data_3LDF # _model_server_result.job_id hQUDIA0XNuEUY-qPgQADfQ _model_server_result.datetime_utc '2024-11-04 23:01:04' _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 3ldf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 3LDF # _exptl.entry_id 3LDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 107.14 _cell.angle_gamma 90 _cell.entry_id 3LDF _cell.length_a 165.684 _cell.length_b 50.828 _cell.length_c 59.569 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _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 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 N CA SAH sing 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 3LDF _atom_sites.fract_transf_matrix[1][1] 0.006036 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001862 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019674 _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] 0.017568 _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 SAH A 1 401 401 SAH SAH . C 3 HOH A 1 501 501 HOH HOH . C 3 HOH A 2 502 502 HOH HOH . C 3 HOH A 3 503 503 HOH HOH . C 3 HOH A 4 504 504 HOH HOH . C 3 HOH A 5 505 505 HOH HOH . C 3 HOH A 6 506 506 HOH HOH . C 3 HOH A 7 507 507 HOH HOH . C 3 HOH A 8 508 508 HOH HOH . C 3 HOH A 9 509 509 HOH HOH . C 3 HOH A 10 510 510 HOH HOH . C 3 HOH A 11 511 511 HOH HOH . C 3 HOH A 12 512 512 HOH HOH . C 3 HOH A 13 513 513 HOH HOH . C 3 HOH A 14 514 514 HOH HOH . C 3 HOH A 15 515 515 HOH HOH . C 3 HOH A 16 516 516 HOH HOH . C 3 HOH A 17 517 517 HOH HOH . C 3 HOH A 18 518 518 HOH HOH . C 3 HOH A 19 519 519 HOH HOH . C 3 HOH A 20 520 520 HOH HOH . C 3 HOH A 21 521 521 HOH HOH . C 3 HOH A 22 522 522 HOH HOH . C 3 HOH A 23 523 523 HOH HOH . C 3 HOH A 24 524 524 HOH HOH . C 3 HOH A 25 525 525 HOH HOH . C 3 HOH A 26 526 526 HOH HOH . C 3 HOH A 27 527 527 HOH HOH . C 3 HOH A 28 528 528 HOH HOH . C 3 HOH A 29 529 529 HOH HOH . C 3 HOH A 30 530 530 HOH HOH . C 3 HOH A 31 531 1 HOH HOH . C 3 HOH A 32 532 532 HOH HOH . C 3 HOH A 33 533 533 HOH HOH . C 3 HOH A 34 534 534 HOH HOH . C 3 HOH A 35 535 535 HOH HOH . C 3 HOH A 36 536 536 HOH HOH . C 3 HOH A 37 537 537 HOH HOH . C 3 HOH A 38 538 538 HOH HOH . C 3 HOH A 39 539 539 HOH HOH . C 3 HOH A 40 540 540 HOH HOH . C 3 HOH A 41 541 541 HOH HOH . C 3 HOH A 42 542 542 HOH HOH . C 3 HOH A 43 543 543 HOH HOH . C 3 HOH A 44 544 544 HOH HOH . C 3 HOH A 45 545 545 HOH HOH . C 3 HOH A 46 546 546 HOH HOH . C 3 HOH A 47 547 547 HOH HOH . C 3 HOH A 48 548 548 HOH HOH . C 3 HOH A 49 549 549 HOH HOH . C 3 HOH A 50 550 550 HOH HOH . C 3 HOH A 51 551 551 HOH HOH . C 3 HOH A 52 552 552 HOH HOH . C 3 HOH A 53 553 553 HOH HOH . C 3 HOH A 54 554 554 HOH HOH . C 3 HOH A 55 555 555 HOH HOH . C 3 HOH A 56 556 556 HOH HOH . C 3 HOH A 57 557 557 HOH HOH . C 3 HOH A 58 558 558 HOH HOH . C 3 HOH A 59 559 559 HOH HOH . C 3 HOH A 60 560 560 HOH HOH . C 3 HOH A 61 561 561 HOH HOH . C 3 HOH A 62 562 562 HOH HOH . C 3 HOH A 63 563 563 HOH HOH . C 3 HOH A 64 564 564 HOH HOH . C 3 HOH A 65 565 565 HOH HOH . C 3 HOH A 66 566 566 HOH HOH . C 3 HOH A 67 567 567 HOH HOH . C 3 HOH A 68 568 568 HOH HOH . C 3 HOH A 69 569 569 HOH HOH . C 3 HOH A 70 570 570 HOH HOH . C 3 HOH A 71 571 571 HOH HOH . C 3 HOH A 72 572 572 HOH HOH . C 3 HOH A 73 573 573 HOH HOH . C 3 HOH A 74 574 2 HOH HOH . C 3 HOH A 75 575 3 HOH HOH . C 3 HOH A 76 576 576 HOH HOH . C 3 HOH A 77 577 5 HOH HOH . C 3 HOH A 78 578 6 HOH HOH . C 3 HOH A 79 579 579 HOH HOH . C 3 HOH A 80 580 580 HOH HOH . C 3 HOH A 81 581 581 HOH HOH . C 3 HOH A 82 582 582 HOH HOH . C 3 HOH A 83 583 583 HOH HOH . C 3 HOH A 84 584 584 HOH HOH . C 3 HOH A 85 585 585 HOH HOH . C 3 HOH A 86 586 586 HOH HOH . C 3 HOH A 87 587 587 HOH HOH . C 3 HOH A 88 588 588 HOH HOH . C 3 HOH A 89 589 589 HOH HOH . C 3 HOH A 90 590 590 HOH HOH . C 3 HOH A 91 591 591 HOH HOH . C 3 HOH A 92 592 592 HOH HOH . C 3 HOH A 93 593 593 HOH HOH . C 3 HOH A 94 594 594 HOH HOH . C 3 HOH A 95 595 595 HOH HOH . C 3 HOH A 96 596 596 HOH HOH . C 3 HOH A 97 597 597 HOH HOH . C 3 HOH A 98 598 598 HOH HOH . C 3 HOH A 99 599 599 HOH HOH . C 3 HOH A 100 600 600 HOH HOH . C 3 HOH A 101 601 601 HOH HOH . C 3 HOH A 102 602 602 HOH HOH . C 3 HOH A 103 603 603 HOH HOH . C 3 HOH A 104 604 604 HOH HOH . C 3 HOH A 105 605 605 HOH HOH . C 3 HOH A 106 606 606 HOH HOH . C 3 HOH A 107 607 607 HOH HOH . C 3 HOH A 108 608 608 HOH HOH . C 3 HOH A 109 609 609 HOH HOH . C 3 HOH A 110 610 610 HOH HOH . C 3 HOH A 111 611 611 HOH HOH . C 3 HOH A 112 612 612 HOH HOH . C 3 HOH A 113 613 613 HOH HOH . C 3 HOH A 114 614 614 HOH HOH . C 3 HOH A 115 615 615 HOH HOH . C 3 HOH A 116 616 616 HOH HOH . C 3 HOH A 117 617 617 HOH HOH . C 3 HOH A 118 618 618 HOH HOH . C 3 HOH A 119 619 619 HOH HOH . C 3 HOH A 120 620 620 HOH HOH . C 3 HOH A 121 621 621 HOH HOH . C 3 HOH A 122 622 622 HOH HOH . C 3 HOH A 123 623 623 HOH HOH . C 3 HOH A 124 624 624 HOH HOH . C 3 HOH A 125 625 625 HOH HOH . C 3 HOH A 126 626 626 HOH HOH . C 3 HOH A 127 627 627 HOH HOH . C 3 HOH A 128 628 628 HOH HOH . C 3 HOH A 129 629 629 HOH HOH . C 3 HOH A 130 630 630 HOH HOH . C 3 HOH A 131 631 631 HOH HOH . C 3 HOH A 132 632 632 HOH HOH . C 3 HOH A 133 633 633 HOH HOH . C 3 HOH A 134 634 634 HOH HOH . C 3 HOH A 135 635 635 HOH HOH . C 3 HOH A 136 636 7 HOH HOH . C 3 HOH A 137 637 637 HOH HOH . C 3 HOH A 138 638 8 HOH HOH . C 3 HOH A 139 639 9 HOH HOH . C 3 HOH A 140 640 10 HOH HOH . C 3 HOH A 141 641 11 HOH HOH . C 3 HOH A 142 642 12 HOH HOH . C 3 HOH A 143 643 13 HOH HOH . C 3 HOH A 144 644 14 HOH HOH . C 3 HOH A 145 645 15 HOH HOH . C 3 HOH A 146 646 16 HOH HOH . C 3 HOH A 147 647 17 HOH HOH . C 3 HOH A 148 648 18 HOH HOH . C 3 HOH A 149 649 19 HOH HOH . C 3 HOH A 150 650 20 HOH HOH . C 3 HOH A 151 651 21 HOH HOH . C 3 HOH A 152 652 22 HOH HOH . C 3 HOH A 153 653 23 HOH HOH . C 3 HOH A 154 654 24 HOH HOH . C 3 HOH A 155 655 25 HOH HOH . C 3 HOH A 156 656 26 HOH HOH . C 3 HOH A 157 657 27 HOH HOH . C 3 HOH A 158 658 28 HOH HOH . C 3 HOH A 159 659 29 HOH HOH . C 3 HOH A 160 660 30 HOH HOH . C 3 HOH A 161 661 31 HOH HOH . C 3 HOH A 162 662 32 HOH HOH . C 3 HOH A 163 663 33 HOH HOH . C 3 HOH A 164 664 34 HOH HOH . C 3 HOH A 165 665 35 HOH HOH . C 3 HOH A 166 666 36 HOH HOH . C 3 HOH A 167 667 37 HOH HOH . C 3 HOH A 168 668 38 HOH HOH . C 3 HOH A 169 669 39 HOH HOH . C 3 HOH A 170 670 40 HOH HOH . C 3 HOH A 171 671 41 HOH HOH . C 3 HOH A 172 672 42 HOH HOH . C 3 HOH A 173 673 43 HOH HOH . C 3 HOH A 174 674 44 HOH HOH . C 3 HOH A 175 675 46 HOH HOH . C 3 HOH A 176 676 47 HOH HOH . C 3 HOH A 177 677 48 HOH HOH . C 3 HOH A 178 678 49 HOH HOH . C 3 HOH A 179 679 50 HOH HOH . C 3 HOH A 180 680 51 HOH HOH . C 3 HOH A 181 681 52 HOH HOH . C 3 HOH A 182 682 53 HOH HOH . C 3 HOH A 183 683 54 HOH HOH . C 3 HOH A 184 684 56 HOH HOH . C 3 HOH A 185 685 58 HOH HOH . C 3 HOH A 186 686 59 HOH HOH . C 3 HOH A 187 687 60 HOH HOH . C 3 HOH A 188 688 61 HOH HOH . C 3 HOH A 189 689 62 HOH HOH . C 3 HOH A 190 690 63 HOH HOH . C 3 HOH A 191 691 64 HOH HOH . C 3 HOH A 192 692 65 HOH HOH . C 3 HOH A 193 693 66 HOH HOH . C 3 HOH A 194 694 67 HOH HOH . C 3 HOH A 195 695 68 HOH HOH . C 3 HOH A 196 696 69 HOH HOH . C 3 HOH A 197 697 70 HOH HOH . C 3 HOH A 198 698 71 HOH HOH . C 3 HOH A 199 699 72 HOH HOH . C 3 HOH A 200 700 73 HOH HOH . C 3 HOH A 201 701 74 HOH HOH . C 3 HOH A 202 702 75 HOH HOH . C 3 HOH A 203 703 76 HOH HOH . C 3 HOH A 204 704 77 HOH HOH . C 3 HOH A 205 705 78 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 N SAH . . . B 2 32.281 -6.799 10.343 1 15.64 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . B 2 31.291 -7.254 9.314 1 16.52 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . B 2 29.843 -7.28 9.905 1 15.21 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . B 2 29.63 -8.436 10.947 1 18.03 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . B 2 28.069 -9.307 10.73 1 21.6 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . B 2 31.508 -6.374 8.121 1 16.65 ? C SAH 401 A 1 HETATM 7 O O SAH . . . B 2 32.499 -5.586 8.107 1 15.46 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . B 2 30.681 -6.409 7.174 1 15.95 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . B 2 28.327 -10.65 11.894 1 15.98 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . B 2 29.158 -11.837 11.348 1 18.62 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . B 2 29.836 -12.522 12.416 1 15.38 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . B 2 28.338 -12.93 10.626 1 16.76 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . B 2 28.905 -13.058 9.327 1 16.14 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . B 2 28.607 -14.247 11.35 1 16.54 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . B 2 28.915 -15.283 10.402 1 17.4 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . B 2 29.917 -13.929 12.1 1 18.18 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . B 2 30.195 -14.678 13.367 1 16.99 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . B 2 29.379 -14.807 14.478 1 14.92 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . B 2 30.02 -15.511 15.454 1 18.44 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . B 2 31.259 -15.829 14.976 1 15.74 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . B 2 32.451 -16.535 15.475 1 18.18 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . B 2 32.439 -17.067 16.733 1 15.3 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . B 2 33.556 -16.61 14.665 1 16.56 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . B 2 33.582 -16.093 13.414 1 19.07 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . B 2 32.536 -15.423 12.903 1 19.75 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . B 2 31.366 -15.278 13.609 1 15.74 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #