data_4RTK # _model_server_result.job_id BBdbGEYsXosPmkMwL7Ce8Q _model_server_result.datetime_utc '2025-02-05 11:55:52' _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 4rtk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4RTK # _exptl.entry_id 4RTK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _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 90 _cell.entry_id 4RTK _cell.length_a 36.331 _cell.length_b 63.044 _cell.length_c 142.185 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RTK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order hydrog WATSON-CRICK hydrog1 B N3 DC 2 F DC 2 1_555 C N1 DG 11 G DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 2 F DC 2 1_555 C O6 DG 11 G DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 2 F DC 2 1_555 C N2 DG 11 G DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 3 F DT 3 1_555 C N1 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 3 F DT 3 1_555 C N6 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 4 F DA 4 1_555 C N3 DT 9 G DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 4 F DA 4 1_555 C O4 DT 9 G DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 5 F DA 5 1_555 C N3 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 5 F DA 5 1_555 C O4 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 6 F DA 6 1_555 C N3 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 6 F DA 6 1_555 C O4 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DG 7 F DG 7 1_555 C N3 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 DG 7 F DG 7 1_555 C O2 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 7 F DG 7 1_555 C N4 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog15 B N1 DA 8 F DA 8 1_555 C N3 DT 5 G DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DT 9 F DT 9 1_555 C N1 DA 4 G DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O4 DT 9 F DT 9 1_555 C N6 DA 4 G DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DC 10 F DC 10 1_555 C N1 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 DC 10 F DC 10 1_555 C O6 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 DC 10 F DC 10 1_555 C N2 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N1 DG 11 F DG 11 1_555 C N3 DC 2 G DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N2 DG 11 F DG 11 1_555 C O2 DC 2 G DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O6 DG 11 F DG 11 1_555 C N4 DC 2 G DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 439 n n N HN1 SAH sing 440 n n N HN2 SAH sing 441 n n CA CB SAH sing 442 n n CA C SAH sing 443 n n CA HA SAH sing 444 n n CB CG SAH sing 445 n n CB HB1 SAH sing 446 n n CB HB2 SAH sing 447 n n CG SD SAH sing 448 n n CG HG1 SAH sing 449 n n CG HG2 SAH sing 450 n n SD C5' SAH sing 451 n n C O SAH doub 452 n n C OXT SAH sing 453 n n OXT HXT SAH sing 454 n n C5' C4' SAH sing 455 n n C5' "H5'1" SAH sing 456 n n C5' "H5'2" SAH sing 457 n n C4' O4' SAH sing 458 n n C4' C3' SAH sing 459 n n C4' H4' SAH sing 460 n n O4' C1' SAH sing 461 n n C3' O3' SAH sing 462 n n C3' C2' SAH sing 463 n n C3' H3' SAH sing 464 n n O3' HO3' SAH sing 465 n n C2' O2' SAH sing 466 n n C2' C1' SAH sing 467 n n C2' H2' SAH sing 468 n n O2' HO2' SAH sing 469 n n C1' N9 SAH sing 470 n n C1' H1' SAH sing 471 n n N9 C8 SAH sing 472 n y N9 C4 SAH sing 473 n y C8 N7 SAH doub 474 n y C8 H8 SAH sing 475 n n N7 C5 SAH sing 476 n y C5 C6 SAH sing 477 n y C5 C4 SAH doub 478 n y C6 N6 SAH sing 479 n n C6 N1 SAH doub 480 n y N6 HN61 SAH sing 481 n n N6 HN62 SAH sing 482 n n N1 C2 SAH sing 483 n y C2 N3 SAH doub 484 n y C2 H2 SAH sing 485 n n N3 C4 SAH sing 486 n y # _atom_sites.entry_id 4RTK _atom_sites.fract_transf_matrix[1][1] 0.027525 _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] 0.015862 _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] 0.007033 _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 D 4 SAH A 1 301 301 SAH SAH . E 5 GOL A 1 302 397 GOL GOL . F 6 HOH A 1 401 1 HOH HOH . F 6 HOH A 2 402 2 HOH HOH . F 6 HOH A 3 403 3 HOH HOH . F 6 HOH A 4 404 4 HOH HOH . F 6 HOH A 5 405 5 HOH HOH . F 6 HOH A 6 406 6 HOH HOH . F 6 HOH A 7 407 7 HOH HOH . F 6 HOH A 8 408 9 HOH HOH . F 6 HOH A 9 409 10 HOH HOH . F 6 HOH A 10 410 12 HOH HOH . F 6 HOH A 11 411 13 HOH HOH . F 6 HOH A 12 412 14 HOH HOH . F 6 HOH A 13 413 15 HOH HOH . F 6 HOH A 14 414 16 HOH HOH . F 6 HOH A 15 415 18 HOH HOH . F 6 HOH A 16 416 19 HOH HOH . F 6 HOH A 17 417 20 HOH HOH . F 6 HOH A 18 418 21 HOH HOH . F 6 HOH A 19 419 22 HOH HOH . F 6 HOH A 20 420 23 HOH HOH . F 6 HOH A 21 421 24 HOH HOH . F 6 HOH A 22 422 25 HOH HOH . F 6 HOH A 23 423 27 HOH HOH . F 6 HOH A 24 424 28 HOH HOH . F 6 HOH A 25 425 29 HOH HOH . F 6 HOH A 26 426 30 HOH HOH . F 6 HOH A 27 427 31 HOH HOH . F 6 HOH A 28 428 32 HOH HOH . F 6 HOH A 29 429 33 HOH HOH . F 6 HOH A 30 430 34 HOH HOH . F 6 HOH A 31 431 35 HOH HOH . F 6 HOH A 32 432 36 HOH HOH . F 6 HOH A 33 433 37 HOH HOH . F 6 HOH A 34 434 38 HOH HOH . F 6 HOH A 35 435 43 HOH HOH . F 6 HOH A 36 436 44 HOH HOH . F 6 HOH A 37 437 47 HOH HOH . F 6 HOH A 38 438 48 HOH HOH . F 6 HOH A 39 439 49 HOH HOH . F 6 HOH A 40 440 50 HOH HOH . F 6 HOH A 41 441 51 HOH HOH . F 6 HOH A 42 442 53 HOH HOH . F 6 HOH A 43 443 54 HOH HOH . F 6 HOH A 44 444 55 HOH HOH . F 6 HOH A 45 445 56 HOH HOH . F 6 HOH A 46 446 57 HOH HOH . F 6 HOH A 47 447 59 HOH HOH . F 6 HOH A 48 448 60 HOH HOH . F 6 HOH A 49 449 61 HOH HOH . F 6 HOH A 50 450 62 HOH HOH . F 6 HOH A 51 451 63 HOH HOH . F 6 HOH A 52 452 64 HOH HOH . F 6 HOH A 53 453 65 HOH HOH . F 6 HOH A 54 454 66 HOH HOH . F 6 HOH A 55 455 67 HOH HOH . F 6 HOH A 56 456 68 HOH HOH . F 6 HOH A 57 457 69 HOH HOH . F 6 HOH A 58 458 71 HOH HOH . F 6 HOH A 59 459 72 HOH HOH . F 6 HOH A 60 460 73 HOH HOH . F 6 HOH A 61 461 75 HOH HOH . F 6 HOH A 62 462 77 HOH HOH . F 6 HOH A 63 463 79 HOH HOH . F 6 HOH A 64 464 82 HOH HOH . F 6 HOH A 65 465 83 HOH HOH . F 6 HOH A 66 466 84 HOH HOH . F 6 HOH A 67 467 85 HOH HOH . F 6 HOH A 68 468 86 HOH HOH . F 6 HOH A 69 469 87 HOH HOH . F 6 HOH A 70 470 88 HOH HOH . F 6 HOH A 71 471 89 HOH HOH . F 6 HOH A 72 472 90 HOH HOH . F 6 HOH A 73 473 91 HOH HOH . F 6 HOH A 74 474 92 HOH HOH . F 6 HOH A 75 475 95 HOH HOH . F 6 HOH A 76 476 96 HOH HOH . F 6 HOH A 77 477 98 HOH HOH . F 6 HOH A 78 478 100 HOH HOH . F 6 HOH A 79 479 101 HOH HOH . F 6 HOH A 80 480 102 HOH HOH . F 6 HOH A 81 481 103 HOH HOH . F 6 HOH A 82 482 104 HOH HOH . F 6 HOH A 83 483 107 HOH HOH . F 6 HOH A 84 484 108 HOH HOH . F 6 HOH A 85 485 81 HOH HOH . G 6 HOH F 1 101 8 HOH HOH . G 6 HOH F 2 102 11 HOH HOH . G 6 HOH F 3 103 17 HOH HOH . G 6 HOH F 4 104 74 HOH HOH . G 6 HOH F 5 105 76 HOH HOH . G 6 HOH F 6 106 80 HOH HOH . H 6 HOH G 1 101 39 HOH HOH . H 6 HOH G 2 102 40 HOH HOH . H 6 HOH G 3 103 45 HOH HOH . H 6 HOH G 4 104 58 HOH HOH . H 6 HOH G 5 105 78 HOH HOH . H 6 HOH G 6 106 93 HOH HOH . H 6 HOH G 7 107 94 HOH HOH . H 6 HOH G 8 108 105 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 4 -7.776 -1.839 87.278 1 55.89 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . D 4 -7.48 -1.144 88.526 1 56.22 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . D 4 -6.334 -0.142 88.385 1 56.5 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . D 4 -5.342 -0.373 87.246 1 56.69 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . D 4 -4.072 0.917 87.255 1 37.25 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . D 4 -8.71 -0.474 89.139 1 56.29 ? C SAH 301 A 1 HETATM 7 O O SAH . . . D 4 -9.846 -0.714 88.729 1 56.23 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . D 4 -8.591 0.319 90.074 1 56.03 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . D 4 -2.715 -0.264 87.035 1 31.54 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . D 4 -2.058 -0.689 88.344 1 31.42 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . D 4 -1.002 -1.589 88.074 1 31.88 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . D 4 -1.453 0.473 89.118 1 31.27 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . D 4 -2.117 0.594 90.353 1 31.36 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . D 4 -0.004 0.092 89.361 1 30.82 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . D 4 0.339 0.283 90.714 1 29.34 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . D 4 0.052 -1.382 88.992 1 31.5 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . D 4 1.34 -1.776 88.389 1 31.62 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . D 4 2.203 -0.994 87.665 1 32.08 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . D 4 3.263 -1.753 87.299 1 32 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . D 4 3.088 -3.005 87.776 1 32.15 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . D 4 3.856 -4.161 87.692 1 32.4 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . D 4 5.016 -4.156 87.038 1 32.36 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . D 4 3.406 -5.317 88.293 1 32.53 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . D 4 2.204 -5.321 88.971 1 32.08 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . D 4 1.447 -4.17 89.051 1 31.84 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . D 4 1.884 -3.031 88.463 1 31.72 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 26 #