data_3EVD # _model_server_result.job_id ffRbWMzS9X0DQx3upsRKDA _model_server_result.datetime_utc '2024-11-24 21:37:39' _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 3evd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":903}' # _entry.id 3EVD # _exptl.entry_id 3EVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _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 90 _cell.angle_gamma 120 _cell.entry_id 3EVD _cell.length_a 104.958 _cell.length_b 104.958 _cell.length_c 51.902 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 3 _struct_asym.id D _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 327 n n N HN1 SAH sing 328 n n N HN2 SAH sing 329 n n CA CB SAH sing 330 n n CA C SAH sing 331 n n CA HA SAH sing 332 n n CB CG SAH sing 333 n n CB HB1 SAH sing 334 n n CB HB2 SAH sing 335 n n CG SD SAH sing 336 n n CG HG1 SAH sing 337 n n CG HG2 SAH sing 338 n n SD C5' SAH sing 339 n n C O SAH doub 340 n n C OXT SAH sing 341 n n OXT HXT SAH sing 342 n n C5' C4' SAH sing 343 n n C5' "H5'1" SAH sing 344 n n C5' "H5'2" SAH sing 345 n n C4' O4' SAH sing 346 n n C4' C3' SAH sing 347 n n C4' H4' SAH sing 348 n n O4' C1' SAH sing 349 n n C3' O3' SAH sing 350 n n C3' C2' SAH sing 351 n n C3' H3' SAH sing 352 n n O3' HO3' SAH sing 353 n n C2' O2' SAH sing 354 n n C2' C1' SAH sing 355 n n C2' H2' SAH sing 356 n n O2' HO2' SAH sing 357 n n C1' N9 SAH sing 358 n n C1' H1' SAH sing 359 n n N9 C8 SAH sing 360 n y N9 C4 SAH sing 361 n y C8 N7 SAH doub 362 n y C8 H8 SAH sing 363 n n N7 C5 SAH sing 364 n y C5 C6 SAH sing 365 n y C5 C4 SAH doub 366 n y C6 N6 SAH sing 367 n n C6 N1 SAH doub 368 n y N6 HN61 SAH sing 369 n n N6 HN62 SAH sing 370 n n N1 C2 SAH sing 371 n y C2 N3 SAH doub 372 n y C2 H2 SAH sing 373 n n N3 C4 SAH sing 374 n y # _atom_sites.entry_id 3EVD _atom_sites.fract_transf_matrix[1][1] 0.009528 _atom_sites.fract_transf_matrix[1][2] 0.005501 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011002 _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] 0.019267 _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 GTP A 1 901 1001 GTP GTP . C 2 GTP A 1 902 1002 GTP GTP . D 3 SAH A 1 903 901 SAH SAH . E 4 HOH A 1 501 501 HOH HOH . E 4 HOH A 2 502 502 HOH HOH . E 4 HOH A 3 503 503 HOH HOH . E 4 HOH A 4 504 504 HOH HOH . E 4 HOH A 5 505 505 HOH HOH . E 4 HOH A 6 506 506 HOH HOH . E 4 HOH A 7 507 507 HOH HOH . E 4 HOH A 8 508 508 HOH HOH . E 4 HOH A 9 509 509 HOH HOH . E 4 HOH A 10 510 510 HOH HOH . E 4 HOH A 11 511 511 HOH HOH . E 4 HOH A 12 512 512 HOH HOH . E 4 HOH A 13 513 513 HOH HOH . E 4 HOH A 14 514 514 HOH HOH . E 4 HOH A 15 515 515 HOH HOH . E 4 HOH A 16 516 516 HOH HOH . E 4 HOH A 17 517 517 HOH HOH . E 4 HOH A 18 518 518 HOH HOH . E 4 HOH A 19 519 519 HOH HOH . E 4 HOH A 20 520 520 HOH HOH . E 4 HOH A 21 521 521 HOH HOH . E 4 HOH A 22 522 522 HOH HOH . E 4 HOH A 23 523 523 HOH HOH . E 4 HOH A 24 524 524 HOH HOH . E 4 HOH A 25 525 525 HOH HOH . E 4 HOH A 26 526 526 HOH HOH . E 4 HOH A 27 527 527 HOH HOH . E 4 HOH A 28 528 528 HOH HOH . E 4 HOH A 29 529 529 HOH HOH . E 4 HOH A 30 530 530 HOH HOH . E 4 HOH A 31 531 531 HOH HOH . E 4 HOH A 32 532 532 HOH HOH . E 4 HOH A 33 533 533 HOH HOH . E 4 HOH A 34 534 534 HOH HOH . E 4 HOH A 35 535 535 HOH HOH . E 4 HOH A 36 536 536 HOH HOH . E 4 HOH A 37 537 537 HOH HOH . E 4 HOH A 38 538 538 HOH HOH . E 4 HOH A 39 539 539 HOH HOH . E 4 HOH A 40 540 540 HOH HOH . E 4 HOH A 41 541 541 HOH HOH . E 4 HOH A 42 542 542 HOH HOH . E 4 HOH A 43 543 543 HOH HOH . E 4 HOH A 44 544 544 HOH HOH . E 4 HOH A 45 545 545 HOH HOH . E 4 HOH A 46 546 546 HOH HOH . E 4 HOH A 47 547 547 HOH HOH . E 4 HOH A 48 548 548 HOH HOH . E 4 HOH A 49 549 549 HOH HOH . E 4 HOH A 50 550 550 HOH HOH . E 4 HOH A 51 551 551 HOH HOH . E 4 HOH A 52 552 552 HOH HOH . E 4 HOH A 53 553 553 HOH HOH . E 4 HOH A 54 554 554 HOH HOH . E 4 HOH A 55 555 555 HOH HOH . E 4 HOH A 56 556 556 HOH HOH . E 4 HOH A 57 557 557 HOH HOH . E 4 HOH A 58 558 558 HOH HOH . E 4 HOH A 59 559 559 HOH HOH . E 4 HOH A 60 560 560 HOH HOH . E 4 HOH A 61 561 561 HOH HOH . E 4 HOH A 62 562 562 HOH HOH . E 4 HOH A 63 563 563 HOH HOH . E 4 HOH A 64 564 564 HOH HOH . E 4 HOH A 65 565 565 HOH HOH . E 4 HOH A 66 566 566 HOH HOH . E 4 HOH A 67 567 567 HOH HOH . E 4 HOH A 68 568 568 HOH HOH . E 4 HOH A 69 569 569 HOH HOH . E 4 HOH A 70 570 570 HOH HOH . E 4 HOH A 71 571 571 HOH HOH . E 4 HOH A 72 572 572 HOH HOH . E 4 HOH A 73 573 573 HOH HOH . E 4 HOH A 74 574 574 HOH HOH . E 4 HOH A 75 575 575 HOH HOH . E 4 HOH A 76 576 576 HOH HOH . E 4 HOH A 77 577 577 HOH HOH . E 4 HOH A 78 578 578 HOH HOH . E 4 HOH A 79 579 579 HOH HOH . E 4 HOH A 80 580 580 HOH HOH . E 4 HOH A 81 581 581 HOH HOH . E 4 HOH A 82 582 582 HOH HOH . E 4 HOH A 83 583 583 HOH HOH . E 4 HOH A 84 584 584 HOH HOH . E 4 HOH A 85 585 585 HOH HOH . E 4 HOH A 86 586 586 HOH HOH . E 4 HOH A 87 587 587 HOH HOH . E 4 HOH A 88 588 588 HOH HOH . E 4 HOH A 89 589 589 HOH HOH . E 4 HOH A 90 590 590 HOH HOH . E 4 HOH A 91 591 591 HOH HOH . E 4 HOH A 92 592 592 HOH HOH . E 4 HOH A 93 593 593 HOH HOH . E 4 HOH A 94 594 594 HOH HOH . E 4 HOH A 95 595 595 HOH HOH . E 4 HOH A 96 596 596 HOH HOH . E 4 HOH A 97 597 597 HOH HOH . E 4 HOH A 98 598 598 HOH HOH . E 4 HOH A 99 599 599 HOH HOH . E 4 HOH A 100 600 600 HOH HOH . E 4 HOH A 101 601 601 HOH HOH . E 4 HOH A 102 602 602 HOH HOH . E 4 HOH A 103 603 603 HOH HOH . E 4 HOH A 104 604 604 HOH HOH . E 4 HOH A 105 605 605 HOH HOH . E 4 HOH A 106 606 606 HOH HOH . E 4 HOH A 107 607 607 HOH HOH . E 4 HOH A 108 608 608 HOH HOH . E 4 HOH A 109 609 609 HOH HOH . E 4 HOH A 110 610 610 HOH HOH . E 4 HOH A 111 611 611 HOH HOH . E 4 HOH A 112 612 612 HOH HOH . E 4 HOH A 113 613 613 HOH HOH . E 4 HOH A 114 614 614 HOH HOH . E 4 HOH A 115 615 615 HOH HOH . E 4 HOH A 116 616 616 HOH HOH . E 4 HOH A 117 617 617 HOH HOH . E 4 HOH A 118 618 618 HOH HOH . E 4 HOH A 119 619 619 HOH HOH . E 4 HOH A 120 620 620 HOH HOH . E 4 HOH A 121 621 621 HOH HOH . E 4 HOH A 122 622 622 HOH HOH . E 4 HOH A 123 623 623 HOH HOH . E 4 HOH A 124 624 624 HOH HOH . E 4 HOH A 125 625 625 HOH HOH . E 4 HOH A 126 626 626 HOH HOH . E 4 HOH A 127 627 627 HOH HOH . E 4 HOH A 128 628 628 HOH HOH . E 4 HOH A 129 629 629 HOH HOH . E 4 HOH A 130 630 630 HOH HOH . E 4 HOH A 131 631 631 HOH HOH . E 4 HOH A 132 632 632 HOH HOH . E 4 HOH A 133 633 633 HOH HOH . E 4 HOH A 134 634 634 HOH HOH . E 4 HOH A 135 635 635 HOH HOH . E 4 HOH A 136 636 636 HOH HOH . E 4 HOH A 137 637 637 HOH HOH . E 4 HOH A 138 638 638 HOH HOH . E 4 HOH A 139 639 639 HOH HOH . E 4 HOH A 140 640 640 HOH HOH . E 4 HOH A 141 641 641 HOH HOH . E 4 HOH A 142 642 642 HOH HOH . E 4 HOH A 143 643 643 HOH HOH . E 4 HOH A 144 644 644 HOH HOH . E 4 HOH A 145 645 645 HOH HOH . E 4 HOH A 146 646 646 HOH HOH . E 4 HOH A 147 647 647 HOH HOH . E 4 HOH A 148 648 648 HOH HOH . E 4 HOH A 149 649 649 HOH HOH . E 4 HOH A 150 650 650 HOH HOH . E 4 HOH A 151 651 651 HOH HOH . E 4 HOH A 152 652 652 HOH HOH . E 4 HOH A 153 653 653 HOH HOH . E 4 HOH A 154 654 654 HOH HOH . E 4 HOH A 155 655 655 HOH HOH . E 4 HOH A 156 656 656 HOH HOH . E 4 HOH A 157 657 657 HOH HOH . E 4 HOH A 158 658 658 HOH HOH . E 4 HOH A 159 659 659 HOH HOH . E 4 HOH A 160 660 660 HOH HOH . E 4 HOH A 161 661 661 HOH HOH . E 4 HOH A 162 662 662 HOH HOH . E 4 HOH A 163 663 663 HOH HOH . E 4 HOH A 164 664 664 HOH HOH . E 4 HOH A 165 665 665 HOH HOH . E 4 HOH A 166 667 667 HOH HOH . E 4 HOH A 167 668 668 HOH HOH . E 4 HOH A 168 669 669 HOH HOH . E 4 HOH A 169 670 670 HOH HOH . E 4 HOH A 170 671 671 HOH HOH . E 4 HOH A 171 672 672 HOH HOH . E 4 HOH A 172 673 673 HOH HOH . E 4 HOH A 173 674 674 HOH HOH . E 4 HOH A 174 675 675 HOH HOH . E 4 HOH A 175 676 676 HOH HOH . E 4 HOH A 176 677 677 HOH HOH . E 4 HOH A 177 678 678 HOH HOH . E 4 HOH A 178 679 679 HOH HOH . E 4 HOH A 179 680 680 HOH HOH . E 4 HOH A 180 681 681 HOH HOH . E 4 HOH A 181 682 682 HOH HOH . E 4 HOH A 182 683 683 HOH HOH . E 4 HOH A 183 684 684 HOH HOH . E 4 HOH A 184 685 685 HOH HOH . E 4 HOH A 185 686 686 HOH HOH . E 4 HOH A 186 687 687 HOH HOH . E 4 HOH A 187 688 688 HOH HOH . E 4 HOH A 188 689 689 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 . . . D 3 24.635 29.931 -26.838 1 15.79 ? N SAH 903 A 1 HETATM 2 C CA SAH . . . D 3 25.701 30.938 -26.958 1 16.84 ? CA SAH 903 A 1 HETATM 3 C CB SAH . . . D 3 26.496 30.701 -28.245 1 20.79 ? CB SAH 903 A 1 HETATM 4 C CG SAH . . . D 3 27.33 29.422 -28.153 1 22.49 ? CG SAH 903 A 1 HETATM 5 S SD SAH . . . D 3 28.401 29.164 -29.615 1 25.9 ? SD SAH 903 A 1 HETATM 6 C C SAH . . . D 3 25.082 32.334 -26.996 1 17.4 ? C SAH 903 A 1 HETATM 7 O O SAH . . . D 3 25.866 33.296 -27.132 1 17.65 ? O SAH 903 A 1 HETATM 8 O OXT SAH . . . D 3 23.839 32.416 -26.86 1 17.2 ? OXT SAH 903 A 1 HETATM 9 C C5' SAH . . . D 3 29.363 27.715 -29.05 1 22.42 ? C5' SAH 903 A 1 HETATM 10 C C4' SAH . . . D 3 30.481 28.076 -28.07 1 21.26 ? C4' SAH 903 A 1 HETATM 11 O O4' SAH . . . D 3 31.015 26.843 -27.563 1 20.59 ? O4' SAH 903 A 1 HETATM 12 C C3' SAH . . . D 3 31.636 28.815 -28.755 1 20.94 ? C3' SAH 903 A 1 HETATM 13 O O3' SAH . . . D 3 32.006 29.966 -27.991 1 23.33 ? O3' SAH 903 A 1 HETATM 14 C C2' SAH . . . D 3 32.766 27.785 -28.733 1 20.68 ? C2' SAH 903 A 1 HETATM 15 O O2' SAH . . . D 3 34.016 28.46 -28.562 1 20.59 ? O2' SAH 903 A 1 HETATM 16 C C1' SAH . . . D 3 32.428 27.05 -27.437 1 21.31 ? C1' SAH 903 A 1 HETATM 17 N N9 SAH . . . D 3 33.083 25.726 -27.365 1 20.7 ? N9 SAH 903 A 1 HETATM 18 C C8 SAH . . . D 3 33.293 24.894 -28.379 1 20.69 ? C8 SAH 903 A 1 HETATM 19 N N7 SAH . . . D 3 33.852 23.77 -27.926 1 21.24 ? N7 SAH 903 A 1 HETATM 20 C C5 SAH . . . D 3 34.002 23.89 -26.618 1 19.29 ? C5 SAH 903 A 1 HETATM 21 C C6 SAH . . . D 3 34.501 23.065 -25.611 1 19.67 ? C6 SAH 903 A 1 HETATM 22 N N6 SAH . . . D 3 34.996 21.866 -25.913 1 22.12 ? N6 SAH 903 A 1 HETATM 23 N N1 SAH . . . D 3 34.488 23.498 -24.35 1 19.32 ? N1 SAH 903 A 1 HETATM 24 C C2 SAH . . . D 3 34.012 24.697 -24.04 1 18.27 ? C2 SAH 903 A 1 HETATM 25 N N3 SAH . . . D 3 33.532 25.508 -24.966 1 18.42 ? N3 SAH 903 A 1 HETATM 26 C C4 SAH . . . D 3 33.513 25.139 -26.246 1 18.96 ? C4 SAH 903 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 446 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #