data_1CBF # _model_server_result.job_id ylkvmC9tgaKLR7z7ecqQHA _model_server_result.datetime_utc '2025-02-27 16:16:34' _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 1cbf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":300}' # _entry.id 1CBF # _exptl.entry_id 1CBF _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 1CBF _cell.length_a 80.7 _cell.length_b 80.7 _cell.length_c 109.4 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CBF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 6_556 -x,-x+y,-z+4/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 145.866667 # _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 281 n n N HN1 SAH sing 282 n n N HN2 SAH sing 283 n n CA CB SAH sing 284 n n CA C SAH sing 285 n n CA HA SAH sing 286 n n CB CG SAH sing 287 n n CB HB1 SAH sing 288 n n CB HB2 SAH sing 289 n n CG SD SAH sing 290 n n CG HG1 SAH sing 291 n n CG HG2 SAH sing 292 n n SD C5' SAH sing 293 n n C O SAH doub 294 n n C OXT SAH sing 295 n n OXT HXT SAH sing 296 n n C5' C4' SAH sing 297 n n C5' "H5'1" SAH sing 298 n n C5' "H5'2" SAH sing 299 n n C4' O4' SAH sing 300 n n C4' C3' SAH sing 301 n n C4' H4' SAH sing 302 n n O4' C1' SAH sing 303 n n C3' O3' SAH sing 304 n n C3' C2' SAH sing 305 n n C3' H3' SAH sing 306 n n O3' HO3' SAH sing 307 n n C2' O2' SAH sing 308 n n C2' C1' SAH sing 309 n n C2' H2' SAH sing 310 n n O2' HO2' SAH sing 311 n n C1' N9 SAH sing 312 n n C1' H1' SAH sing 313 n n N9 C8 SAH sing 314 n y N9 C4 SAH sing 315 n y C8 N7 SAH doub 316 n y C8 H8 SAH sing 317 n n N7 C5 SAH sing 318 n y C5 C6 SAH sing 319 n y C5 C4 SAH doub 320 n y C6 N6 SAH sing 321 n n C6 N1 SAH doub 322 n y N6 HN61 SAH sing 323 n n N6 HN62 SAH sing 324 n n N1 C2 SAH sing 325 n y C2 N3 SAH doub 326 n y C2 H2 SAH sing 327 n n N3 C4 SAH sing 328 n y # _atom_sites.entry_id 1CBF _atom_sites.fract_transf_matrix[1][1] 0.012392 _atom_sites.fract_transf_matrix[1][2] 0.007154 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014309 _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] 0.009141 _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 PO4 A 1 400 400 PO4 PO4 . C 2 PO4 A 1 401 401 PO4 PO4 . D 3 SAH A 1 300 300 SAH SAH . E 4 HOH A 1 500 500 HOH HOH . E 4 HOH A 2 501 501 HOH HOH . E 4 HOH A 3 502 502 HOH HOH . E 4 HOH A 4 503 503 HOH HOH . E 4 HOH A 5 504 504 HOH HOH . E 4 HOH A 6 505 505 HOH HOH . E 4 HOH A 7 506 506 HOH HOH . E 4 HOH A 8 507 507 HOH HOH . E 4 HOH A 9 508 508 HOH HOH . E 4 HOH A 10 509 509 HOH HOH . E 4 HOH A 11 510 510 HOH HOH . E 4 HOH A 12 511 511 HOH HOH . E 4 HOH A 13 512 512 HOH HOH . E 4 HOH A 14 513 513 HOH HOH . E 4 HOH A 15 514 514 HOH HOH . E 4 HOH A 16 515 515 HOH HOH . E 4 HOH A 17 516 516 HOH HOH . E 4 HOH A 18 517 517 HOH HOH . E 4 HOH A 19 518 518 HOH HOH . E 4 HOH A 20 519 519 HOH HOH . E 4 HOH A 21 520 520 HOH HOH . E 4 HOH A 22 521 521 HOH HOH . E 4 HOH A 23 522 522 HOH HOH . E 4 HOH A 24 523 523 HOH HOH . E 4 HOH A 25 524 524 HOH HOH . E 4 HOH A 26 525 525 HOH HOH . E 4 HOH A 27 526 526 HOH HOH . E 4 HOH A 28 527 527 HOH HOH . E 4 HOH A 29 528 528 HOH HOH . E 4 HOH A 30 529 529 HOH HOH . E 4 HOH A 31 530 530 HOH HOH . E 4 HOH A 32 531 531 HOH HOH . E 4 HOH A 33 532 532 HOH HOH . E 4 HOH A 34 533 533 HOH HOH . E 4 HOH A 35 534 534 HOH HOH . E 4 HOH A 36 535 535 HOH HOH . E 4 HOH A 37 536 536 HOH HOH . E 4 HOH A 38 537 537 HOH HOH . E 4 HOH A 39 538 538 HOH HOH . E 4 HOH A 40 539 539 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 105 606 606 HOH HOH . E 4 HOH A 106 607 607 HOH HOH . E 4 HOH A 107 608 608 HOH HOH . E 4 HOH A 108 609 609 HOH HOH . E 4 HOH A 109 610 610 HOH HOH . E 4 HOH A 110 611 611 HOH HOH . E 4 HOH A 111 612 612 HOH HOH . E 4 HOH A 112 613 613 HOH HOH . E 4 HOH A 113 614 614 HOH HOH . E 4 HOH A 114 615 615 HOH HOH . E 4 HOH A 115 616 616 HOH HOH . E 4 HOH A 116 617 617 HOH HOH . E 4 HOH A 117 618 618 HOH HOH . E 4 HOH A 118 619 619 HOH HOH . E 4 HOH A 119 620 620 HOH HOH . E 4 HOH A 120 622 622 HOH HOH . E 4 HOH A 121 623 623 HOH HOH . E 4 HOH A 122 624 624 HOH HOH . E 4 HOH A 123 625 625 HOH HOH . E 4 HOH A 124 626 626 HOH HOH . E 4 HOH A 125 627 627 HOH HOH . E 4 HOH A 126 628 628 HOH HOH . E 4 HOH A 127 629 629 HOH HOH . E 4 HOH A 128 630 630 HOH HOH . E 4 HOH A 129 631 631 HOH HOH . E 4 HOH A 130 632 632 HOH HOH . E 4 HOH A 131 633 633 HOH HOH . E 4 HOH A 132 634 634 HOH HOH . E 4 HOH A 133 635 635 HOH HOH . E 4 HOH A 134 636 636 HOH HOH . E 4 HOH A 135 637 637 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 -13.86 33.077 81.097 1 23.55 ? N SAH 300 A 1 HETATM 2 C CA SAH . . . D 3 -12.879 33.807 80.261 1 23.02 ? CA SAH 300 A 1 HETATM 3 C CB SAH . . . D 3 -11.47 33.248 80.647 1 22.12 ? CB SAH 300 A 1 HETATM 4 C CG SAH . . . D 3 -10.998 33.492 82.133 1 19.04 ? CG SAH 300 A 1 HETATM 5 S SD SAH . . . D 3 -9.427 32.658 82.433 1 22.41 ? SD SAH 300 A 1 HETATM 6 C C SAH . . . D 3 -13.227 33.725 78.773 1 26.84 ? C SAH 300 A 1 HETATM 7 O O SAH . . . D 3 -14.249 33.009 78.382 1 24.63 ? O SAH 300 A 1 HETATM 8 O OXT SAH . . . D 3 -12.462 34.274 77.914 1 26.09 ? OXT SAH 300 A 1 HETATM 9 C C5' SAH . . . D 3 -8.3 34.012 81.852 1 19.95 ? C5' SAH 300 A 1 HETATM 10 C C4' SAH . . . D 3 -7.642 33.717 80.518 1 23.44 ? C4' SAH 300 A 1 HETATM 11 O O4' SAH . . . D 3 -8.544 33.996 79.428 1 23.59 ? O4' SAH 300 A 1 HETATM 12 C C3' SAH . . . D 3 -6.379 34.507 80.132 1 23.67 ? C3' SAH 300 A 1 HETATM 13 O O3' SAH . . . D 3 -5.2 33.913 80.703 1 20.91 ? O3' SAH 300 A 1 HETATM 14 C C2' SAH . . . D 3 -6.357 34.343 78.611 1 22.75 ? C2' SAH 300 A 1 HETATM 15 O O2' SAH . . . D 3 -5.967 33.012 78.232 1 22.51 ? O2' SAH 300 A 1 HETATM 16 C C1' SAH . . . D 3 -7.865 34.461 78.288 1 23.22 ? C1' SAH 300 A 1 HETATM 17 N N9 SAH . . . D 3 -8.281 35.808 78.102 1 23.92 ? N9 SAH 300 A 1 HETATM 18 C C8 SAH . . . D 3 -9.27 36.508 78.762 1 20.25 ? C8 SAH 300 A 1 HETATM 19 N N7 SAH . . . D 3 -9.546 37.647 78.116 1 19.45 ? N7 SAH 300 A 1 HETATM 20 C C5 SAH . . . D 3 -8.716 37.659 77.014 1 21.48 ? C5 SAH 300 A 1 HETATM 21 C C6 SAH . . . D 3 -8.527 38.544 75.98 1 23.52 ? C6 SAH 300 A 1 HETATM 22 N N6 SAH . . . D 3 -9.276 39.648 75.876 1 23.59 ? N6 SAH 300 A 1 HETATM 23 N N1 SAH . . . D 3 -7.573 38.289 75.042 1 23.34 ? N1 SAH 300 A 1 HETATM 24 C C2 SAH . . . D 3 -6.862 37.156 75.167 1 23.08 ? C2 SAH 300 A 1 HETATM 25 N N3 SAH . . . D 3 -6.981 36.214 76.12 1 23.33 ? N3 SAH 300 A 1 HETATM 26 C C4 SAH . . . D 3 -7.905 36.541 77.011 1 22.64 ? C4 SAH 300 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #