data_5ISC # _model_server_result.job_id HDa-tR_UdUgVvrfy8lrJnA _model_server_result.datetime_utc '2024-10-12 19:23:42' _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":"K","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 . . . K 2 22.023 37.596 179.513 1 89.43 ? N SAO 501 C 1 HETATM 2 C CA SAO . . . K 2 23.184 36.988 178.805 1 84.53 ? CA SAO 501 C 1 HETATM 3 C CB SAO . . . K 2 24.207 36.436 179.803 1 81.14 ? CB SAO 501 C 1 HETATM 4 C CG SAO . . . K 2 23.592 35.646 180.953 1 78.08 ? CG SAO 501 C 1 HETATM 5 S SD SAO . . . K 2 24.972 35.282 182.078 1 75.2 ? SD SAO 501 C 1 HETATM 6 C C SAO . . . K 2 22.685 35.901 177.848 1 82.8 ? C SAO 501 C 1 HETATM 7 O O SAO . . . K 2 23.534 35.329 177.126 1 82.35 ? O SAO 501 C 1 HETATM 8 O OXT SAO . . . K 2 21.455 35.66 177.865 1 82.16 ? OXT SAO 501 C 1 HETATM 9 C C5' SAO . . . K 2 24.793 36.535 183.377 1 70.83 ? C5' SAO 501 C 1 HETATM 10 C C4' SAO . . . K 2 25.59 37.778 183.028 1 67.16 ? C4' SAO 501 C 1 HETATM 11 O O4' SAO . . . K 2 25.296 38.786 184.018 1 65.93 ? O4' SAO 501 C 1 HETATM 12 C C3' SAO . . . K 2 27.113 37.574 183.031 1 65.46 ? C3' SAO 501 C 1 HETATM 13 O O3' SAO . . . K 2 27.689 38.074 181.827 1 65.06 ? O3' SAO 501 C 1 HETATM 14 C C2' SAO . . . K 2 27.589 38.328 184.287 1 64.08 ? C2' SAO 501 C 1 HETATM 15 O O2' SAO . . . K 2 28.861 38.945 184.092 1 62.45 ? O2' SAO 501 C 1 HETATM 16 C C1' SAO . . . K 2 26.493 39.382 184.474 1 64.69 ? C1' SAO 501 C 1 HETATM 17 N N9 SAO . . . K 2 26.285 39.81 185.856 1 63.42 ? N9 SAO 501 C 1 HETATM 18 C C8 SAO . . . K 2 26.165 39.011 186.954 1 63.06 ? C8 SAO 501 C 1 HETATM 19 N N7 SAO . . . K 2 25.916 39.645 188.082 1 62.17 ? N7 SAO 501 C 1 HETATM 20 C C5 SAO . . . K 2 25.875 40.974 187.671 1 61.54 ? C5 SAO 501 C 1 HETATM 21 C C6 SAO . . . K 2 25.633 42.165 188.393 1 60.17 ? C6 SAO 501 C 1 HETATM 22 N N6 SAO . . . K 2 25.364 42.206 189.699 1 58.37 ? N6 SAO 501 C 1 HETATM 23 N N1 SAO . . . K 2 25.656 43.327 187.696 1 60.58 ? N1 SAO 501 C 1 HETATM 24 C C2 SAO . . . K 2 25.893 43.287 186.383 1 61.02 ? C2 SAO 501 C 1 HETATM 25 N N3 SAO . . . K 2 26.126 42.224 185.602 1 61.81 ? N3 SAO 501 C 1 HETATM 26 C C4 SAO . . . K 2 26.103 41.096 186.317 1 62.37 ? C4 SAO 501 C 1 HETATM 27 H H2 SAO . . . K 2 25.897 44.257 185.888 1 73.22 ? H2 SAO 501 C 1 HETATM 28 H HN2 SAO . . . K 2 21.494 36.795 179.84 1 107.31 ? HN2 SAO 501 C 1 HETATM 29 H H3 SAO . . . K 2 21.441 38.155 178.897 1 107.31 ? H3 SAO 501 C 1 HETATM 30 H HN1 SAO . . . K 2 22.288 38.166 180.31 1 107.31 ? HN1 SAO 501 C 1 HETATM 31 H HA SAO . . . K 2 23.66 37.753 178.194 1 101.44 ? HA SAO 501 C 1 HETATM 32 H HB1 SAO . . . K 2 24.761 37.282 180.205 1 97.37 ? HB1 SAO 501 C 1 HETATM 33 H HB2 SAO . . . K 2 24.967 35.847 179.292 1 97.37 ? HB2 SAO 501 C 1 HETATM 34 H HG2 SAO . . . K 2 22.82 36.21 181.474 1 93.7 ? HG2 SAO 501 C 1 HETATM 35 H HG1 SAO . . . K 2 23.125 34.713 180.639 1 93.7 ? HG1 SAO 501 C 1 HETATM 36 H "H5'2" SAO . . . K 2 25.112 36.116 184.33 1 84.99 ? "H5'2" SAO 501 C 1 HETATM 37 H "H5'1" SAO . . . K 2 23.733 36.751 183.503 1 84.99 ? "H5'1" SAO 501 C 1 HETATM 38 H H4' SAO . . . K 2 25.22 38.202 182.097 1 80.59 ? H4' SAO 501 C 1 HETATM 39 H H3' SAO . . . K 2 27.437 36.535 183.01 1 78.55 ? H3' SAO 501 C 1 HETATM 40 H HO3' SAO . . . K 2 27.889 39.04 181.945 1 78.07 ? HO3' SAO 501 C 1 HETATM 41 H H2' SAO . . . K 2 27.75 37.679 185.146 1 76.89 ? H2' SAO 501 C 1 HETATM 42 H HO2' SAO . . . K 2 28.787 39.678 183.426 1 74.94 ? HO2' SAO 501 C 1 HETATM 43 H H1' SAO . . . K 2 26.656 40.283 183.884 1 77.63 ? H1' SAO 501 C 1 HETATM 44 H H8 SAO . . . K 2 26.268 37.928 186.901 1 75.68 ? H8 SAO 501 C 1 HETATM 45 H HN61 SAO . . . K 2 25.323 41.348 190.238 1 70.04 ? HN61 SAO 501 C 1 HETATM 46 H HN62 SAO . . . K 2 25.196 43.085 190.178 1 70.04 ? HN62 SAO 501 C 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #