data_1VP3 # _model_server_result.job_id q1YesESzWyEa69doNW0jaQ _model_server_result.datetime_utc '2024-11-13 18:50:48' _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 1vp3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 1VP3 # _exptl.entry_id 1VP3 _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 117.3 _cell.angle_gamma 90 _cell.entry_id 1VP3 _cell.length_a 84.6 _cell.length_b 67.3 _cell.length_c 79.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VP3 _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 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 '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 1VP3 _atom_sites.fract_transf_matrix[1][1] 0.01182 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006101 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014859 _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] 0.014137 _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 1 400 400 SAH SAH . C 3 HOH A 1 501 501 HOH HOH . C 3 HOH A 2 502 502 HOH HOH . C 3 HOH A 3 504 504 HOH HOH . C 3 HOH A 4 505 505 HOH HOH . C 3 HOH A 5 506 506 HOH HOH . C 3 HOH A 6 507 507 HOH HOH . C 3 HOH A 7 508 508 HOH HOH . C 3 HOH A 8 509 509 HOH HOH . C 3 HOH A 9 510 510 HOH HOH . C 3 HOH A 10 511 511 HOH HOH . C 3 HOH A 11 512 512 HOH HOH . C 3 HOH A 12 513 513 HOH HOH . C 3 HOH A 13 517 517 HOH HOH . C 3 HOH A 14 518 518 HOH HOH . C 3 HOH A 15 519 519 HOH HOH . C 3 HOH A 16 520 520 HOH HOH . C 3 HOH A 17 521 521 HOH HOH . C 3 HOH A 18 522 522 HOH HOH . C 3 HOH A 19 523 523 HOH HOH . C 3 HOH A 20 524 524 HOH HOH . C 3 HOH A 21 525 525 HOH HOH . C 3 HOH A 22 526 526 HOH HOH . C 3 HOH A 23 527 527 HOH HOH . C 3 HOH A 24 528 528 HOH HOH . C 3 HOH A 25 529 529 HOH HOH . C 3 HOH A 26 530 530 HOH HOH . C 3 HOH A 27 531 531 HOH HOH . C 3 HOH A 28 532 532 HOH HOH . C 3 HOH A 29 533 533 HOH HOH . C 3 HOH A 30 534 534 HOH HOH . C 3 HOH A 31 535 535 HOH HOH . C 3 HOH A 32 536 536 HOH HOH . C 3 HOH A 33 537 537 HOH HOH . C 3 HOH A 34 538 538 HOH HOH . C 3 HOH A 35 539 539 HOH HOH . C 3 HOH A 36 540 540 HOH HOH . C 3 HOH A 37 541 541 HOH HOH . C 3 HOH A 38 542 542 HOH HOH . C 3 HOH A 39 543 543 HOH HOH . C 3 HOH A 40 544 544 HOH HOH . C 3 HOH A 41 545 545 HOH HOH . C 3 HOH A 42 546 546 HOH HOH . C 3 HOH A 43 547 547 HOH HOH . C 3 HOH A 44 548 548 HOH HOH . C 3 HOH A 45 549 549 HOH HOH . C 3 HOH A 46 550 550 HOH HOH . C 3 HOH A 47 551 551 HOH HOH . C 3 HOH A 48 552 552 HOH HOH . C 3 HOH A 49 553 553 HOH HOH . C 3 HOH A 50 554 554 HOH HOH . C 3 HOH A 51 555 555 HOH HOH . C 3 HOH A 52 556 556 HOH HOH . C 3 HOH A 53 557 557 HOH HOH . C 3 HOH A 54 558 558 HOH HOH . C 3 HOH A 55 559 559 HOH HOH . C 3 HOH A 56 560 560 HOH HOH . C 3 HOH A 57 561 561 HOH HOH . C 3 HOH A 58 562 562 HOH HOH . C 3 HOH A 59 563 563 HOH HOH . C 3 HOH A 60 564 564 HOH HOH . C 3 HOH A 61 565 565 HOH HOH . C 3 HOH A 62 566 566 HOH HOH . C 3 HOH A 63 568 568 HOH HOH . C 3 HOH A 64 569 569 HOH HOH . C 3 HOH A 65 570 570 HOH HOH . C 3 HOH A 66 571 571 HOH HOH . C 3 HOH A 67 572 572 HOH HOH . C 3 HOH A 68 574 574 HOH HOH . C 3 HOH A 69 575 575 HOH HOH . C 3 HOH A 70 576 576 HOH HOH . C 3 HOH A 71 577 577 HOH HOH . C 3 HOH A 72 578 578 HOH HOH . C 3 HOH A 73 579 579 HOH HOH . C 3 HOH A 74 580 580 HOH HOH . C 3 HOH A 75 581 581 HOH HOH . C 3 HOH A 76 582 582 HOH HOH . C 3 HOH A 77 583 583 HOH HOH . C 3 HOH A 78 584 584 HOH HOH . C 3 HOH A 79 585 585 HOH HOH . C 3 HOH A 80 586 586 HOH HOH . C 3 HOH A 81 587 587 HOH HOH . C 3 HOH A 82 588 588 HOH HOH . C 3 HOH A 83 589 589 HOH HOH . C 3 HOH A 84 590 590 HOH HOH . C 3 HOH A 85 591 591 HOH HOH . C 3 HOH A 86 592 592 HOH HOH . C 3 HOH A 87 593 593 HOH HOH . C 3 HOH A 88 595 595 HOH HOH . C 3 HOH A 89 596 596 HOH HOH . C 3 HOH A 90 597 597 HOH HOH . C 3 HOH A 91 598 598 HOH HOH . C 3 HOH A 92 599 599 HOH HOH . C 3 HOH A 93 600 600 HOH HOH . C 3 HOH A 94 601 601 HOH HOH . C 3 HOH A 95 602 602 HOH HOH . C 3 HOH A 96 603 603 HOH HOH . C 3 HOH A 97 604 604 HOH HOH . C 3 HOH A 98 605 605 HOH HOH . C 3 HOH A 99 606 606 HOH HOH . C 3 HOH A 100 607 607 HOH HOH . C 3 HOH A 101 609 609 HOH HOH . C 3 HOH A 102 610 610 HOH HOH . C 3 HOH A 103 611 611 HOH HOH . C 3 HOH A 104 612 612 HOH HOH . C 3 HOH A 105 613 613 HOH HOH . C 3 HOH A 106 614 614 HOH HOH . C 3 HOH A 107 615 615 HOH HOH . C 3 HOH A 108 616 616 HOH HOH . C 3 HOH A 109 618 618 HOH HOH . C 3 HOH A 110 619 619 HOH HOH . C 3 HOH A 111 620 620 HOH HOH . C 3 HOH A 112 621 621 HOH HOH . C 3 HOH A 113 622 622 HOH HOH . C 3 HOH A 114 623 623 HOH HOH . C 3 HOH A 115 624 624 HOH HOH . C 3 HOH A 116 625 625 HOH HOH . C 3 HOH A 117 626 626 HOH HOH . C 3 HOH A 118 627 627 HOH HOH . C 3 HOH A 119 628 628 HOH HOH . C 3 HOH A 120 629 629 HOH HOH . C 3 HOH A 121 630 630 HOH HOH . C 3 HOH A 122 631 631 HOH HOH . C 3 HOH A 123 632 632 HOH HOH . C 3 HOH A 124 633 633 HOH HOH . C 3 HOH A 125 634 634 HOH HOH . C 3 HOH A 126 635 635 HOH HOH . C 3 HOH A 127 636 636 HOH HOH . C 3 HOH A 128 637 637 HOH HOH . C 3 HOH A 129 638 638 HOH HOH . C 3 HOH A 130 639 639 HOH HOH . C 3 HOH A 131 640 640 HOH HOH . C 3 HOH A 132 641 641 HOH HOH . C 3 HOH A 133 642 642 HOH HOH . C 3 HOH A 134 643 643 HOH HOH . C 3 HOH A 135 644 644 HOH HOH . C 3 HOH A 136 645 645 HOH HOH . C 3 HOH A 137 646 646 HOH HOH . C 3 HOH A 138 647 647 HOH HOH . C 3 HOH A 139 648 648 HOH HOH . C 3 HOH A 140 649 649 HOH HOH . C 3 HOH A 141 650 650 HOH HOH . C 3 HOH A 142 651 651 HOH HOH . C 3 HOH A 143 652 652 HOH HOH . C 3 HOH A 144 653 653 HOH HOH . C 3 HOH A 145 654 654 HOH HOH . C 3 HOH A 146 655 655 HOH HOH . C 3 HOH A 147 656 656 HOH HOH . C 3 HOH A 148 657 657 HOH HOH . C 3 HOH A 149 658 658 HOH HOH . C 3 HOH A 150 659 659 HOH HOH . C 3 HOH A 151 660 660 HOH HOH . C 3 HOH A 152 661 661 HOH HOH . C 3 HOH A 153 662 662 HOH HOH . C 3 HOH A 154 663 663 HOH HOH . C 3 HOH A 155 664 664 HOH HOH . C 3 HOH A 156 665 665 HOH HOH . C 3 HOH A 157 666 666 HOH HOH . C 3 HOH A 158 667 667 HOH HOH . C 3 HOH A 159 668 668 HOH HOH . C 3 HOH A 160 669 669 HOH HOH . C 3 HOH A 161 670 670 HOH HOH . C 3 HOH A 162 671 671 HOH HOH . C 3 HOH A 163 672 672 HOH HOH . C 3 HOH A 164 673 673 HOH HOH . C 3 HOH A 165 674 674 HOH HOH . C 3 HOH A 166 675 675 HOH HOH . C 3 HOH A 167 676 676 HOH HOH . C 3 HOH A 168 677 677 HOH HOH . C 3 HOH A 169 678 678 HOH HOH . C 3 HOH A 170 679 679 HOH HOH . C 3 HOH A 171 680 680 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 -4.189 12.808 24.041 1 11.23 ? N SAH 400 A 1 HETATM 2 C CA SAH . . . B 2 -4.311 11.789 25.074 1 14.51 ? CA SAH 400 A 1 HETATM 3 C CB SAH . . . B 2 -3.027 10.963 25.169 1 13.13 ? CB SAH 400 A 1 HETATM 4 C CG SAH . . . B 2 -2.621 10.346 23.845 1 15.96 ? CG SAH 400 A 1 HETATM 5 S SD SAH . . . B 2 -1.345 9.101 23.979 1 16.56 ? SD SAH 400 A 1 HETATM 6 C C SAH . . . B 2 -4.591 12.461 26.41 1 15.32 ? C SAH 400 A 1 HETATM 7 O O SAH . . . B 2 -5.151 13.572 26.368 1 15.51 ? O SAH 400 A 1 HETATM 8 O OXT SAH . . . B 2 -4.542 11.748 27.442 1 18.8 ? OXT SAH 400 A 1 HETATM 9 C C5' SAH . . . B 2 -1.29 8.594 22.251 1 19.95 ? C5' SAH 400 A 1 HETATM 10 C C4' SAH . . . B 2 -2.497 7.806 21.813 1 21.04 ? C4' SAH 400 A 1 HETATM 11 O O4' SAH . . . B 2 -2.57 7.737 20.384 1 19.47 ? O4' SAH 400 A 1 HETATM 12 C C3' SAH . . . B 2 -2.748 6.413 22.471 1 21.19 ? C3' SAH 400 A 1 HETATM 13 O O3' SAH . . . B 2 -3.867 6.45 23.391 1 21.6 ? O3' SAH 400 A 1 HETATM 14 C C2' SAH . . . B 2 -3.064 5.602 21.215 1 18.18 ? C2' SAH 400 A 1 HETATM 15 O O2' SAH . . . B 2 -3.991 4.49 21.403 1 22.57 ? O2' SAH 400 A 1 HETATM 16 C C1' SAH . . . B 2 -3.504 6.688 20.201 1 20.95 ? C1' SAH 400 A 1 HETATM 17 N N9 SAH . . . B 2 -3.469 6.313 18.765 1 22.57 ? N9 SAH 400 A 1 HETATM 18 C C8 SAH . . . B 2 -2.459 5.668 18.08 1 19.05 ? C8 SAH 400 A 1 HETATM 19 N N7 SAH . . . B 2 -2.867 5.343 16.906 1 22.13 ? N7 SAH 400 A 1 HETATM 20 C C5 SAH . . . B 2 -4.177 5.817 16.76 1 21.9 ? C5 SAH 400 A 1 HETATM 21 C C6 SAH . . . B 2 -5.142 5.781 15.735 1 24.71 ? C6 SAH 400 A 1 HETATM 22 N N6 SAH . . . B 2 -4.921 5.234 14.544 1 25.37 ? N6 SAH 400 A 1 HETATM 23 N N1 SAH . . . B 2 -6.374 6.262 15.991 1 23.33 ? N1 SAH 400 A 1 HETATM 24 C C2 SAH . . . B 2 -6.703 6.645 17.193 1 24.43 ? C2 SAH 400 A 1 HETATM 25 N N3 SAH . . . B 2 -5.892 6.721 18.226 1 25.16 ? N3 SAH 400 A 1 HETATM 26 C C4 SAH . . . B 2 -4.61 6.311 17.937 1 24.02 ? C4 SAH 400 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #