data_1VP9 # _model_server_result.job_id R_HvMeUdDVPbg3hB0ozcEA _model_server_result.datetime_utc '2024-11-20 09:17:03' _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 1vp9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 1VP9 # _exptl.entry_id 1VP9 _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 1VP9 _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 1VP9 _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 1VP9 _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 33 538 538 HOH HOH . C 3 HOH A 34 539 539 HOH HOH . C 3 HOH A 35 540 540 HOH HOH . C 3 HOH A 36 541 541 HOH HOH . C 3 HOH A 37 542 542 HOH HOH . C 3 HOH A 38 543 543 HOH HOH . C 3 HOH A 39 544 544 HOH HOH . C 3 HOH A 40 545 545 HOH HOH . C 3 HOH A 41 546 546 HOH HOH . C 3 HOH A 42 547 547 HOH HOH . C 3 HOH A 43 548 548 HOH HOH . C 3 HOH A 44 549 549 HOH HOH . C 3 HOH A 45 550 550 HOH HOH . C 3 HOH A 46 551 551 HOH HOH . C 3 HOH A 47 552 552 HOH HOH . C 3 HOH A 48 553 553 HOH HOH . C 3 HOH A 49 554 554 HOH HOH . C 3 HOH A 50 555 555 HOH HOH . C 3 HOH A 51 556 556 HOH HOH . C 3 HOH A 52 557 557 HOH HOH . C 3 HOH A 53 558 558 HOH HOH . C 3 HOH A 54 560 560 HOH HOH . C 3 HOH A 55 561 561 HOH HOH . C 3 HOH A 56 562 562 HOH HOH . C 3 HOH A 57 563 563 HOH HOH . C 3 HOH A 58 564 564 HOH HOH . C 3 HOH A 59 565 565 HOH HOH . C 3 HOH A 60 566 566 HOH HOH . C 3 HOH A 61 568 568 HOH HOH . C 3 HOH A 62 569 569 HOH HOH . C 3 HOH A 63 570 570 HOH HOH . C 3 HOH A 64 571 571 HOH HOH . C 3 HOH A 65 572 572 HOH HOH . C 3 HOH A 66 574 574 HOH HOH . C 3 HOH A 67 575 575 HOH HOH . C 3 HOH A 68 576 576 HOH HOH . C 3 HOH A 69 577 577 HOH HOH . C 3 HOH A 70 578 578 HOH HOH . C 3 HOH A 71 579 579 HOH HOH . C 3 HOH A 72 580 580 HOH HOH . C 3 HOH A 73 581 581 HOH HOH . C 3 HOH A 74 582 582 HOH HOH . C 3 HOH A 75 583 583 HOH HOH . C 3 HOH A 76 584 584 HOH HOH . C 3 HOH A 77 585 585 HOH HOH . C 3 HOH A 78 586 586 HOH HOH . C 3 HOH A 79 587 587 HOH HOH . C 3 HOH A 80 588 588 HOH HOH . C 3 HOH A 81 589 589 HOH HOH . C 3 HOH A 82 590 590 HOH HOH . C 3 HOH A 83 591 591 HOH HOH . C 3 HOH A 84 592 592 HOH HOH . C 3 HOH A 85 593 593 HOH HOH . C 3 HOH A 86 595 595 HOH HOH . C 3 HOH A 87 596 596 HOH HOH . C 3 HOH A 88 597 597 HOH HOH . C 3 HOH A 89 598 598 HOH HOH . C 3 HOH A 90 599 599 HOH HOH . C 3 HOH A 91 600 600 HOH HOH . C 3 HOH A 92 601 601 HOH HOH . C 3 HOH A 93 602 602 HOH HOH . C 3 HOH A 94 603 603 HOH HOH . C 3 HOH A 95 604 604 HOH HOH . C 3 HOH A 96 605 605 HOH HOH . C 3 HOH A 97 606 606 HOH HOH . C 3 HOH A 98 607 607 HOH HOH . C 3 HOH A 99 609 609 HOH HOH . C 3 HOH A 100 610 610 HOH HOH . C 3 HOH A 101 611 611 HOH HOH . C 3 HOH A 102 612 612 HOH HOH . C 3 HOH A 103 613 613 HOH HOH . C 3 HOH A 104 614 614 HOH HOH . C 3 HOH A 105 615 615 HOH HOH . C 3 HOH A 106 616 616 HOH HOH . C 3 HOH A 107 619 619 HOH HOH . C 3 HOH A 108 620 620 HOH HOH . C 3 HOH A 109 621 621 HOH HOH . C 3 HOH A 110 622 622 HOH HOH . C 3 HOH A 111 623 623 HOH HOH . C 3 HOH A 112 624 624 HOH HOH . C 3 HOH A 113 625 625 HOH HOH . C 3 HOH A 114 626 626 HOH HOH . C 3 HOH A 115 627 627 HOH HOH . C 3 HOH A 116 628 628 HOH HOH . C 3 HOH A 117 629 629 HOH HOH . C 3 HOH A 118 630 630 HOH HOH . C 3 HOH A 119 631 631 HOH HOH . C 3 HOH A 120 632 632 HOH HOH . C 3 HOH A 121 633 633 HOH HOH . C 3 HOH A 122 634 634 HOH HOH . C 3 HOH A 123 635 635 HOH HOH . C 3 HOH A 124 636 636 HOH HOH . C 3 HOH A 125 637 637 HOH HOH . C 3 HOH A 126 638 638 HOH HOH . C 3 HOH A 127 639 639 HOH HOH . C 3 HOH A 128 640 640 HOH HOH . C 3 HOH A 129 641 641 HOH HOH . C 3 HOH A 130 642 642 HOH HOH . C 3 HOH A 131 643 643 HOH HOH . C 3 HOH A 132 644 644 HOH HOH . C 3 HOH A 133 645 645 HOH HOH . C 3 HOH A 134 646 646 HOH HOH . C 3 HOH A 135 647 647 HOH HOH . C 3 HOH A 136 648 648 HOH HOH . C 3 HOH A 137 649 649 HOH HOH . C 3 HOH A 138 650 650 HOH HOH . C 3 HOH A 139 651 651 HOH HOH . C 3 HOH A 140 653 653 HOH HOH . C 3 HOH A 141 654 654 HOH HOH . C 3 HOH A 142 655 655 HOH HOH . C 3 HOH A 143 656 656 HOH HOH . C 3 HOH A 144 657 657 HOH HOH . C 3 HOH A 145 658 658 HOH HOH . C 3 HOH A 146 659 659 HOH HOH . C 3 HOH A 147 661 661 HOH HOH . C 3 HOH A 148 662 662 HOH HOH . C 3 HOH A 149 663 663 HOH HOH . C 3 HOH A 150 664 664 HOH HOH . C 3 HOH A 151 666 666 HOH HOH . C 3 HOH A 152 667 667 HOH HOH . C 3 HOH A 153 668 668 HOH HOH . C 3 HOH A 154 670 670 HOH HOH . C 3 HOH A 155 671 671 HOH HOH . C 3 HOH A 156 672 672 HOH HOH . C 3 HOH A 157 674 674 HOH HOH . C 3 HOH A 158 675 675 HOH HOH . C 3 HOH A 159 677 677 HOH HOH . C 3 HOH A 160 678 678 HOH HOH . C 3 HOH A 161 680 680 HOH HOH . C 3 HOH A 162 701 701 HOH HOH . C 3 HOH A 163 702 702 HOH HOH . C 3 HOH A 164 703 703 HOH HOH . C 3 HOH A 165 704 704 HOH HOH . C 3 HOH A 166 705 705 HOH HOH . C 3 HOH A 167 706 706 HOH HOH . C 3 HOH A 168 707 707 HOH HOH . C 3 HOH A 169 708 708 HOH HOH . C 3 HOH A 170 801 801 HOH HOH . C 3 HOH A 171 802 802 HOH HOH . C 3 HOH A 172 803 803 HOH HOH . C 3 HOH A 173 804 804 HOH HOH . C 3 HOH A 174 805 805 HOH HOH . C 3 HOH A 175 806 806 HOH HOH . C 3 HOH A 176 807 807 HOH HOH . C 3 HOH A 177 808 808 HOH HOH . C 3 HOH A 178 809 809 HOH HOH . C 3 HOH A 179 810 810 HOH HOH . C 3 HOH A 180 811 811 HOH HOH . C 3 HOH A 181 812 812 HOH HOH . C 3 HOH A 182 813 813 HOH HOH . C 3 HOH A 183 814 814 HOH HOH . C 3 HOH A 184 815 815 HOH HOH . C 3 HOH A 185 816 816 HOH HOH . C 3 HOH A 186 817 817 HOH HOH . C 3 HOH A 187 818 818 HOH HOH . C 3 HOH A 188 819 819 HOH HOH . C 3 HOH A 189 820 820 HOH HOH . C 3 HOH A 190 821 821 HOH HOH . C 3 HOH A 191 822 822 HOH HOH . C 3 HOH A 192 823 823 HOH HOH . C 3 HOH A 193 824 824 HOH HOH . C 3 HOH A 194 825 825 HOH HOH . C 3 HOH A 195 826 826 HOH HOH . C 3 HOH A 196 827 827 HOH HOH . C 3 HOH A 197 828 828 HOH HOH . C 3 HOH A 198 829 829 HOH HOH . C 3 HOH A 199 830 830 HOH HOH . C 3 HOH A 200 831 831 HOH HOH . C 3 HOH A 201 832 832 HOH HOH . C 3 HOH A 202 833 833 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 -3.939 12.949 23.901 1 30.78 ? N SAH 400 A 1 HETATM 2 C CA SAH . . . B 2 -4.2 11.982 24.96 1 35.51 ? CA SAH 400 A 1 HETATM 3 C CB SAH . . . B 2 -2.943 11.132 25.184 1 36.11 ? CB SAH 400 A 1 HETATM 4 C CG SAH . . . B 2 -2.492 10.496 23.863 1 42.21 ? CG SAH 400 A 1 HETATM 5 S SD SAH . . . B 2 -1.157 9.287 23.889 1 43.55 ? SD SAH 400 A 1 HETATM 6 C C SAH . . . B 2 -4.719 12.651 26.25 1 35.39 ? C SAH 400 A 1 HETATM 7 O O SAH . . . B 2 -5.617 13.513 26.083 1 32.33 ? O SAH 400 A 1 HETATM 8 O OXT SAH . . . B 2 -4.557 12.062 27.354 1 31.37 ? OXT SAH 400 A 1 HETATM 9 C C5' SAH . . . B 2 -1.266 8.748 22.187 1 46.73 ? C5' SAH 400 A 1 HETATM 10 C C4' SAH . . . B 2 -2.548 8.017 21.888 1 50.09 ? C4' SAH 400 A 1 HETATM 11 O O4' SAH . . . B 2 -2.591 7.839 20.44 1 50.13 ? O4' SAH 400 A 1 HETATM 12 C C3' SAH . . . B 2 -2.781 6.59 22.615 1 52.17 ? C3' SAH 400 A 1 HETATM 13 O O3' SAH . . . B 2 -3.878 6.611 23.589 1 49.44 ? O3' SAH 400 A 1 HETATM 14 C C2' SAH . . . B 2 -3.023 5.688 21.355 1 51.97 ? C2' SAH 400 A 1 HETATM 15 O O2' SAH . . . B 2 -3.902 4.527 21.448 1 50.15 ? O2' SAH 400 A 1 HETATM 16 C C1' SAH . . . B 2 -3.483 6.739 20.313 1 51.99 ? C1' SAH 400 A 1 HETATM 17 N N9 SAH . . . B 2 -3.468 6.341 18.914 1 54.64 ? N9 SAH 400 A 1 HETATM 18 C C8 SAH . . . B 2 -2.455 5.677 18.202 1 55.27 ? C8 SAH 400 A 1 HETATM 19 N N7 SAH . . . B 2 -2.858 5.266 17.036 1 55.31 ? N7 SAH 400 A 1 HETATM 20 C C5 SAH . . . B 2 -4.192 5.728 16.955 1 54.53 ? C5 SAH 400 A 1 HETATM 21 C C6 SAH . . . B 2 -5.166 5.614 15.968 1 53.81 ? C6 SAH 400 A 1 HETATM 22 N N6 SAH . . . B 2 -4.869 5.106 14.769 1 54.09 ? N6 SAH 400 A 1 HETATM 23 N N1 SAH . . . B 2 -6.425 5.947 16.306 1 52.89 ? N1 SAH 400 A 1 HETATM 24 C C2 SAH . . . B 2 -6.694 6.366 17.522 1 51.69 ? C2 SAH 400 A 1 HETATM 25 N N3 SAH . . . B 2 -5.859 6.623 18.501 1 52.73 ? N3 SAH 400 A 1 HETATM 26 C C4 SAH . . . B 2 -4.599 6.29 18.133 1 53.28 ? C4 SAH 400 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #