data_3I58 # _model_server_result.job_id EBDmjehdXgi376XQ1F8Udg _model_server_result.datetime_utc '2024-11-30 07:15:55' _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 3i58 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 3I58 # _exptl.entry_id 3I58 _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 2 _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 3I58 _cell.length_a 108.392 _cell.length_b 108.392 _cell.length_c 210.321 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I58 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N 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 320 n n N HN1 SAH sing 321 n n N HN2 SAH sing 322 n n CA CB SAH sing 323 n n CA C SAH sing 324 n n CA HA SAH sing 325 n n CB CG SAH sing 326 n n CB HB1 SAH sing 327 n n CB HB2 SAH sing 328 n n CG SD SAH sing 329 n n CG HG1 SAH sing 330 n n CG HG2 SAH sing 331 n n SD C5' SAH sing 332 n n C O SAH doub 333 n n C OXT SAH sing 334 n n OXT HXT SAH sing 335 n n C5' C4' SAH sing 336 n n C5' "H5'1" SAH sing 337 n n C5' "H5'2" SAH sing 338 n n C4' O4' SAH sing 339 n n C4' C3' SAH sing 340 n n C4' H4' SAH sing 341 n n O4' C1' SAH sing 342 n n C3' O3' SAH sing 343 n n C3' C2' SAH sing 344 n n C3' H3' SAH sing 345 n n O3' HO3' SAH sing 346 n n C2' O2' SAH sing 347 n n C2' C1' SAH sing 348 n n C2' H2' SAH sing 349 n n O2' HO2' SAH sing 350 n n C1' N9 SAH sing 351 n n C1' H1' SAH sing 352 n n N9 C8 SAH sing 353 n y N9 C4 SAH sing 354 n y C8 N7 SAH doub 355 n y C8 H8 SAH sing 356 n n N7 C5 SAH sing 357 n y C5 C6 SAH sing 358 n y C5 C4 SAH doub 359 n y C6 N6 SAH sing 360 n n C6 N1 SAH doub 361 n y N6 HN61 SAH sing 362 n n N6 HN62 SAH sing 363 n n N1 C2 SAH sing 364 n y C2 N3 SAH doub 365 n y C2 H2 SAH sing 366 n n N3 C4 SAH sing 367 n y # _atom_sites.entry_id 3I58 _atom_sites.fract_transf_matrix[1][1] 0.009226 _atom_sites.fract_transf_matrix[1][2] 0.005327 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010653 _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] 0.004755 _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 C 2 SAH A 1 401 1 SAH SAH . D 3 7NA A 1 402 3 7NA NA . E 4 GOL A 1 403 5 GOL GOL . F 2 SAH B 1 401 2 SAH SAH . G 3 7NA B 1 402 4 7NA NA . H 4 GOL B 1 404 6 GOL GOL . I 5 HOH A 1 502 2 HOH HOH . I 5 HOH A 2 503 3 HOH HOH . I 5 HOH A 3 506 6 HOH HOH . I 5 HOH A 4 510 10 HOH HOH . I 5 HOH A 5 511 11 HOH HOH . I 5 HOH A 6 513 13 HOH HOH . I 5 HOH A 7 520 20 HOH HOH . I 5 HOH A 8 524 24 HOH HOH . I 5 HOH A 9 526 26 HOH HOH . I 5 HOH A 10 527 27 HOH HOH . I 5 HOH A 11 528 28 HOH HOH . I 5 HOH A 12 530 30 HOH HOH . I 5 HOH A 13 531 31 HOH HOH . I 5 HOH A 14 532 32 HOH HOH . I 5 HOH A 15 533 33 HOH HOH . I 5 HOH A 16 545 45 HOH HOH . I 5 HOH A 17 546 46 HOH HOH . I 5 HOH A 18 547 47 HOH HOH . I 5 HOH A 19 549 49 HOH HOH . I 5 HOH A 20 550 50 HOH HOH . I 5 HOH A 21 556 56 HOH HOH . I 5 HOH A 22 559 59 HOH HOH . I 5 HOH A 23 561 61 HOH HOH . I 5 HOH A 24 562 62 HOH HOH . I 5 HOH A 25 564 64 HOH HOH . I 5 HOH A 26 566 66 HOH HOH . I 5 HOH A 27 568 68 HOH HOH . I 5 HOH A 28 576 76 HOH HOH . I 5 HOH A 29 577 77 HOH HOH . I 5 HOH A 30 580 80 HOH HOH . I 5 HOH A 31 581 81 HOH HOH . I 5 HOH A 32 584 84 HOH HOH . I 5 HOH A 33 586 86 HOH HOH . I 5 HOH A 34 587 87 HOH HOH . I 5 HOH A 35 593 93 HOH HOH . I 5 HOH A 36 594 94 HOH HOH . I 5 HOH A 37 595 95 HOH HOH . I 5 HOH A 38 597 97 HOH HOH . I 5 HOH A 39 598 98 HOH HOH . I 5 HOH A 40 601 101 HOH HOH . I 5 HOH A 41 602 102 HOH HOH . I 5 HOH A 42 604 104 HOH HOH . I 5 HOH A 43 609 109 HOH HOH . I 5 HOH A 44 610 110 HOH HOH . I 5 HOH A 45 611 111 HOH HOH . I 5 HOH A 46 613 113 HOH HOH . I 5 HOH A 47 615 115 HOH HOH . I 5 HOH A 48 616 116 HOH HOH . I 5 HOH A 49 621 121 HOH HOH . I 5 HOH A 50 622 122 HOH HOH . I 5 HOH A 51 623 123 HOH HOH . I 5 HOH A 52 624 124 HOH HOH . I 5 HOH A 53 626 126 HOH HOH . I 5 HOH A 54 627 127 HOH HOH . I 5 HOH A 55 629 129 HOH HOH . I 5 HOH A 56 630 130 HOH HOH . I 5 HOH A 57 631 131 HOH HOH . I 5 HOH A 58 632 132 HOH HOH . I 5 HOH A 59 633 133 HOH HOH . I 5 HOH A 60 634 134 HOH HOH . I 5 HOH A 61 636 136 HOH HOH . I 5 HOH A 62 637 137 HOH HOH . I 5 HOH A 63 638 138 HOH HOH . I 5 HOH A 64 640 140 HOH HOH . I 5 HOH A 65 641 141 HOH HOH . I 5 HOH A 66 642 142 HOH HOH . I 5 HOH A 67 644 144 HOH HOH . I 5 HOH A 68 646 146 HOH HOH . I 5 HOH A 69 647 147 HOH HOH . I 5 HOH A 70 652 152 HOH HOH . I 5 HOH A 71 654 154 HOH HOH . I 5 HOH A 72 659 159 HOH HOH . I 5 HOH A 73 660 160 HOH HOH . I 5 HOH A 74 661 161 HOH HOH . I 5 HOH A 75 663 163 HOH HOH . J 5 HOH B 1 501 1 HOH HOH . J 5 HOH B 2 504 4 HOH HOH . J 5 HOH B 3 505 5 HOH HOH . J 5 HOH B 4 507 7 HOH HOH . J 5 HOH B 5 508 8 HOH HOH . J 5 HOH B 6 509 9 HOH HOH . J 5 HOH B 7 512 12 HOH HOH . J 5 HOH B 8 514 14 HOH HOH . J 5 HOH B 9 515 15 HOH HOH . J 5 HOH B 10 516 16 HOH HOH . J 5 HOH B 11 517 17 HOH HOH . J 5 HOH B 12 518 18 HOH HOH . J 5 HOH B 13 519 19 HOH HOH . J 5 HOH B 14 521 21 HOH HOH . J 5 HOH B 15 522 22 HOH HOH . J 5 HOH B 16 523 23 HOH HOH . J 5 HOH B 17 525 25 HOH HOH . J 5 HOH B 18 529 29 HOH HOH . J 5 HOH B 19 534 34 HOH HOH . J 5 HOH B 20 535 35 HOH HOH . J 5 HOH B 21 536 36 HOH HOH . J 5 HOH B 22 537 37 HOH HOH . J 5 HOH B 23 538 38 HOH HOH . J 5 HOH B 24 539 39 HOH HOH . J 5 HOH B 25 540 40 HOH HOH . J 5 HOH B 26 541 41 HOH HOH . J 5 HOH B 27 542 42 HOH HOH . J 5 HOH B 28 543 43 HOH HOH . J 5 HOH B 29 544 44 HOH HOH . J 5 HOH B 30 548 48 HOH HOH . J 5 HOH B 31 551 51 HOH HOH . J 5 HOH B 32 552 52 HOH HOH . J 5 HOH B 33 553 53 HOH HOH . J 5 HOH B 34 554 54 HOH HOH . J 5 HOH B 35 555 55 HOH HOH . J 5 HOH B 36 557 57 HOH HOH . J 5 HOH B 37 558 58 HOH HOH . J 5 HOH B 38 560 60 HOH HOH . J 5 HOH B 39 563 63 HOH HOH . J 5 HOH B 40 565 65 HOH HOH . J 5 HOH B 41 567 67 HOH HOH . J 5 HOH B 42 569 69 HOH HOH . J 5 HOH B 43 570 70 HOH HOH . J 5 HOH B 44 571 71 HOH HOH . J 5 HOH B 45 572 72 HOH HOH . J 5 HOH B 46 573 73 HOH HOH . J 5 HOH B 47 574 74 HOH HOH . J 5 HOH B 48 575 75 HOH HOH . J 5 HOH B 49 578 78 HOH HOH . J 5 HOH B 50 579 79 HOH HOH . J 5 HOH B 51 582 82 HOH HOH . J 5 HOH B 52 583 83 HOH HOH . J 5 HOH B 53 585 85 HOH HOH . J 5 HOH B 54 588 88 HOH HOH . J 5 HOH B 55 589 89 HOH HOH . J 5 HOH B 56 590 90 HOH HOH . J 5 HOH B 57 591 91 HOH HOH . J 5 HOH B 58 592 92 HOH HOH . J 5 HOH B 59 596 96 HOH HOH . J 5 HOH B 60 599 99 HOH HOH . J 5 HOH B 61 600 100 HOH HOH . J 5 HOH B 62 603 103 HOH HOH . J 5 HOH B 63 605 105 HOH HOH . J 5 HOH B 64 606 106 HOH HOH . J 5 HOH B 65 607 107 HOH HOH . J 5 HOH B 66 608 108 HOH HOH . J 5 HOH B 67 612 112 HOH HOH . J 5 HOH B 68 614 114 HOH HOH . J 5 HOH B 69 617 117 HOH HOH . J 5 HOH B 70 618 118 HOH HOH . J 5 HOH B 71 619 119 HOH HOH . J 5 HOH B 72 620 120 HOH HOH . J 5 HOH B 73 625 125 HOH HOH . J 5 HOH B 74 628 128 HOH HOH . J 5 HOH B 75 635 135 HOH HOH . J 5 HOH B 76 639 139 HOH HOH . J 5 HOH B 77 643 143 HOH HOH . J 5 HOH B 78 645 145 HOH HOH . J 5 HOH B 79 648 148 HOH HOH . J 5 HOH B 80 649 149 HOH HOH . J 5 HOH B 81 650 150 HOH HOH . J 5 HOH B 82 651 151 HOH HOH . J 5 HOH B 83 653 153 HOH HOH . J 5 HOH B 84 655 155 HOH HOH . J 5 HOH B 85 656 156 HOH HOH . J 5 HOH B 86 657 157 HOH HOH . J 5 HOH B 87 658 158 HOH HOH . J 5 HOH B 88 662 162 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 . . . F 2 -36.993 36.293 15.847 1 58.49 ? N SAH 401 B 1 HETATM 2 C CA SAH . . . F 2 -36.684 36.291 14.41 1 57.85 ? CA SAH 401 B 1 HETATM 3 C CB SAH . . . F 2 -36.736 34.854 13.889 1 58.73 ? CB SAH 401 B 1 HETATM 4 C CG SAH . . . F 2 -36.154 34.777 12.477 1 57 ? CG SAH 401 B 1 HETATM 5 S SD SAH . . . F 2 -36.307 33.126 11.705 1 58.51 ? SD SAH 401 B 1 HETATM 6 C C SAH . . . F 2 -37.694 37.152 13.645 1 58.39 ? C SAH 401 B 1 HETATM 7 O O SAH . . . F 2 -37.276 37.744 12.626 1 60.33 ? O SAH 401 B 1 HETATM 8 O OXT SAH . . . F 2 -38.862 37.204 14.087 1 55.03 ? OXT SAH 401 B 1 HETATM 9 C C5' SAH . . . F 2 -35.595 32.007 12.967 1 57.76 ? C5' SAH 401 B 1 HETATM 10 C C4' SAH . . . F 2 -34.242 32.439 13.534 1 57.45 ? C4' SAH 401 B 1 HETATM 11 O O4' SAH . . . F 2 -33.689 31.306 14.228 1 57.78 ? O4' SAH 401 B 1 HETATM 12 C C3' SAH . . . F 2 -33.234 32.802 12.439 1 57.09 ? C3' SAH 401 B 1 HETATM 13 O O3' SAH . . . F 2 -32.544 33.998 12.812 1 55.19 ? O3' SAH 401 B 1 HETATM 14 C C2' SAH . . . F 2 -32.273 31.614 12.454 1 58.32 ? C2' SAH 401 B 1 HETATM 15 O O2' SAH . . . F 2 -30.964 32.042 12.067 1 57.65 ? O2' SAH 401 B 1 HETATM 16 C C1' SAH . . . F 2 -32.282 31.328 13.953 1 58.8 ? C1' SAH 401 B 1 HETATM 17 N N9 SAH . . . F 2 -31.681 30.01 14.259 1 62.78 ? N9 SAH 401 B 1 HETATM 18 C C8 SAH . . . F 2 -31.808 28.902 13.532 1 63.63 ? C8 SAH 401 B 1 HETATM 19 N N7 SAH . . . F 2 -31.218 27.887 14.162 1 64.12 ? N7 SAH 401 B 1 HETATM 20 C C5 SAH . . . F 2 -30.708 28.35 15.299 1 63.58 ? C5 SAH 401 B 1 HETATM 21 C C6 SAH . . . F 2 -30.023 27.776 16.363 1 63.99 ? C6 SAH 401 B 1 HETATM 22 N N6 SAH . . . F 2 -29.767 26.472 16.389 1 63.59 ? N6 SAH 401 B 1 HETATM 23 N N1 SAH . . . F 2 -29.657 28.551 17.393 1 65.12 ? N1 SAH 401 B 1 HETATM 24 C C2 SAH . . . F 2 -29.937 29.842 17.408 1 64.62 ? C2 SAH 401 B 1 HETATM 25 N N3 SAH . . . F 2 -30.591 30.42 16.417 1 63.83 ? N3 SAH 401 B 1 HETATM 26 C C4 SAH . . . F 2 -30.993 29.707 15.356 1 63.6 ? C4 SAH 401 B 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #