data_8E9U # _model_server_result.job_id GcI1_vRriWPdyzMyKDHGeg _model_server_result.datetime_utc '2024-11-24 20:31:57' _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 8e9u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8E9U # _exptl.entry_id 8E9U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 8E9U _cell.length_a 143.83 _cell.length_b 143.83 _cell.length_c 81.57 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E9U _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall 'P 6c' _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 PLP doub 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 8E9U _atom_sites.fract_transf_matrix[1][1] 0.006953 _atom_sites.fract_transf_matrix[1][2] 0.004014 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008028 _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] 0.012259 _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 C 2 PLP A 1 401 500 PLP PLP . D 3 SO4 A 1 402 600 SO4 SO4 . E 2 PLP B 1 401 500 PLP PLP . F 3 SO4 B 1 402 600 SO4 SO4 . G 4 HOH A 1 501 18 HOH HOH . G 4 HOH A 2 502 260 HOH HOH . G 4 HOH A 3 503 237 HOH HOH . G 4 HOH A 4 504 266 HOH HOH . G 4 HOH A 5 505 59 HOH HOH . G 4 HOH A 6 506 281 HOH HOH . G 4 HOH A 7 507 270 HOH HOH . G 4 HOH A 8 508 122 HOH HOH . G 4 HOH A 9 509 292 HOH HOH . G 4 HOH A 10 510 262 HOH HOH . G 4 HOH A 11 511 286 HOH HOH . G 4 HOH A 12 512 275 HOH HOH . G 4 HOH A 13 513 10 HOH HOH . G 4 HOH A 14 514 54 HOH HOH . G 4 HOH A 15 515 196 HOH HOH . G 4 HOH A 16 516 289 HOH HOH . G 4 HOH A 17 517 40 HOH HOH . G 4 HOH A 18 518 97 HOH HOH . G 4 HOH A 19 519 214 HOH HOH . G 4 HOH A 20 520 12 HOH HOH . G 4 HOH A 21 521 28 HOH HOH . G 4 HOH A 22 522 45 HOH HOH . G 4 HOH A 23 523 140 HOH HOH . G 4 HOH A 24 524 288 HOH HOH . G 4 HOH A 25 525 169 HOH HOH . G 4 HOH A 26 526 107 HOH HOH . G 4 HOH A 27 527 128 HOH HOH . G 4 HOH A 28 528 192 HOH HOH . G 4 HOH A 29 529 24 HOH HOH . G 4 HOH A 30 530 272 HOH HOH . G 4 HOH A 31 531 47 HOH HOH . G 4 HOH A 32 532 264 HOH HOH . G 4 HOH A 33 533 145 HOH HOH . G 4 HOH A 34 534 36 HOH HOH . G 4 HOH A 35 535 48 HOH HOH . G 4 HOH A 36 536 46 HOH HOH . G 4 HOH A 37 537 120 HOH HOH . G 4 HOH A 38 538 124 HOH HOH . G 4 HOH A 39 539 19 HOH HOH . G 4 HOH A 40 540 63 HOH HOH . G 4 HOH A 41 541 126 HOH HOH . G 4 HOH A 42 542 6 HOH HOH . G 4 HOH A 43 543 115 HOH HOH . G 4 HOH A 44 544 245 HOH HOH . G 4 HOH A 45 545 138 HOH HOH . G 4 HOH A 46 546 5 HOH HOH . G 4 HOH A 47 547 147 HOH HOH . G 4 HOH A 48 548 3 HOH HOH . G 4 HOH A 49 549 242 HOH HOH . G 4 HOH A 50 550 284 HOH HOH . G 4 HOH A 51 551 121 HOH HOH . G 4 HOH A 52 552 93 HOH HOH . G 4 HOH A 53 553 14 HOH HOH . G 4 HOH A 54 554 52 HOH HOH . G 4 HOH A 55 555 79 HOH HOH . G 4 HOH A 56 556 132 HOH HOH . G 4 HOH A 57 557 50 HOH HOH . G 4 HOH A 58 558 27 HOH HOH . G 4 HOH A 59 559 85 HOH HOH . G 4 HOH A 60 560 146 HOH HOH . G 4 HOH A 61 561 190 HOH HOH . G 4 HOH A 62 562 26 HOH HOH . G 4 HOH A 63 563 76 HOH HOH . G 4 HOH A 64 564 100 HOH HOH . G 4 HOH A 65 565 32 HOH HOH . G 4 HOH A 66 566 89 HOH HOH . G 4 HOH A 67 567 99 HOH HOH . G 4 HOH A 68 568 35 HOH HOH . G 4 HOH A 69 569 173 HOH HOH . G 4 HOH A 70 570 280 HOH HOH . G 4 HOH A 71 571 160 HOH HOH . G 4 HOH A 72 572 205 HOH HOH . G 4 HOH A 73 573 110 HOH HOH . G 4 HOH A 74 574 9 HOH HOH . G 4 HOH A 75 575 15 HOH HOH . G 4 HOH A 76 576 101 HOH HOH . G 4 HOH A 77 577 170 HOH HOH . G 4 HOH A 78 578 193 HOH HOH . G 4 HOH A 79 579 178 HOH HOH . G 4 HOH A 80 580 1 HOH HOH . G 4 HOH A 81 581 29 HOH HOH . G 4 HOH A 82 582 185 HOH HOH . G 4 HOH A 83 583 143 HOH HOH . G 4 HOH A 84 584 7 HOH HOH . G 4 HOH A 85 585 166 HOH HOH . G 4 HOH A 86 586 68 HOH HOH . G 4 HOH A 87 587 17 HOH HOH . G 4 HOH A 88 588 116 HOH HOH . G 4 HOH A 89 589 20 HOH HOH . G 4 HOH A 90 590 77 HOH HOH . G 4 HOH A 91 591 207 HOH HOH . G 4 HOH A 92 592 133 HOH HOH . G 4 HOH A 93 593 149 HOH HOH . G 4 HOH A 94 594 252 HOH HOH . G 4 HOH A 95 595 159 HOH HOH . G 4 HOH A 96 596 86 HOH HOH . G 4 HOH A 97 597 194 HOH HOH . G 4 HOH A 98 598 34 HOH HOH . G 4 HOH A 99 599 246 HOH HOH . G 4 HOH A 100 600 134 HOH HOH . G 4 HOH A 101 601 154 HOH HOH . G 4 HOH A 102 602 78 HOH HOH . G 4 HOH A 103 603 130 HOH HOH . G 4 HOH A 104 604 251 HOH HOH . G 4 HOH A 105 605 222 HOH HOH . G 4 HOH A 106 606 153 HOH HOH . G 4 HOH A 107 607 204 HOH HOH . G 4 HOH A 108 608 197 HOH HOH . G 4 HOH A 109 609 234 HOH HOH . G 4 HOH A 110 610 235 HOH HOH . G 4 HOH A 111 611 94 HOH HOH . G 4 HOH A 112 612 156 HOH HOH . G 4 HOH A 113 613 229 HOH HOH . G 4 HOH A 114 614 165 HOH HOH . G 4 HOH A 115 615 238 HOH HOH . G 4 HOH A 116 616 42 HOH HOH . G 4 HOH A 117 617 39 HOH HOH . G 4 HOH A 118 618 102 HOH HOH . G 4 HOH A 119 619 249 HOH HOH . G 4 HOH A 120 620 183 HOH HOH . G 4 HOH A 121 621 215 HOH HOH . G 4 HOH A 122 622 182 HOH HOH . G 4 HOH A 123 623 293 HOH HOH . G 4 HOH A 124 624 4 HOH HOH . G 4 HOH A 125 625 296 HOH HOH . G 4 HOH A 126 626 208 HOH HOH . G 4 HOH A 127 627 75 HOH HOH . G 4 HOH A 128 628 22 HOH HOH . G 4 HOH A 129 629 224 HOH HOH . G 4 HOH A 130 630 139 HOH HOH . G 4 HOH A 131 631 91 HOH HOH . G 4 HOH A 132 632 202 HOH HOH . G 4 HOH A 133 633 290 HOH HOH . G 4 HOH A 134 634 276 HOH HOH . G 4 HOH A 135 635 223 HOH HOH . G 4 HOH A 136 636 244 HOH HOH . G 4 HOH A 137 637 168 HOH HOH . G 4 HOH A 138 638 82 HOH HOH . G 4 HOH A 139 639 141 HOH HOH . G 4 HOH A 140 640 218 HOH HOH . G 4 HOH A 141 641 162 HOH HOH . G 4 HOH A 142 642 250 HOH HOH . H 4 HOH B 1 501 83 HOH HOH . H 4 HOH B 2 502 261 HOH HOH . H 4 HOH B 3 503 61 HOH HOH . H 4 HOH B 4 504 271 HOH HOH . H 4 HOH B 5 505 216 HOH HOH . H 4 HOH B 6 506 87 HOH HOH . H 4 HOH B 7 507 177 HOH HOH . H 4 HOH B 8 508 163 HOH HOH . H 4 HOH B 9 509 151 HOH HOH . H 4 HOH B 10 510 213 HOH HOH . H 4 HOH B 11 511 127 HOH HOH . H 4 HOH B 12 512 44 HOH HOH . H 4 HOH B 13 513 98 HOH HOH . H 4 HOH B 14 514 277 HOH HOH . H 4 HOH B 15 515 74 HOH HOH . H 4 HOH B 16 516 106 HOH HOH . H 4 HOH B 17 517 152 HOH HOH . H 4 HOH B 18 518 57 HOH HOH . H 4 HOH B 19 519 233 HOH HOH . H 4 HOH B 20 520 291 HOH HOH . H 4 HOH B 21 521 84 HOH HOH . H 4 HOH B 22 522 148 HOH HOH . H 4 HOH B 23 523 33 HOH HOH . H 4 HOH B 24 524 203 HOH HOH . H 4 HOH B 25 525 13 HOH HOH . H 4 HOH B 26 526 137 HOH HOH . H 4 HOH B 27 527 273 HOH HOH . H 4 HOH B 28 528 198 HOH HOH . H 4 HOH B 29 529 16 HOH HOH . H 4 HOH B 30 530 104 HOH HOH . H 4 HOH B 31 531 8 HOH HOH . H 4 HOH B 32 532 105 HOH HOH . H 4 HOH B 33 533 73 HOH HOH . H 4 HOH B 34 534 164 HOH HOH . H 4 HOH B 35 535 184 HOH HOH . H 4 HOH B 36 536 11 HOH HOH . H 4 HOH B 37 537 287 HOH HOH . H 4 HOH B 38 538 96 HOH HOH . H 4 HOH B 39 539 188 HOH HOH . H 4 HOH B 40 540 60 HOH HOH . H 4 HOH B 41 541 70 HOH HOH . H 4 HOH B 42 542 80 HOH HOH . H 4 HOH B 43 543 274 HOH HOH . H 4 HOH B 44 544 282 HOH HOH . H 4 HOH B 45 545 65 HOH HOH . H 4 HOH B 46 546 55 HOH HOH . H 4 HOH B 47 547 174 HOH HOH . H 4 HOH B 48 548 150 HOH HOH . H 4 HOH B 49 549 278 HOH HOH . H 4 HOH B 50 550 2 HOH HOH . H 4 HOH B 51 551 199 HOH HOH . H 4 HOH B 52 552 112 HOH HOH . H 4 HOH B 53 553 95 HOH HOH . H 4 HOH B 54 554 53 HOH HOH . H 4 HOH B 55 555 21 HOH HOH . H 4 HOH B 56 556 123 HOH HOH . H 4 HOH B 57 557 108 HOH HOH . H 4 HOH B 58 558 125 HOH HOH . H 4 HOH B 59 559 167 HOH HOH . H 4 HOH B 60 560 259 HOH HOH . H 4 HOH B 61 561 176 HOH HOH . H 4 HOH B 62 562 231 HOH HOH . H 4 HOH B 63 563 211 HOH HOH . H 4 HOH B 64 564 38 HOH HOH . H 4 HOH B 65 565 265 HOH HOH . H 4 HOH B 66 566 131 HOH HOH . H 4 HOH B 67 567 136 HOH HOH . H 4 HOH B 68 568 90 HOH HOH . H 4 HOH B 69 569 37 HOH HOH . H 4 HOH B 70 570 64 HOH HOH . H 4 HOH B 71 571 230 HOH HOH . H 4 HOH B 72 572 210 HOH HOH . H 4 HOH B 73 573 283 HOH HOH . H 4 HOH B 74 574 56 HOH HOH . H 4 HOH B 75 575 179 HOH HOH . H 4 HOH B 76 576 118 HOH HOH . H 4 HOH B 77 577 23 HOH HOH . H 4 HOH B 78 578 255 HOH HOH . H 4 HOH B 79 579 114 HOH HOH . H 4 HOH B 80 580 49 HOH HOH . H 4 HOH B 81 581 243 HOH HOH . H 4 HOH B 82 582 221 HOH HOH . H 4 HOH B 83 583 157 HOH HOH . H 4 HOH B 84 584 31 HOH HOH . H 4 HOH B 85 585 71 HOH HOH . H 4 HOH B 86 586 103 HOH HOH . H 4 HOH B 87 587 240 HOH HOH . H 4 HOH B 88 588 279 HOH HOH . H 4 HOH B 89 589 92 HOH HOH . H 4 HOH B 90 590 66 HOH HOH . H 4 HOH B 91 591 111 HOH HOH . H 4 HOH B 92 592 187 HOH HOH . H 4 HOH B 93 593 43 HOH HOH . H 4 HOH B 94 594 25 HOH HOH . H 4 HOH B 95 595 241 HOH HOH . H 4 HOH B 96 596 41 HOH HOH . H 4 HOH B 97 597 294 HOH HOH . H 4 HOH B 98 598 155 HOH HOH . H 4 HOH B 99 599 72 HOH HOH . H 4 HOH B 100 600 30 HOH HOH . H 4 HOH B 101 601 263 HOH HOH . H 4 HOH B 102 602 172 HOH HOH . H 4 HOH B 103 603 135 HOH HOH . H 4 HOH B 104 604 269 HOH HOH . H 4 HOH B 105 605 186 HOH HOH . H 4 HOH B 106 606 117 HOH HOH . H 4 HOH B 107 607 142 HOH HOH . H 4 HOH B 108 608 295 HOH HOH . H 4 HOH B 109 609 200 HOH HOH . H 4 HOH B 110 610 254 HOH HOH . H 4 HOH B 111 611 239 HOH HOH . H 4 HOH B 112 612 58 HOH HOH . H 4 HOH B 113 613 109 HOH HOH . H 4 HOH B 114 614 69 HOH HOH . H 4 HOH B 115 615 51 HOH HOH . H 4 HOH B 116 616 228 HOH HOH . H 4 HOH B 117 617 113 HOH HOH . H 4 HOH B 118 618 201 HOH HOH . H 4 HOH B 119 619 285 HOH HOH . H 4 HOH B 120 620 268 HOH HOH . H 4 HOH B 121 621 257 HOH HOH . H 4 HOH B 122 622 267 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 PLP . . . C 2 40.137 -47.076 0.674 1 31.55 ? N1 PLP 401 A 1 HETATM 2 C C2 PLP . . . C 2 39.996 -48.44 0.675 1 33.33 ? C2 PLP 401 A 1 HETATM 3 C C2A PLP . . . C 2 40.474 -49.237 -0.497 1 33.49 ? C2A PLP 401 A 1 HETATM 4 C C3 PLP . . . C 2 39.418 -49.074 1.763 1 41.21 ? C3 PLP 401 A 1 HETATM 5 O O3 PLP . . . C 2 39.305 -50.439 1.738 1 40.14 ? O3 PLP 401 A 1 HETATM 6 C C4 PLP . . . C 2 38.977 -48.328 2.863 1 51.27 ? C4 PLP 401 A 1 HETATM 7 C C4A PLP . . . C 2 38.483 -49.056 4.084 1 63.68 ? C4A PLP 401 A 1 HETATM 8 O O4A PLP . . . C 2 37.511 -48.64 4.705 1 71.89 ? O4A PLP 401 A 1 HETATM 9 C C5 PLP . . . C 2 39.124 -46.94 2.855 1 47.37 ? C5 PLP 401 A 1 HETATM 10 C C6 PLP . . . C 2 39.7 -46.332 1.751 1 40.82 ? C6 PLP 401 A 1 HETATM 11 C C5A PLP . . . C 2 38.634 -46.052 3.974 1 43.95 ? C5A PLP 401 A 1 HETATM 12 O O4P PLP . . . C 2 39.49 -45.932 5.067 1 34.49 ? O4P PLP 401 A 1 HETATM 13 P P PLP . . . C 2 39.108 -44.932 6.266 1 28.58 ? P PLP 401 A 1 HETATM 14 O O1P PLP . . . C 2 38.345 -43.702 5.823 1 26.5 ? O1P PLP 401 A 1 HETATM 15 O O2P PLP . . . C 2 40.465 -44.528 6.791 1 31.49 ? O2P PLP 401 A 1 HETATM 16 O O3P PLP . . . C 2 38.254 -45.648 7.282 1 29.28 ? O3P PLP 401 A 1 HETATM 17 H H2A1 PLP . . . C 2 40.3 -50.297 -0.312 1 40.19 ? H2A1 PLP 401 A 1 HETATM 18 H H2A2 PLP . . . C 2 41.541 -49.064 -0.643 1 40.19 ? H2A2 PLP 401 A 1 HETATM 19 H H2A3 PLP . . . C 2 39.931 -48.93 -1.391 1 40.19 ? H2A3 PLP 401 A 1 HETATM 20 H HO3 PLP . . . C 2 39.297 -50.783 2.656 1 48.17 ? HO3 PLP 401 A 1 HETATM 21 H H4A PLP . . . C 2 38.979 -49.98 4.367 1 76.42 ? H4A PLP 401 A 1 HETATM 22 H H6 PLP . . . C 2 39.81 -45.248 1.733 1 48.98 ? H6 PLP 401 A 1 HETATM 23 H H5A1 PLP . . . C 2 37.68 -46.443 4.329 1 52.74 ? H5A1 PLP 401 A 1 HETATM 24 H H5A2 PLP . . . C 2 38.457 -45.056 3.568 1 52.74 ? H5A2 PLP 401 A 1 # _model_server_stats.io_time_ms 115 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #