data_1BKY # _model_server_result.job_id HL3fBfk7C51XaMcKJsqi6g _model_server_result.datetime_utc '2024-11-20 01:12:27' _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 1bky # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 1BKY # _exptl.entry_id 1BKY _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 1BKY _cell.length_a 84.5 _cell.length_b 67.21 _cell.length_c 79.56 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BKY _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,D _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 293 n n N HN1 SAH sing 294 n n N HN2 SAH sing 295 n n CA CB SAH sing 296 n n CA C SAH sing 297 n n CA HA SAH sing 298 n n CB CG SAH sing 299 n n CB HB1 SAH sing 300 n n CB HB2 SAH sing 301 n n CG SD SAH sing 302 n n CG HG1 SAH sing 303 n n CG HG2 SAH sing 304 n n SD C5' SAH sing 305 n n C O SAH doub 306 n n C OXT SAH sing 307 n n OXT HXT SAH sing 308 n n C5' C4' SAH sing 309 n n C5' "H5'1" SAH sing 310 n n C5' "H5'2" SAH sing 311 n n C4' O4' SAH sing 312 n n C4' C3' SAH sing 313 n n C4' H4' SAH sing 314 n n O4' C1' SAH sing 315 n n C3' O3' SAH sing 316 n n C3' C2' SAH sing 317 n n C3' H3' SAH sing 318 n n O3' HO3' SAH sing 319 n n C2' O2' SAH sing 320 n n C2' C1' SAH sing 321 n n C2' H2' SAH sing 322 n n O2' HO2' SAH sing 323 n n C1' N9 SAH sing 324 n n C1' H1' SAH sing 325 n n N9 C8 SAH sing 326 n y N9 C4 SAH sing 327 n y C8 N7 SAH doub 328 n y C8 H8 SAH sing 329 n n N7 C5 SAH sing 330 n y C5 C6 SAH sing 331 n y C5 C4 SAH doub 332 n y C6 N6 SAH sing 333 n n C6 N1 SAH doub 334 n y N6 HN61 SAH sing 335 n n N6 HN62 SAH sing 336 n n N1 C2 SAH sing 337 n y C2 N3 SAH doub 338 n y C2 H2 SAH sing 339 n n N3 C4 SAH sing 340 n y # _atom_sites.entry_id 1BKY _atom_sites.fract_transf_matrix[1][1] 0.011834 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006108 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014879 _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] 0.014145 _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 1MC A 1 600 600 1MC 1MC . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 2 HOH HOH . D 4 HOH A 3 603 3 HOH HOH . D 4 HOH A 4 604 4 HOH HOH . D 4 HOH A 5 605 5 HOH HOH . D 4 HOH A 6 606 6 HOH HOH . D 4 HOH A 7 607 7 HOH HOH . D 4 HOH A 8 608 8 HOH HOH . D 4 HOH A 9 609 9 HOH HOH . D 4 HOH A 10 610 10 HOH HOH . D 4 HOH A 11 611 11 HOH HOH . D 4 HOH A 12 612 12 HOH HOH . D 4 HOH A 13 613 13 HOH HOH . D 4 HOH A 14 614 14 HOH HOH . D 4 HOH A 15 615 15 HOH HOH . D 4 HOH A 16 616 16 HOH HOH . D 4 HOH A 17 617 17 HOH HOH . D 4 HOH A 18 618 18 HOH HOH . D 4 HOH A 19 619 19 HOH HOH . D 4 HOH A 20 620 20 HOH HOH . D 4 HOH A 21 621 21 HOH HOH . D 4 HOH A 22 622 22 HOH HOH . D 4 HOH A 23 623 23 HOH HOH . D 4 HOH A 24 624 24 HOH HOH . D 4 HOH A 25 625 25 HOH HOH . D 4 HOH A 26 626 26 HOH HOH . D 4 HOH A 27 627 27 HOH HOH . D 4 HOH A 28 628 28 HOH HOH . D 4 HOH A 29 629 29 HOH HOH . D 4 HOH A 30 630 30 HOH HOH . D 4 HOH A 31 631 31 HOH HOH . D 4 HOH A 32 632 32 HOH HOH . D 4 HOH A 33 633 33 HOH HOH . D 4 HOH A 34 634 34 HOH HOH . D 4 HOH A 35 635 35 HOH HOH . D 4 HOH A 36 636 36 HOH HOH . D 4 HOH A 37 637 37 HOH HOH . D 4 HOH A 38 638 38 HOH HOH . D 4 HOH A 39 639 39 HOH HOH . D 4 HOH A 40 640 40 HOH HOH . D 4 HOH A 41 641 41 HOH HOH . D 4 HOH A 42 642 42 HOH HOH . D 4 HOH A 43 643 43 HOH HOH . D 4 HOH A 44 644 44 HOH HOH . D 4 HOH A 45 645 45 HOH HOH . D 4 HOH A 46 646 46 HOH HOH . D 4 HOH A 47 647 47 HOH HOH . D 4 HOH A 48 648 48 HOH HOH . D 4 HOH A 49 649 49 HOH HOH . D 4 HOH A 50 650 50 HOH HOH . D 4 HOH A 51 651 51 HOH HOH . D 4 HOH A 52 652 52 HOH HOH . D 4 HOH A 53 653 53 HOH HOH . D 4 HOH A 54 654 54 HOH HOH . D 4 HOH A 55 655 55 HOH HOH . D 4 HOH A 56 656 56 HOH HOH . D 4 HOH A 57 657 57 HOH HOH . D 4 HOH A 58 658 58 HOH HOH . D 4 HOH A 59 659 59 HOH HOH . D 4 HOH A 60 660 60 HOH HOH . D 4 HOH A 61 661 61 HOH HOH . D 4 HOH A 62 662 62 HOH HOH . D 4 HOH A 63 663 63 HOH HOH . D 4 HOH A 64 664 64 HOH HOH . D 4 HOH A 65 665 65 HOH HOH . D 4 HOH A 66 666 66 HOH HOH . D 4 HOH A 67 667 67 HOH HOH . D 4 HOH A 68 668 68 HOH HOH . D 4 HOH A 69 669 69 HOH HOH . D 4 HOH A 70 670 70 HOH HOH . D 4 HOH A 71 671 71 HOH HOH . D 4 HOH A 72 672 72 HOH HOH . D 4 HOH A 73 673 73 HOH HOH . D 4 HOH A 74 674 74 HOH HOH . D 4 HOH A 75 675 75 HOH HOH . D 4 HOH A 76 676 76 HOH HOH . D 4 HOH A 77 677 77 HOH HOH . D 4 HOH A 78 678 78 HOH HOH . D 4 HOH A 79 679 79 HOH HOH . D 4 HOH A 80 680 80 HOH HOH . D 4 HOH A 81 681 81 HOH HOH . D 4 HOH A 82 682 82 HOH HOH . D 4 HOH A 83 683 83 HOH HOH . D 4 HOH A 84 684 84 HOH HOH . D 4 HOH A 85 685 85 HOH HOH . D 4 HOH A 86 686 86 HOH HOH . D 4 HOH A 87 687 87 HOH HOH . D 4 HOH A 88 688 88 HOH HOH . D 4 HOH A 89 689 89 HOH HOH . D 4 HOH A 90 690 90 HOH HOH . D 4 HOH A 91 691 91 HOH HOH . D 4 HOH A 92 692 92 HOH HOH . D 4 HOH A 93 693 93 HOH HOH . D 4 HOH A 94 694 94 HOH HOH . D 4 HOH A 95 695 95 HOH HOH . D 4 HOH A 96 696 96 HOH HOH . D 4 HOH A 97 697 97 HOH HOH . D 4 HOH A 98 698 98 HOH HOH . D 4 HOH A 99 699 8 HOH HOH . D 4 HOH A 100 700 9 HOH HOH . D 4 HOH A 101 701 10 HOH HOH . D 4 HOH A 102 702 11 HOH HOH . D 4 HOH A 103 703 12 HOH HOH . D 4 HOH A 104 704 13 HOH HOH . D 4 HOH A 105 705 14 HOH HOH . D 4 HOH A 106 706 15 HOH HOH . D 4 HOH A 107 707 16 HOH HOH . D 4 HOH A 108 708 17 HOH HOH . D 4 HOH A 109 709 18 HOH HOH . D 4 HOH A 110 710 19 HOH HOH . D 4 HOH A 111 711 20 HOH HOH . D 4 HOH A 112 712 21 HOH HOH . D 4 HOH A 113 713 22 HOH HOH . D 4 HOH A 114 714 23 HOH HOH . D 4 HOH A 115 715 24 HOH HOH . D 4 HOH A 116 716 25 HOH HOH . D 4 HOH A 117 717 26 HOH HOH . D 4 HOH A 118 718 27 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 -4.066 12.805 24.187 1 2 ? N SAH 400 A 1 HETATM 2 C CA SAH . . . B 2 -4.232 11.791 25.212 1 2 ? CA SAH 400 A 1 HETATM 3 C CB SAH . . . B 2 -2.94 10.991 25.335 1 2 ? CB SAH 400 A 1 HETATM 4 C CG SAH . . . B 2 -2.552 10.287 24.025 1 2 ? CG SAH 400 A 1 HETATM 5 S SD SAH . . . B 2 -1.255 9.05 24.176 1 2 ? SD SAH 400 A 1 HETATM 6 C C SAH . . . B 2 -4.638 12.402 26.553 1 4.01 ? C SAH 400 A 1 HETATM 7 O O SAH . . . B 2 -5 13.595 26.549 1 2.11 ? O SAH 400 A 1 HETATM 8 O OXT SAH . . . B 2 -4.49 11.726 27.606 1 2.42 ? OXT SAH 400 A 1 HETATM 9 C C5' SAH . . . B 2 -1.245 8.486 22.459 1 6.71 ? C5' SAH 400 A 1 HETATM 10 C C4' SAH . . . B 2 -2.559 7.854 22.012 1 7.78 ? C4' SAH 400 A 1 HETATM 11 O O4' SAH . . . B 2 -2.593 7.721 20.574 1 6.31 ? O4' SAH 400 A 1 HETATM 12 C C3' SAH . . . B 2 -2.745 6.443 22.574 1 10.22 ? C3' SAH 400 A 1 HETATM 13 O O3' SAH . . . B 2 -3.908 6.391 23.429 1 12.06 ? O3' SAH 400 A 1 HETATM 14 C C2' SAH . . . B 2 -2.939 5.646 21.352 1 9.09 ? C2' SAH 400 A 1 HETATM 15 O O2' SAH . . . B 2 -3.842 4.472 21.523 1 13.45 ? O2' SAH 400 A 1 HETATM 16 C C1' SAH . . . B 2 -3.504 6.628 20.412 1 8.76 ? C1' SAH 400 A 1 HETATM 17 N N9 SAH . . . B 2 -3.465 6.144 19.01 1 11.74 ? N9 SAH 400 A 1 HETATM 18 C C8 SAH . . . B 2 -2.413 5.579 18.261 1 10.76 ? C8 SAH 400 A 1 HETATM 19 N N7 SAH . . . B 2 -2.761 5.321 17.017 1 11.43 ? N7 SAH 400 A 1 HETATM 20 C C5 SAH . . . B 2 -4.116 5.732 16.936 1 13.27 ? C5 SAH 400 A 1 HETATM 21 C C6 SAH . . . B 2 -5.066 5.72 15.911 1 12.3 ? C6 SAH 400 A 1 HETATM 22 N N6 SAH . . . B 2 -4.836 5.287 14.678 1 14.51 ? N6 SAH 400 A 1 HETATM 23 N N1 SAH . . . B 2 -6.271 6.165 16.199 1 11.69 ? N1 SAH 400 A 1 HETATM 24 C C2 SAH . . . B 2 -6.54 6.608 17.406 1 12.58 ? C2 SAH 400 A 1 HETATM 25 N N3 SAH . . . B 2 -5.78 6.692 18.445 1 10.59 ? N3 SAH 400 A 1 HETATM 26 C C4 SAH . . . B 2 -4.549 6.225 18.139 1 12.52 ? C4 SAH 400 A 1 HETATM 27 H HN1 SAH . . . B 2 -4.391 12.608 23.285 1 0 ? HN1 SAH 400 A 1 HETATM 28 H HO2' SAH . . . B 2 -3.645 3.986 20.73 1 0 ? HO2' SAH 400 A 1 HETATM 29 H HN61 SAH . . . B 2 -3.908 4.98 14.457 1 0 ? HN61 SAH 400 A 1 HETATM 30 H HN62 SAH . . . B 2 -5.571 5.239 13.988 1 0 ? HN62 SAH 400 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 30 #