data_3HT5 # _model_server_result.job_id SgKJf22Vkvbvo-NfunadRg _model_server_result.datetime_utc '2024-10-11 09:21:21' _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 3ht5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":6236}' # _entry.id 3HT5 # _exptl.entry_id 3HT5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 248.173 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _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 3HT5 _cell.length_a 65.454 _cell.length_b 85.351 _cell.length_c 59.715 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HT5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 65.454 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C8 H13 N2 O5 P' _chem_comp.formula_weight 248.173 _chem_comp.id PMP _chem_comp.mon_nstd_flag . _chem_comp.name "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "PYRIDOXAMINE-5'-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 PMP doub 260 n y N1 C6 PMP sing 261 n y C2 C2A PMP sing 262 n n C2 C3 PMP sing 263 n y C2A H2A1 PMP sing 264 n n C2A H2A2 PMP sing 265 n n C2A H2A3 PMP sing 266 n n C3 O3 PMP sing 267 n n C3 C4 PMP doub 268 n y O3 HO3 PMP sing 269 n n C4 C4A PMP sing 270 n n C4 C5 PMP sing 271 n y C4A N4A PMP sing 272 n n C4A H4A1 PMP sing 273 n n C4A H4A2 PMP sing 274 n n N4A HNA1 PMP sing 275 n n N4A HNA2 PMP sing 276 n n C5 C6 PMP doub 277 n y C5 C5A PMP sing 278 n n C6 H6 PMP sing 279 n n C5A O4P PMP sing 280 n n C5A H5A1 PMP sing 281 n n C5A H5A2 PMP sing 282 n n O4P P PMP sing 283 n n P O1P PMP doub 284 n n P O2P PMP sing 285 n n P O3P PMP sing 286 n n O2P HOP2 PMP sing 287 n n O3P HOP3 PMP sing 288 n n # _atom_sites.entry_id 3HT5 _atom_sites.fract_transf_matrix[1][1] 0.015278 _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] 0.011716 _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] 0.016746 _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 PMP A 1 6236 6236 PMP PMP . C 3 HOH A 1 369 369 HOH HOH . C 3 HOH A 2 370 370 HOH HOH . C 3 HOH A 3 371 371 HOH HOH . C 3 HOH A 4 372 372 HOH HOH . C 3 HOH A 5 373 373 HOH HOH . C 3 HOH A 6 374 374 HOH HOH . C 3 HOH A 7 375 375 HOH HOH . C 3 HOH A 8 376 376 HOH HOH . C 3 HOH A 9 377 377 HOH HOH . C 3 HOH A 10 378 378 HOH HOH . C 3 HOH A 11 379 379 HOH HOH . C 3 HOH A 12 380 380 HOH HOH . C 3 HOH A 13 381 381 HOH HOH . C 3 HOH A 14 382 382 HOH HOH . C 3 HOH A 15 383 383 HOH HOH . C 3 HOH A 16 384 384 HOH HOH . C 3 HOH A 17 385 385 HOH HOH . C 3 HOH A 18 386 386 HOH HOH . C 3 HOH A 19 387 387 HOH HOH . C 3 HOH A 20 388 388 HOH HOH . C 3 HOH A 21 389 389 HOH HOH . C 3 HOH A 22 390 390 HOH HOH . C 3 HOH A 23 391 391 HOH HOH . C 3 HOH A 24 392 392 HOH HOH . C 3 HOH A 25 393 393 HOH HOH . C 3 HOH A 26 394 394 HOH HOH . C 3 HOH A 27 395 395 HOH HOH . C 3 HOH A 28 396 396 HOH HOH . C 3 HOH A 29 397 397 HOH HOH . C 3 HOH A 30 398 398 HOH HOH . C 3 HOH A 31 399 399 HOH HOH . C 3 HOH A 32 400 400 HOH HOH . C 3 HOH A 33 401 401 HOH HOH . C 3 HOH A 34 402 402 HOH HOH . C 3 HOH A 35 403 403 HOH HOH . C 3 HOH A 36 405 405 HOH HOH . C 3 HOH A 37 406 406 HOH HOH . C 3 HOH A 38 407 407 HOH HOH . C 3 HOH A 39 408 408 HOH HOH . C 3 HOH A 40 409 409 HOH HOH . C 3 HOH A 41 410 410 HOH HOH . C 3 HOH A 42 411 411 HOH HOH . C 3 HOH A 43 412 412 HOH HOH . C 3 HOH A 44 413 413 HOH HOH . C 3 HOH A 45 415 415 HOH HOH . C 3 HOH A 46 416 416 HOH HOH . C 3 HOH A 47 417 417 HOH HOH . C 3 HOH A 48 418 418 HOH HOH . C 3 HOH A 49 419 419 HOH HOH . C 3 HOH A 50 420 420 HOH HOH . C 3 HOH A 51 421 421 HOH HOH . C 3 HOH A 52 422 422 HOH HOH . C 3 HOH A 53 423 423 HOH HOH . C 3 HOH A 54 424 424 HOH HOH . C 3 HOH A 55 425 425 HOH HOH . C 3 HOH A 56 427 427 HOH HOH . C 3 HOH A 57 428 428 HOH HOH . C 3 HOH A 58 429 429 HOH HOH . C 3 HOH A 59 430 430 HOH HOH . C 3 HOH A 60 431 431 HOH HOH . C 3 HOH A 61 432 432 HOH HOH . C 3 HOH A 62 433 433 HOH HOH . C 3 HOH A 63 434 434 HOH HOH . C 3 HOH A 64 435 435 HOH HOH . C 3 HOH A 65 436 436 HOH HOH . C 3 HOH A 66 437 437 HOH HOH . C 3 HOH A 67 438 438 HOH HOH . C 3 HOH A 68 439 439 HOH HOH . C 3 HOH A 69 441 441 HOH HOH . C 3 HOH A 70 442 442 HOH HOH . C 3 HOH A 71 443 443 HOH HOH . C 3 HOH A 72 444 444 HOH HOH . C 3 HOH A 73 445 445 HOH HOH . C 3 HOH A 74 446 446 HOH HOH . C 3 HOH A 75 447 447 HOH HOH . C 3 HOH A 76 448 448 HOH HOH . C 3 HOH A 77 449 449 HOH HOH . C 3 HOH A 78 450 450 HOH HOH . C 3 HOH A 79 451 451 HOH HOH . C 3 HOH A 80 452 452 HOH HOH . C 3 HOH A 81 453 453 HOH HOH . C 3 HOH A 82 454 454 HOH HOH . C 3 HOH A 83 455 455 HOH HOH . C 3 HOH A 84 457 457 HOH HOH . C 3 HOH A 85 458 458 HOH HOH . C 3 HOH A 86 460 460 HOH HOH . C 3 HOH A 87 461 461 HOH HOH . C 3 HOH A 88 462 462 HOH HOH . C 3 HOH A 89 463 463 HOH HOH . C 3 HOH A 90 464 464 HOH HOH . C 3 HOH A 91 465 465 HOH HOH . C 3 HOH A 92 466 466 HOH HOH . C 3 HOH A 93 467 467 HOH HOH . C 3 HOH A 94 468 468 HOH HOH . C 3 HOH A 95 469 469 HOH HOH . C 3 HOH A 96 470 470 HOH HOH . C 3 HOH A 97 473 473 HOH HOH . C 3 HOH A 98 474 474 HOH HOH . C 3 HOH A 99 476 476 HOH HOH . C 3 HOH A 100 477 477 HOH HOH . C 3 HOH A 101 478 478 HOH HOH . C 3 HOH A 102 479 479 HOH HOH . C 3 HOH A 103 480 480 HOH HOH . C 3 HOH A 104 481 481 HOH HOH . C 3 HOH A 105 482 482 HOH HOH . C 3 HOH A 106 483 483 HOH HOH . C 3 HOH A 107 484 484 HOH HOH . C 3 HOH A 108 485 485 HOH HOH . C 3 HOH A 109 486 486 HOH HOH . C 3 HOH A 110 488 488 HOH HOH . C 3 HOH A 111 490 490 HOH HOH . C 3 HOH A 112 491 491 HOH HOH . C 3 HOH A 113 492 492 HOH HOH . C 3 HOH A 114 496 496 HOH HOH . C 3 HOH A 115 498 498 HOH HOH . C 3 HOH A 116 500 500 HOH HOH . C 3 HOH A 117 501 501 HOH HOH . C 3 HOH A 118 502 502 HOH HOH . C 3 HOH A 119 503 503 HOH HOH . C 3 HOH A 120 507 507 HOH HOH . C 3 HOH A 121 510 510 HOH HOH . C 3 HOH A 122 511 511 HOH HOH . C 3 HOH A 123 512 512 HOH HOH . C 3 HOH A 124 513 513 HOH HOH . C 3 HOH A 125 514 514 HOH HOH . C 3 HOH A 126 516 516 HOH HOH . C 3 HOH A 127 517 517 HOH HOH . C 3 HOH A 128 518 518 HOH HOH . C 3 HOH A 129 519 519 HOH HOH . C 3 HOH A 130 520 520 HOH HOH . C 3 HOH A 131 523 523 HOH HOH . C 3 HOH A 132 524 524 HOH HOH . C 3 HOH A 133 526 526 HOH HOH . C 3 HOH A 134 527 527 HOH HOH . C 3 HOH A 135 528 528 HOH HOH . C 3 HOH A 136 529 529 HOH HOH . C 3 HOH A 137 530 530 HOH HOH . C 3 HOH A 138 531 531 HOH HOH . C 3 HOH A 139 533 533 HOH HOH . C 3 HOH A 140 534 534 HOH HOH . C 3 HOH A 141 536 536 HOH HOH . C 3 HOH A 142 537 537 HOH HOH . C 3 HOH A 143 538 538 HOH HOH . C 3 HOH A 144 539 539 HOH HOH . C 3 HOH A 145 540 540 HOH HOH . C 3 HOH A 146 541 541 HOH HOH . C 3 HOH A 147 542 542 HOH HOH . C 3 HOH A 148 543 543 HOH HOH . C 3 HOH A 149 544 544 HOH HOH . C 3 HOH A 150 545 545 HOH HOH . C 3 HOH A 151 546 546 HOH HOH . C 3 HOH A 152 547 547 HOH HOH . C 3 HOH A 153 548 548 HOH HOH . C 3 HOH A 154 550 550 HOH HOH . C 3 HOH A 155 553 553 HOH HOH . C 3 HOH A 156 554 554 HOH HOH . C 3 HOH A 157 557 557 HOH HOH . C 3 HOH A 158 558 558 HOH HOH . C 3 HOH A 159 559 559 HOH HOH . C 3 HOH A 160 560 560 HOH HOH . C 3 HOH A 161 561 561 HOH HOH . C 3 HOH A 162 562 562 HOH HOH . C 3 HOH A 163 563 563 HOH HOH . C 3 HOH A 164 564 564 HOH HOH . C 3 HOH A 165 565 565 HOH HOH . C 3 HOH A 166 567 567 HOH HOH . C 3 HOH A 167 575 575 HOH HOH . C 3 HOH A 168 576 576 HOH HOH . C 3 HOH A 169 579 579 HOH HOH . C 3 HOH A 170 580 580 HOH HOH . C 3 HOH A 171 581 581 HOH HOH . C 3 HOH A 172 582 582 HOH HOH . C 3 HOH A 173 584 584 HOH HOH . C 3 HOH A 174 588 588 HOH HOH . C 3 HOH A 175 589 589 HOH HOH . C 3 HOH A 176 590 590 HOH HOH . C 3 HOH A 177 591 591 HOH HOH . C 3 HOH A 178 592 592 HOH HOH . C 3 HOH A 179 593 593 HOH HOH . C 3 HOH A 180 595 595 HOH HOH . C 3 HOH A 181 596 596 HOH HOH . C 3 HOH A 182 597 597 HOH HOH . C 3 HOH A 183 598 598 HOH HOH . C 3 HOH A 184 605 605 HOH HOH . C 3 HOH A 185 607 607 HOH HOH . C 3 HOH A 186 609 609 HOH HOH . C 3 HOH A 187 611 611 HOH HOH . C 3 HOH A 188 612 612 HOH HOH . C 3 HOH A 189 613 613 HOH HOH . C 3 HOH A 190 614 614 HOH HOH . C 3 HOH A 191 619 619 HOH HOH . C 3 HOH A 192 624 624 HOH HOH . C 3 HOH A 193 628 628 HOH HOH . C 3 HOH A 194 629 629 HOH HOH . C 3 HOH A 195 630 630 HOH HOH . C 3 HOH A 196 633 633 HOH HOH . C 3 HOH A 197 634 634 HOH HOH . C 3 HOH A 198 637 637 HOH HOH . C 3 HOH A 199 643 643 HOH HOH . C 3 HOH A 200 644 644 HOH HOH . C 3 HOH A 201 645 645 HOH HOH . C 3 HOH A 202 646 646 HOH HOH . C 3 HOH A 203 647 647 HOH HOH . C 3 HOH A 204 649 649 HOH HOH . C 3 HOH A 205 651 651 HOH HOH . C 3 HOH A 206 652 652 HOH HOH . C 3 HOH A 207 654 654 HOH HOH . C 3 HOH A 208 657 657 HOH HOH . C 3 HOH A 209 658 658 HOH HOH . C 3 HOH A 210 659 659 HOH HOH . C 3 HOH A 211 660 660 HOH HOH . C 3 HOH A 212 661 661 HOH HOH . C 3 HOH A 213 662 662 HOH HOH . C 3 HOH A 214 663 663 HOH HOH . C 3 HOH A 215 664 664 HOH HOH . C 3 HOH A 216 666 666 HOH HOH . C 3 HOH A 217 669 669 HOH HOH . C 3 HOH A 218 671 671 HOH HOH . C 3 HOH A 219 672 672 HOH HOH . C 3 HOH A 220 674 674 HOH HOH . C 3 HOH A 221 675 675 HOH HOH . C 3 HOH A 222 676 676 HOH HOH . C 3 HOH A 223 677 677 HOH HOH . C 3 HOH A 224 679 679 HOH HOH . C 3 HOH A 225 680 680 HOH HOH . C 3 HOH A 226 681 681 HOH HOH . C 3 HOH A 227 683 683 HOH HOH . C 3 HOH A 228 684 684 HOH HOH . C 3 HOH A 229 686 686 HOH HOH . C 3 HOH A 230 687 687 HOH HOH . C 3 HOH A 231 689 689 HOH HOH . C 3 HOH A 232 697 697 HOH HOH . C 3 HOH A 233 705 705 HOH HOH . C 3 HOH A 234 709 709 HOH HOH . C 3 HOH A 235 710 710 HOH HOH . C 3 HOH A 236 713 713 HOH HOH . C 3 HOH A 237 717 717 HOH HOH . C 3 HOH A 238 718 718 HOH HOH . C 3 HOH A 239 722 722 HOH HOH . C 3 HOH A 240 725 725 HOH HOH . C 3 HOH A 241 728 728 HOH HOH . C 3 HOH A 242 735 735 HOH HOH . C 3 HOH A 243 740 740 HOH HOH . C 3 HOH A 244 741 741 HOH HOH . C 3 HOH A 245 742 742 HOH HOH . C 3 HOH A 246 747 747 HOH HOH . C 3 HOH A 247 748 748 HOH HOH . C 3 HOH A 248 750 750 HOH HOH . C 3 HOH A 249 751 751 HOH HOH . C 3 HOH A 250 752 752 HOH HOH . C 3 HOH A 251 753 753 HOH HOH . C 3 HOH A 252 754 754 HOH HOH . C 3 HOH A 253 755 755 HOH HOH . C 3 HOH A 254 756 756 HOH HOH . C 3 HOH A 255 757 757 HOH HOH . C 3 HOH A 256 759 759 HOH HOH . C 3 HOH A 257 760 760 HOH HOH . C 3 HOH A 258 761 761 HOH HOH . C 3 HOH A 259 762 762 HOH HOH . C 3 HOH A 260 764 764 HOH HOH . C 3 HOH A 261 766 766 HOH HOH . C 3 HOH A 262 768 768 HOH HOH . C 3 HOH A 263 769 769 HOH HOH . C 3 HOH A 264 770 770 HOH HOH . C 3 HOH A 265 771 771 HOH HOH . C 3 HOH A 266 772 772 HOH HOH . C 3 HOH A 267 773 773 HOH HOH . C 3 HOH A 268 774 774 HOH HOH . C 3 HOH A 269 775 775 HOH HOH . C 3 HOH A 270 776 776 HOH HOH . C 3 HOH A 271 777 777 HOH HOH . C 3 HOH A 272 778 778 HOH HOH . C 3 HOH A 273 782 782 HOH HOH . C 3 HOH A 274 783 783 HOH HOH . C 3 HOH A 275 784 784 HOH HOH . C 3 HOH A 276 785 785 HOH HOH . C 3 HOH A 277 786 786 HOH HOH . C 3 HOH A 278 787 787 HOH HOH . C 3 HOH A 279 788 788 HOH HOH . C 3 HOH A 280 789 789 HOH HOH . C 3 HOH A 281 790 790 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 PMP . . . B 2 29.753 14.201 20.246 1 20 ? N1 PMP 6236 A 1 HETATM 2 C C2 PMP . . . B 2 29.603 13.363 19.207 1 20 ? C2 PMP 6236 A 1 HETATM 3 C C2A PMP . . . B 2 29.365 11.909 19.438 1 20 ? C2A PMP 6236 A 1 HETATM 4 C C3 PMP . . . B 2 29.6 13.856 17.91 1 20 ? C3 PMP 6236 A 1 HETATM 5 O O3 PMP . . . B 2 29.387 13.06 16.851 1 20 ? O3 PMP 6236 A 1 HETATM 6 C C4 PMP . . . B 2 29.774 15.242 17.729 1 20 ? C4 PMP 6236 A 1 HETATM 7 C C4A PMP . . . B 2 29.762 15.785 16.329 1 20 ? C4A PMP 6236 A 1 HETATM 8 N N4A PMP . . . B 2 31.075 15.514 15.882 1 20 ? N4A PMP 6236 A 1 HETATM 9 C C5 PMP . . . B 2 29.963 16.061 18.815 1 20 ? C5 PMP 6236 A 1 HETATM 10 C C6 PMP . . . B 2 29.924 15.513 20.069 1 20 ? C6 PMP 6236 A 1 HETATM 11 C C5A PMP . . . B 2 30.246 17.536 18.658 1 20 ? C5A PMP 6236 A 1 HETATM 12 O O4P PMP . . . B 2 31.416 17.753 17.996 1 20 ? O4P PMP 6236 A 1 HETATM 13 P P PMP . . . B 2 31.775 19.071 17.279 1 20 ? P PMP 6236 A 1 HETATM 14 O O1P PMP . . . B 2 30.975 19.12 16.098 1 20 ? O1P PMP 6236 A 1 HETATM 15 O O2P PMP . . . B 2 31.452 20.157 18.085 1 20 ? O2P PMP 6236 A 1 HETATM 16 O O3P PMP . . . B 2 33.143 19.031 16.942 1 20 ? O3P PMP 6236 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 16 #