data_3EVF # _model_server_result.job_id ifXjvFDO8KWSSVqeX9iLvQ _model_server_result.datetime_utc '2024-11-08 17:54:48' _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 3evf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":901}' # _entry.id 3EVF # _exptl.entry_id 3EVF _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 3EVF _cell.length_a 104.791 _cell.length_b 104.791 _cell.length_c 51.842 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EVF _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 363 n n N HN1 SAH sing 364 n n N HN2 SAH sing 365 n n CA CB SAH sing 366 n n CA C SAH sing 367 n n CA HA SAH sing 368 n n CB CG SAH sing 369 n n CB HB1 SAH sing 370 n n CB HB2 SAH sing 371 n n CG SD SAH sing 372 n n CG HG1 SAH sing 373 n n CG HG2 SAH sing 374 n n SD C5' SAH sing 375 n n C O SAH doub 376 n n C OXT SAH sing 377 n n OXT HXT SAH sing 378 n n C5' C4' SAH sing 379 n n C5' "H5'1" SAH sing 380 n n C5' "H5'2" SAH sing 381 n n C4' O4' SAH sing 382 n n C4' C3' SAH sing 383 n n C4' H4' SAH sing 384 n n O4' C1' SAH sing 385 n n C3' O3' SAH sing 386 n n C3' C2' SAH sing 387 n n C3' H3' SAH sing 388 n n O3' HO3' SAH sing 389 n n C2' O2' SAH sing 390 n n C2' C1' SAH sing 391 n n C2' H2' SAH sing 392 n n O2' HO2' SAH sing 393 n n C1' N9 SAH sing 394 n n C1' H1' SAH sing 395 n n N9 C8 SAH sing 396 n y N9 C4 SAH sing 397 n y C8 N7 SAH doub 398 n y C8 H8 SAH sing 399 n n N7 C5 SAH sing 400 n y C5 C6 SAH sing 401 n y C5 C4 SAH doub 402 n y C6 N6 SAH sing 403 n n C6 N1 SAH doub 404 n y N6 HN61 SAH sing 405 n n N6 HN62 SAH sing 406 n n N1 C2 SAH sing 407 n y C2 N3 SAH doub 408 n y C2 H2 SAH sing 409 n n N3 C4 SAH sing 410 n y # _atom_sites.entry_id 3EVF _atom_sites.fract_transf_matrix[1][1] 0.009543 _atom_sites.fract_transf_matrix[1][2] 0.00551 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011019 _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] 0.019289 _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 GTA A 1 902 1001 GTA GTA . C 2 GTA A 1 903 1002 GTA GTA . D 3 SAH A 1 901 901 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 166 666 666 HOH HOH . E 4 HOH A 167 667 667 HOH HOH . E 4 HOH A 168 668 668 HOH HOH . E 4 HOH A 169 669 669 HOH HOH . E 4 HOH A 170 670 670 HOH HOH . E 4 HOH A 171 671 671 HOH HOH . E 4 HOH A 172 672 672 HOH HOH . E 4 HOH A 173 673 673 HOH HOH . E 4 HOH A 174 674 674 HOH HOH . E 4 HOH A 175 675 675 HOH HOH . E 4 HOH A 176 676 676 HOH HOH . E 4 HOH A 177 677 677 HOH HOH . E 4 HOH A 178 678 678 HOH HOH . E 4 HOH A 179 679 679 HOH HOH . E 4 HOH A 180 680 680 HOH HOH . E 4 HOH A 181 681 681 HOH HOH . E 4 HOH A 182 682 682 HOH HOH . E 4 HOH A 183 683 683 HOH HOH . E 4 HOH A 184 684 684 HOH HOH . E 4 HOH A 185 685 685 HOH HOH . E 4 HOH A 186 686 686 HOH HOH . E 4 HOH A 187 687 687 HOH HOH . E 4 HOH A 188 688 688 HOH HOH . E 4 HOH A 189 689 689 HOH HOH . E 4 HOH A 190 690 690 HOH HOH . E 4 HOH A 191 691 691 HOH HOH . E 4 HOH A 192 692 692 HOH HOH . E 4 HOH A 193 693 693 HOH HOH . E 4 HOH A 194 694 694 HOH HOH . E 4 HOH A 195 695 695 HOH HOH . E 4 HOH A 196 696 696 HOH HOH . E 4 HOH A 197 697 697 HOH HOH . E 4 HOH A 198 698 698 HOH HOH . E 4 HOH A 199 699 699 HOH HOH . E 4 HOH A 200 700 700 HOH HOH . E 4 HOH A 201 701 701 HOH HOH . E 4 HOH A 202 702 702 HOH HOH . E 4 HOH A 203 703 703 HOH HOH . E 4 HOH A 204 704 704 HOH HOH . E 4 HOH A 205 705 705 HOH HOH . E 4 HOH A 206 706 706 HOH HOH . E 4 HOH A 207 707 707 HOH HOH . E 4 HOH A 208 708 708 HOH HOH . E 4 HOH A 209 709 709 HOH HOH . E 4 HOH A 210 710 710 HOH HOH . E 4 HOH A 211 711 711 HOH HOH . E 4 HOH A 212 712 712 HOH HOH . E 4 HOH A 213 713 713 HOH HOH . E 4 HOH A 214 714 714 HOH HOH . E 4 HOH A 215 715 715 HOH HOH . E 4 HOH A 216 716 716 HOH HOH . E 4 HOH A 217 717 717 HOH HOH . E 4 HOH A 218 718 718 HOH HOH . E 4 HOH A 219 719 719 HOH HOH . E 4 HOH A 220 720 720 HOH HOH . E 4 HOH A 221 721 721 HOH HOH . E 4 HOH A 222 722 722 HOH HOH . E 4 HOH A 223 723 723 HOH HOH . E 4 HOH A 224 724 724 HOH HOH . E 4 HOH A 225 725 725 HOH HOH . E 4 HOH A 226 726 726 HOH HOH . E 4 HOH A 227 727 727 HOH HOH . E 4 HOH A 228 728 728 HOH HOH . E 4 HOH A 229 729 729 HOH HOH . E 4 HOH A 230 730 730 HOH HOH . E 4 HOH A 231 731 731 HOH HOH . E 4 HOH A 232 732 732 HOH HOH . E 4 HOH A 233 733 733 HOH HOH . E 4 HOH A 234 734 734 HOH HOH . E 4 HOH A 235 735 735 HOH HOH . E 4 HOH A 236 736 736 HOH HOH . E 4 HOH A 237 737 737 HOH HOH . E 4 HOH A 238 738 738 HOH HOH . E 4 HOH A 239 739 739 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 24.65 29.921 -26.844 1 15.28 ? N SAH 901 A 1 HETATM 2 C CA SAH . . . D 3 25.712 30.935 -26.933 1 15.16 ? CA SAH 901 A 1 HETATM 3 C CB SAH . . . D 3 26.528 30.721 -28.21 1 18.9 ? CB SAH 901 A 1 HETATM 4 C CG SAH . . . D 3 27.313 29.41 -28.141 1 21.29 ? CG SAH 901 A 1 HETATM 5 S SD SAH . . . D 3 28.415 29.132 -29.575 1 24 ? SD SAH 901 A 1 HETATM 6 C C SAH . . . D 3 25.073 32.325 -26.953 1 16.19 ? C SAH 901 A 1 HETATM 7 O O SAH . . . D 3 25.85 33.296 -27.086 1 16.08 ? O SAH 901 A 1 HETATM 8 O OXT SAH . . . D 3 23.831 32.386 -26.838 1 15.66 ? OXT SAH 901 A 1 HETATM 9 C C5' SAH . . . D 3 29.351 27.677 -28.979 1 21.15 ? C5' SAH 901 A 1 HETATM 10 C C4' SAH . . . D 3 30.46 28.027 -27.985 1 19.54 ? C4' SAH 901 A 1 HETATM 11 O O4' SAH . . . D 3 30.983 26.797 -27.456 1 18.73 ? O4' SAH 901 A 1 HETATM 12 C C3' SAH . . . D 3 31.632 28.758 -28.648 1 19.15 ? C3' SAH 901 A 1 HETATM 13 O O3' SAH . . . D 3 31.989 29.918 -27.891 1 19.96 ? O3' SAH 901 A 1 HETATM 14 C C2' SAH . . . D 3 32.759 27.726 -28.592 1 18.46 ? C2' SAH 901 A 1 HETATM 15 O O2' SAH . . . D 3 34.004 28.409 -28.42 1 20.3 ? O2' SAH 901 A 1 HETATM 16 C C1' SAH . . . D 3 32.395 27 -27.298 1 18.68 ? C1' SAH 901 A 1 HETATM 17 N N9 SAH . . . D 3 33.054 25.678 -27.201 1 18.51 ? N9 SAH 901 A 1 HETATM 18 C C8 SAH . . . D 3 33.286 24.837 -28.207 1 18.28 ? C8 SAH 901 A 1 HETATM 19 N N7 SAH . . . D 3 33.858 23.73 -27.739 1 17.87 ? N7 SAH 901 A 1 HETATM 20 C C5 SAH . . . D 3 33.989 23.86 -26.422 1 17.12 ? C5 SAH 901 A 1 HETATM 21 C C6 SAH . . . D 3 34.491 23.054 -25.41 1 17.19 ? C6 SAH 901 A 1 HETATM 22 N N6 SAH . . . D 3 35.021 21.865 -25.686 1 18.86 ? N6 SAH 901 A 1 HETATM 23 N N1 SAH . . . D 3 34.45 23.499 -24.147 1 16.95 ? N1 SAH 901 A 1 HETATM 24 C C2 SAH . . . D 3 33.95 24.691 -23.859 1 16.99 ? C2 SAH 901 A 1 HETATM 25 N N3 SAH . . . D 3 33.47 25.485 -24.795 1 16.88 ? N3 SAH 901 A 1 HETATM 26 C C4 SAH . . . D 3 33.472 25.102 -26.081 1 17.31 ? C4 SAH 901 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 26 #