data_5ISC # _model_server_result.job_id dn-t64WH_LlZ6DBJ0HqwhQ _model_server_result.datetime_utc '2024-11-25 06:55:43' _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 5isc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 5ISC # _exptl.entry_id 5ISC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 385.419 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine" _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 90 _cell.entry_id 5ISC _cell.length_a 79.123 _cell.length_b 101.043 _cell.length_c 211.349 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ISC _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details 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,K,L,M,N,O,P,Q,R,S,T,U _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 E N N ? 2 K N N # _chem_comp.formula 'C14 H21 N6 O5 S 1' _chem_comp.formula_weight 385.419 _chem_comp.id SAO _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine" _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms S-ADENOSYL-L-HOMOCYSTEINE # 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 N6 C6 SAO sing 380 n n C6 C5 SAO doub 381 n y C6 N1 SAO sing 382 n y N7 C5 SAO sing 383 n y N7 C8 SAO doub 384 n y C5 C4 SAO sing 385 n y N1 C2 SAO doub 386 n y C8 N9 SAO sing 387 n y C4 N9 SAO sing 388 n y C4 N3 SAO doub 389 n y C2 N3 SAO sing 390 n y N9 C1' SAO sing 391 n n C1' C2' SAO sing 392 n n C1' O4' SAO sing 393 n n C2' O2' SAO sing 394 n n C2' C3' SAO sing 395 n n O4' C4' SAO sing 396 n n C5' C4' SAO sing 397 n n C5' SD SAO sing 398 n n C3' C4' SAO sing 399 n n C3' O3' SAO sing 400 n n SD CG SAO sing 401 n n CG CB SAO sing 402 n n CB CA SAO sing 403 n n N CA SAO sing 404 n n CA C SAO sing 405 n n O C SAO doub 406 n n C OXT SAO sing 407 n n N HN2 SAO sing 408 n n N H3 SAO sing 409 n n N HN1 SAO sing 410 n n CA HA SAO sing 411 n n CB HB1 SAO sing 412 n n CB HB2 SAO sing 413 n n CG HG2 SAO sing 414 n n CG HG1 SAO sing 415 n n OXT H1 SAO sing 416 n n C5' "H5'2" SAO sing 417 n n C5' "H5'1" SAO sing 418 n n C4' H4' SAO sing 419 n n C3' H3' SAO sing 420 n n O3' HO3' SAO sing 421 n n C2' H2' SAO sing 422 n n O2' HO2' SAO sing 423 n n C1' H1' SAO sing 424 n n C8 H8 SAO sing 425 n n N6 HN61 SAO sing 426 n n N6 HN62 SAO sing 427 n n C2 H2 SAO sing 428 n n # _atom_sites.entry_id 5ISC _atom_sites.fract_transf_matrix[1][1] 0.012639 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009897 _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] 0.004732 _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 E 2 SAO A 1 501 1 SAO SAH . F 3 EDO A 1 502 2 EDO EDO . G 3 EDO A 1 503 3 EDO EDO . H 3 EDO A 1 504 6 EDO EDO . I 4 6D0 B 1 501 2 6D0 491 . J 3 EDO B 1 502 1 EDO EDO . K 2 SAO C 1 501 3 SAO SAH . L 3 EDO C 1 502 4 EDO EDO . M 5 DXE C 1 503 7 DXE DXE . N 6 M2M C 1 504 9 M2M M2M . O 4 6D0 D 1 501 4 6D0 491 . P 3 EDO D 1 502 5 EDO EDO . Q 5 DXE D 1 503 8 DXE DXE . R 7 HOH A 1 601 119 HOH HOH . R 7 HOH A 2 602 37 HOH HOH . R 7 HOH A 3 603 60 HOH HOH . R 7 HOH A 4 604 30 HOH HOH . R 7 HOH A 5 605 48 HOH HOH . R 7 HOH A 6 606 92 HOH HOH . R 7 HOH A 7 607 32 HOH HOH . R 7 HOH A 8 608 73 HOH HOH . R 7 HOH A 9 609 26 HOH HOH . R 7 HOH A 10 610 50 HOH HOH . R 7 HOH A 11 611 28 HOH HOH . R 7 HOH A 12 612 99 HOH HOH . R 7 HOH A 13 613 118 HOH HOH . R 7 HOH A 14 614 96 HOH HOH . R 7 HOH A 15 615 88 HOH HOH . R 7 HOH A 16 616 120 HOH HOH . R 7 HOH A 17 617 103 HOH HOH . R 7 HOH A 18 618 15 HOH HOH . R 7 HOH A 19 619 54 HOH HOH . R 7 HOH A 20 620 57 HOH HOH . R 7 HOH A 21 621 97 HOH HOH . R 7 HOH A 22 622 27 HOH HOH . R 7 HOH A 23 623 53 HOH HOH . R 7 HOH A 24 624 20 HOH HOH . R 7 HOH A 25 625 72 HOH HOH . R 7 HOH A 26 626 83 HOH HOH . R 7 HOH A 27 627 34 HOH HOH . R 7 HOH A 28 628 25 HOH HOH . R 7 HOH A 29 629 71 HOH HOH . R 7 HOH A 30 630 62 HOH HOH . R 7 HOH A 31 631 106 HOH HOH . R 7 HOH A 32 632 80 HOH HOH . R 7 HOH A 33 633 100 HOH HOH . R 7 HOH A 34 634 93 HOH HOH . S 7 HOH B 1 601 87 HOH HOH . S 7 HOH B 2 602 3 HOH HOH . S 7 HOH B 3 603 78 HOH HOH . S 7 HOH B 4 604 75 HOH HOH . S 7 HOH B 5 605 70 HOH HOH . S 7 HOH B 6 606 21 HOH HOH . S 7 HOH B 7 607 16 HOH HOH . S 7 HOH B 8 608 17 HOH HOH . S 7 HOH B 9 609 102 HOH HOH . S 7 HOH B 10 610 91 HOH HOH . S 7 HOH B 11 611 23 HOH HOH . S 7 HOH B 12 612 51 HOH HOH . S 7 HOH B 13 613 82 HOH HOH . S 7 HOH B 14 614 98 HOH HOH . S 7 HOH B 15 615 22 HOH HOH . S 7 HOH B 16 616 69 HOH HOH . S 7 HOH B 17 617 116 HOH HOH . S 7 HOH B 18 618 38 HOH HOH . S 7 HOH B 19 619 101 HOH HOH . S 7 HOH B 20 620 109 HOH HOH . S 7 HOH B 21 621 86 HOH HOH . T 7 HOH C 1 601 29 HOH HOH . T 7 HOH C 2 602 67 HOH HOH . T 7 HOH C 3 603 43 HOH HOH . T 7 HOH C 4 604 74 HOH HOH . T 7 HOH C 5 605 117 HOH HOH . T 7 HOH C 6 606 11 HOH HOH . T 7 HOH C 7 607 1 HOH HOH . T 7 HOH C 8 608 2 HOH HOH . T 7 HOH C 9 609 6 HOH HOH . T 7 HOH C 10 610 5 HOH HOH . T 7 HOH C 11 611 104 HOH HOH . T 7 HOH C 12 612 79 HOH HOH . T 7 HOH C 13 613 84 HOH HOH . T 7 HOH C 14 614 85 HOH HOH . T 7 HOH C 15 615 95 HOH HOH . T 7 HOH C 16 616 4 HOH HOH . T 7 HOH C 17 617 113 HOH HOH . T 7 HOH C 18 618 59 HOH HOH . T 7 HOH C 19 619 24 HOH HOH . T 7 HOH C 20 620 90 HOH HOH . T 7 HOH C 21 621 12 HOH HOH . T 7 HOH C 22 622 64 HOH HOH . T 7 HOH C 23 623 18 HOH HOH . T 7 HOH C 24 624 47 HOH HOH . T 7 HOH C 25 625 10 HOH HOH . T 7 HOH C 26 626 14 HOH HOH . T 7 HOH C 27 627 52 HOH HOH . T 7 HOH C 28 628 76 HOH HOH . T 7 HOH C 29 629 89 HOH HOH . T 7 HOH C 30 630 41 HOH HOH . T 7 HOH C 31 631 45 HOH HOH . T 7 HOH C 32 632 31 HOH HOH . T 7 HOH C 33 633 111 HOH HOH . T 7 HOH C 34 634 56 HOH HOH . T 7 HOH C 35 635 108 HOH HOH . T 7 HOH C 36 636 55 HOH HOH . T 7 HOH C 37 637 63 HOH HOH . T 7 HOH C 38 638 44 HOH HOH . T 7 HOH C 39 639 40 HOH HOH . U 7 HOH D 1 601 107 HOH HOH . U 7 HOH D 2 602 81 HOH HOH . U 7 HOH D 3 603 66 HOH HOH . U 7 HOH D 4 604 61 HOH HOH . U 7 HOH D 5 605 33 HOH HOH . U 7 HOH D 6 606 77 HOH HOH . U 7 HOH D 7 607 7 HOH HOH . U 7 HOH D 8 608 94 HOH HOH . U 7 HOH D 9 609 42 HOH HOH . U 7 HOH D 10 610 8 HOH HOH . U 7 HOH D 11 611 68 HOH HOH . U 7 HOH D 12 612 13 HOH HOH . U 7 HOH D 13 613 58 HOH HOH . U 7 HOH D 14 614 19 HOH HOH . U 7 HOH D 15 615 39 HOH HOH . U 7 HOH D 16 616 49 HOH HOH . U 7 HOH D 17 617 110 HOH HOH . U 7 HOH D 18 618 114 HOH HOH . U 7 HOH D 19 619 105 HOH HOH . U 7 HOH D 20 620 9 HOH HOH . U 7 HOH D 21 621 115 HOH HOH . U 7 HOH D 22 622 112 HOH HOH . U 7 HOH D 23 623 46 HOH HOH . U 7 HOH D 24 624 35 HOH HOH . U 7 HOH D 25 625 65 HOH HOH . U 7 HOH D 26 626 36 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 SAO . . . E 2 54.29 39.429 138.07 1 72.01 ? N SAO 501 A 1 HETATM 2 C CA SAO . . . E 2 53.362 38.305 138.383 1 71.73 ? CA SAO 501 A 1 HETATM 3 C CB SAO . . . E 2 52.582 37.864 137.139 1 70.3 ? CB SAO 501 A 1 HETATM 4 C CG SAO . . . E 2 53.444 37.282 136.023 1 69.1 ? CG SAO 501 A 1 HETATM 5 S SD SAO . . . E 2 52.27 36.445 134.909 1 67.94 ? SD SAO 501 A 1 HETATM 6 C C SAO . . . E 2 54.149 37.151 139.019 1 72.54 ? C SAO 501 A 1 HETATM 7 O O SAO . . . E 2 55.293 36.907 138.563 1 72.35 ? O SAO 501 A 1 HETATM 8 O OXT SAO . . . E 2 53.591 36.542 139.966 1 72.89 ? OXT SAO 501 A 1 HETATM 9 C C5' SAO . . . E 2 52.156 37.541 133.467 1 66.05 ? C5' SAO 501 A 1 HETATM 10 C C4' SAO . . . E 2 51.326 38.776 133.762 1 64.61 ? C4' SAO 501 A 1 HETATM 11 O O4' SAO . . . E 2 51.614 39.744 132.728 1 63.86 ? O4' SAO 501 A 1 HETATM 12 C C3' SAO . . . E 2 49.8 38.564 133.752 1 63.95 ? C3' SAO 501 A 1 HETATM 13 O O3' SAO . . . E 2 49.186 39.146 134.9 1 63.67 ? O3' SAO 501 A 1 HETATM 14 C C2' SAO . . . E 2 49.345 39.263 132.462 1 63.32 ? C2' SAO 501 A 1 HETATM 15 O O2' SAO . . . E 2 48.033 39.816 132.571 1 62.35 ? O2' SAO 501 A 1 HETATM 16 C C1' SAO . . . E 2 50.406 40.353 132.322 1 63.62 ? C1' SAO 501 A 1 HETATM 17 N N9 SAO . . . E 2 50.577 40.867 130.967 1 63.45 ? N9 SAO 501 A 1 HETATM 18 C C8 SAO . . . E 2 50.701 40.148 129.817 1 63.02 ? C8 SAO 501 A 1 HETATM 19 N N7 SAO . . . E 2 50.862 40.866 128.722 1 62.44 ? N7 SAO 501 A 1 HETATM 20 C C5 SAO . . . E 2 50.834 42.166 129.216 1 62.55 ? C5 SAO 501 A 1 HETATM 21 C C6 SAO . . . E 2 50.939 43.417 128.558 1 62.1 ? C6 SAO 501 A 1 HETATM 22 N N6 SAO . . . E 2 51.08 43.558 127.238 1 61.07 ? N6 SAO 501 A 1 HETATM 23 N N1 SAO . . . E 2 50.868 44.528 129.327 1 62.45 ? N1 SAO 501 A 1 HETATM 24 C C2 SAO . . . E 2 50.701 44.392 130.647 1 62.59 ? C2 SAO 501 A 1 HETATM 25 N N3 SAO . . . E 2 50.586 43.272 131.368 1 62.79 ? N3 SAO 501 A 1 HETATM 26 C C4 SAO . . . E 2 50.662 42.193 130.583 1 63.1 ? C4 SAO 501 A 1 HETATM 27 H H2 SAO . . . E 2 50.655 45.328 131.202 1 75.1 ? H2 SAO 501 A 1 HETATM 28 H HN2 SAO . . . E 2 53.829 39.915 137.307 1 86.41 ? HN2 SAO 501 A 1 HETATM 29 H H3 SAO . . . E 2 55.202 39.107 137.762 1 86.41 ? H3 SAO 501 A 1 HETATM 30 H HN1 SAO . . . E 2 54.419 40.073 138.843 1 86.41 ? HN1 SAO 501 A 1 HETATM 31 H HA SAO . . . E 2 52.655 38.647 139.136 1 86.08 ? HA SAO 501 A 1 HETATM 32 H HB1 SAO . . . E 2 52.05 38.736 136.762 1 84.36 ? HB1 SAO 501 A 1 HETATM 33 H HB2 SAO . . . E 2 51.785 37.173 137.41 1 84.36 ? HB2 SAO 501 A 1 HETATM 34 H HG2 SAO . . . E 2 53.995 38.051 135.483 1 82.92 ? HG2 SAO 501 A 1 HETATM 35 H HG1 SAO . . . E 2 54.185 36.566 136.374 1 82.92 ? HG1 SAO 501 A 1 HETATM 36 H "H5'2" SAO . . . E 2 51.744 36.984 132.627 1 79.26 ? "H5'2" SAO 501 A 1 HETATM 37 H "H5'1" SAO . . . E 2 53.169 37.801 133.161 1 79.26 ? "H5'1" SAO 501 A 1 HETATM 38 H H4' SAO . . . E 2 51.683 39.248 134.676 1 77.53 ? H4' SAO 501 A 1 HETATM 39 H H3' SAO . . . E 2 49.472 37.528 133.824 1 76.74 ? H3' SAO 501 A 1 HETATM 40 H HO3' SAO . . . E 2 49.145 40.131 134.776 1 76.4 ? HO3' SAO 501 A 1 HETATM 41 H H2' SAO . . . E 2 49.267 38.589 131.61 1 75.99 ? H2' SAO 501 A 1 HETATM 42 H HO2' SAO . . . E 2 47.959 40.357 133.4 1 74.82 ? HO2' SAO 501 A 1 HETATM 43 H H1' SAO . . . E 2 50.235 41.211 132.97 1 76.34 ? H1' SAO 501 A 1 HETATM 44 H H8 SAO . . . E 2 50.67 39.06 129.806 1 75.63 ? H8 SAO 501 A 1 HETATM 45 H HN61 SAO . . . E 2 51.119 42.74 126.638 1 73.28 ? HN61 SAO 501 A 1 HETATM 46 H HN62 SAO . . . E 2 51.151 44.474 126.807 1 73.28 ? HN62 SAO 501 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #