5 HOH A 60 660 79 HOH HOH . L 5 HOH A 61 661 202 HOH HOH . L 5 HOH A 62 662 87 HOH HOH . L 5 HOH A 63 663 42 HOH HOH . L 5 HOH A 64 664 206 HOH HOH . L 5 HOH A 65 665 198 HOH HOH . L 5 HOH A 66 666 128 HOH HOH . L 5 HOH A 67 667 85 HOH HOH . L 5 HOH A 68 668 172 HOH HOH . L 5 HOH A 69 669 35 HOH HOH . L 5 HOH A 70 670 144 HOH HOH . L 5 HOH A 71 671 193 HOH HOH . L 5 HOH A 72 672 151 HOH HOH . L 5 HOH A 73 673 100 HOH HOH . L 5 HOH A 74 674 123 HOH HOH . L 5 HOH A 75 675 70 HOH HOH . L 5 HOH A 76 676 250 HOH HOH . L 5 HOH A 77 677 160 HOH HOH . L 5 HOH A 78 678 246 HOH HOH . L 5 HOH A 79 679 186 HOH HOH . L 5 HOH A 80 680 184 HOH HOH . L 5 HOH A 81 681 45 HOH HOH . L 5 HOH A 82 682 233 HOH HOH . L 5 HOH A 83 683 148 HOH HOH . L 5 HOH A 84 684 174 HOH HOH . L 5 HOH A 85 685 225 HOH HOH . M 5 HOH B 1 601 175 HOH HOH . M 5 HOH B 2 602 82 HOH HOH . M 5 HOH B 3 603 222 HOH HOH . M 5 HOH B 4 604 223 HOH HOH . M 5 HOH B 5 605 19 HOH HOH . M 5 HOH B 6 606 91 HOH HOH . M 5 HOH B 7 607 171 HOH HOH . M 5 HOH B 8 608 196 HOH HOH . M 5 HOH B 9 609 13 HOH HOH . M 5 HOH B 10 610 239 HOH HOH . M 5 HOH B 11 611 88 HOH HOH . M 5 HOH B 12 612 102 HOH HOH . M 5 HOH B 13 613 147 HOH HOH . M 5 HOH B 14 614 212 HOH HOH . M 5 HOH B 15 615 64 HOH HOH . M 5 HOH B 16 616 205 HOH HOH . M 5 HOH B 17 617 63 HOH HOH . M 5 HOH B 18 618 105 HOH HOH . M 5 HOH B 19 619 72 HOH HOH . M 5 HOH B 20 620 104 HOH HOH . M 5 HOH B 21 621 40 HOH HOH . M 5 HOH B 22 622 254 HOH HOH . M 5 HOH B 23 623 214 HOH HOH . M 5 HOH B 24 624 166 HOH HOH . M 5 HOH B 25 625 96 HOH HOH . M 5 HOH B 26 626 201 HOH HOH . M 5 HOH B 27 627 216 HOH HOH . M 5 HOH B 28 628 248 HOH HOH . M 5 HOH B 29 629 50 HOH HOH . M 5 HOH B 30 630 180 HOH HOH . M 5 HOH B 31 631 252 HOH HOH . M 5 HOH B 32 632 60 HOH HOH . M 5 HOH B 33 633 221 HOH HOH . M 5 HOH B 34 634 69 HOH HOH . M 5 HOH B 35 635 25 HOH HOH . M 5 HOH B 36 636 209 HOH HOH . M 5 HOH B 37 637 111 HOH HOH . M 5 HOH B 38 638 89 HOH HOH . M 5 HOH B 39 639 20 HOH HOH . M 5 HOH B 40 640 190 HOH HOH . M 5 HOH B 41 641 32 HOH HOH . M 5 HOH B 42 642 149 HOH HOH . M 5 HOH B 43 643 113 HOH HOH . M 5 HOH B 44 644 54 HOH HOH . M 5 HOH B 45 645 47 HOH HOH . M 5 HOH B 46 646 229 HOH HOH . M 5 HOH B 47 647 76 HOH HOH . M 5 HOH B 48 648 127 HOH HOH . M 5 HOH B 49 649 199 HOH HOH . M 5 HOH B 50 650 155 HOH HOH . M 5 HOH B 51 651 125 HOH HOH . M 5 HOH B 52 652 118 HOH HOH . M 5 HOH B 53 653 29 HOH HOH . M 5 HOH B 54 654 137 HOH HOH . M 5 HOH B 55 655 107 HOH HOH . M 5 HOH B 56 656 80 HOH HOH . M 5 HOH B 57 657 237 HOH HOH . M 5 HOH B 58 658 159 HOH HOH . M 5 HOH B 59 659 78 HOH HOH . M 5 HOH B 60 660 56 HOH HOH . M 5 HOH B 61 661 53 HOH HOH . M 5 HOH B 62 662 30 HOH HOH . M 5 HOH B 63 663 207 HOH HOH . M 5 HOH B 64 664 71 HOH HOH . M 5 HOH B 65 665 34 HOH HOH . M 5 HOH B 66 666 98 HOH HOH . M 5 HOH B 67 667 48 HOH HOH . M 5 HOH B 68 668 83 HOH HOH . M 5 HOH B 69 669 256 HOH HOH . M 5 HOH B 70 670 154 HOH HOH . M 5 HOH B 71 671 43 HOH HOH . M 5 HOH B 72 672 129 HOH HOH . M 5 HOH B 73 673 120 HOH HOH . M 5 HOH B 74 674 245 HOH HOH . M 5 HOH B 75 675 114 HOH HOH . M 5 HOH B 76 676 240 HOH HOH . M 5 HOH B 77 677 153 HOH HOH . M 5 HOH B 78 678 187 HOH HOH . M 5 HOH B 79 679 232 HOH HOH . M 5 HOH B 80 680 121 HOH HOH . M 5 HOH B 81 681 259 HOH HOH . M 5 HOH B 82 682 134 HOH HOH . M 5 HOH B 83 683 185 HOH HOH . M 5 HOH B 84 684 247 HOH HOH . M 5 HOH B 85 685 162 HOH HOH . M 5 HOH B 86 686 243 HOH HOH . M 5 HOH B 87 687 226 HOH HOH . N 5 HOH C 1 601 135 HOH HOH . N 5 HOH C 2 602 253 HOH HOH . N 5 HOH C 3 603 94 HOH HOH . N 5 HOH C 4 604 228 HOH HOH . N 5 HOH C 5 605 170 HOH HOH . N 5 HOH C 6 606 194 HOH HOH . N 5 HOH C 7 607 92 HOH HOH . N 5 HOH C 8 608 163 HOH HOH . N 5 HOH C 9 609 131 HOH HOH . N 5 HOH C 10 610 68 HOH HOH . N 5 HOH C 11 611 124 HOH HOH . N 5 HOH C 12 612 103 HOH HOH . N 5 HOH C 13 613 46 HOH HOH . N 5 HOH C 14 614 16 HOH HOH . N 5 HOH C 15 615 4 HOH HOH . N 5 HOH C 16 616 67 HOH HOH . N 5 HOH C 17 617 183 HOH HOH . N 5 HOH C 18 618 141 HOH HOH . N 5 HOH C 19 619 157 HOH HOH . N 5 HOH C 20 620 14 HOH HOH . N 5 HOH C 21 621 241 HOH HOH . N 5 HOH C 22 622 3 HOH HOH . N 5 HOH C 23 623 167 HOH HOH . N 5 HOH C 24 624 136 HOH HOH . N 5 HOH C 25 625 27 HOH HOH . N 5 HOH C 26 626 59 HOH HOH . N 5 HOH C 27 627 203 HOH HOH . N 5 HOH C 28 628 143 HOH HOH . N 5 HOH C 29 629 12 HOH HOH . N 5 HOH C 30 630 178 HOH HOH . N 5 HOH C 31 631 74 HOH HOH . N 5 HOH C 32 632 224 HOH HOH . N 5 HOH C 33 633 210 HOH HOH . N 5 HOH C 34 634 244 HOH HOH . N 5 HOH C 35 635 5 HOH HOH . N 5 HOH C 36 636 200 HOH HOH . N 5 HOH C 37 637 189 HOH HOH . N 5 HOH C 38 638 97 HOH HOH . N 5 HOH C 39 639 164 HOH HOH . N 5 HOH C 40 640 9 HOH HOH . N 5 HOH C 41 641 179 HOH HOH . N 5 HOH C 42 642 77 HOH HOH . N 5 HOH C 43 643 217 HOH HOH . N 5 HOH C 44 644 10 HOH HOH . N 5 HOH C 45 645 126 HOH HOH . N 5 HOH C 46 646 231 HOH HOH . N 5 HOH C 47 647 117 HOH HOH . N 5 HOH C 48 648 219 HOH HOH . N 5 HOH C 49 649 138 HOH HOH . N 5 HOH C 50 650 84 HOH HOH . N 5 HOH C 51 651 33 HOH HOH . N 5 HOH C 52 652 161 HOH HOH . N 5 HOH C 53 653 38 HOH HOH . N 5 HOH C 54 654 28 HOH HOH . N 5 HOH C 55 655 150 HOH HOH . N 5 HOH C 56 656 55 HOH HOH . N 5 HOH C 57 657 235 HOH HOH . N 5 HOH C 58 658 11 HOH HOH . N 5 HOH C 59 659 197 HOH HOH . N 5 HOH C 60 660 57 HOH HOH . N 5 HOH C 61 661 133 HOH HOH . N 5 HOH C 62 662 44 HOH HOH . N 5 HOH C 63 663 26 HOH HOH . N 5 HOH C 64 664 52 HOH HOH . N 5 HOH C 65 665 7 HOH HOH . N 5 HOH C 66 666 191 HOH HOH . N 5 HOH C 67 667 8 HOH HOH . N 5 HOH C 68 668 1 HOH HOH . N 5 HOH C 69 669 6 HOH HOH . N 5 HOH C 70 670 188 HOH HOH . N 5 HOH C 71 671 181 HOH HOH . N 5 HOH C 72 672 257 HOH HOH . N 5 HOH C 73 673 115 HOH HOH . N 5 HOH C 74 674 119 HOH HOH . N 5 HOH C 75 675 130 HOH HOH . N 5 HOH C 76 676 152 HOH HOH . N 5 HOH C 77 677 208 HOH HOH . N 5 HOH C 78 678 99 HOH HOH . N 5 HOH C 79 679 122 HOH HOH . N 5 HOH C 80 680 234 HOH HOH . N 5 HOH C 81 681 156 HOH HOH . N 5 HOH C 82 682 182 HOH HOH . N 5 HOH C 83 683 249 HOH HOH . N 5 HOH C 84 684 169 HOH HOH . N 5 HOH C 85 685 173 HOH HOH . N 5 HOH C 86 686 2 HOH HOH . N 5 HOH C 87 687 227 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 PLG . . . I 2 3.588 49.792 13.004 1 21.78 ? N1 PLG 501 C 1 HETATM 2 C C2 PLG . . . I 2 3.24 50.166 14.247 1 22.27 ? C2 PLG 501 C 1 HETATM 3 C C2A PLG . . . I 2 4.068 49.72 15.43 1 21.92 ? C2A PLG 501 C 1 HETATM 4 C C3 PLG . . . I 2 2.04 51.023 14.44 1 22.28 ? C3 PLG 501 C 1 HETATM 5 O O3 PLG . . . I 2 1.662 51.413 15.686 1 19.59 ? O3 PLG 501 C 1 HETATM 6 C C4 PLG . . . I 2 1.289 51.408 13.23 1 23.09 ? C4 PLG 501 C 1 HETATM 7 C C4A PLG . . . I 2 0.037 52.257 13.309 1 25.59 ? C4A PLG 501 C 1 HETATM 8 C C5 PLG . . . I 2 1.785 50.907 11.915 1 22.88 ? C5 PLG 501 C 1 HETATM 9 C C6 PLG . . . I 2 2.927 50.103 11.887 1 22.07 ? C6 PLG 501 C 1 HETATM 10 C C5A PLG . . . I 2 1.091 51.182 10.591 1 22.79 ? C5A PLG 501 C 1 HETATM 11 O OP4 PLG . . . I 2 0.9 52.538 10.249 1 22.49 ? OP4 PLG 501 C 1 HETATM 12 P P PLG . . . I 2 -0.065 52.999 9.036 1 21.59 ? P PLG 501 C 1 HETATM 13 O OP1 PLG . . . I 2 -0.283 51.913 8.052 1 21.18 ? OP1 PLG 501 C 1 HETATM 14 O OP2 PLG . . . I 2 -1.336 53.374 9.745 1 23.02 ? OP2 PLG 501 C 1 HETATM 15 O OP3 PLG . . . I 2 0.775 54.161 8.575 1 22.58 ? OP3 PLG 501 C 1 HETATM 16 C C PLG . . . I 2 -1.67 53.699 16.325 1 24.51 ? C PLG 501 C 1 HETATM 17 O O PLG . . . I 2 -2.522 54.553 16.585 1 22.29 ? O PLG 501 C 1 HETATM 18 O OXT PLG . . . I 2 -0.761 53.423 17.124 1 24.74 ? OXT PLG 501 C 1 HETATM 19 C CA PLG . . . I 2 -1.672 52.993 14.989 1 25.32 ? CA PLG 501 C 1 HETATM 20 N N PLG . . . I 2 -0.292 52.765 14.62 1 25.02 ? N PLG 501 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #