data_8KDZ # _model_server_result.job_id 10h_DxOw1IIz5JhzbpmKgQ _model_server_result.datetime_utc '2025-02-23 19:27:08' _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 8kdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 8KDZ # _exptl.entry_id 8KDZ _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 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 8KDZ _cell.length_a 51.648 _cell.length_b 60.722 _cell.length_c 184.36 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type non-polymer _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 315 n n N HN1 SAH sing 316 n n N HN2 SAH sing 317 n n CA CB SAH sing 318 n n CA C SAH sing 319 n n CA HA SAH sing 320 n n CB CG SAH sing 321 n n CB HB1 SAH sing 322 n n CB HB2 SAH sing 323 n n CG SD SAH sing 324 n n CG HG1 SAH sing 325 n n CG HG2 SAH sing 326 n n SD C5' SAH sing 327 n n C O SAH doub 328 n n C OXT SAH sing 329 n n OXT HXT SAH sing 330 n n C5' C4' SAH sing 331 n n C5' "H5'1" SAH sing 332 n n C5' "H5'2" SAH sing 333 n n C4' O4' SAH sing 334 n n C4' C3' SAH sing 335 n n C4' H4' SAH sing 336 n n O4' C1' SAH sing 337 n n C3' O3' SAH sing 338 n n C3' C2' SAH sing 339 n n C3' H3' SAH sing 340 n n O3' HO3' SAH sing 341 n n C2' O2' SAH sing 342 n n C2' C1' SAH sing 343 n n C2' H2' SAH sing 344 n n O2' HO2' SAH sing 345 n n C1' N9 SAH sing 346 n n C1' H1' SAH sing 347 n n N9 C8 SAH sing 348 n y N9 C4 SAH sing 349 n y C8 N7 SAH doub 350 n y C8 H8 SAH sing 351 n n N7 C5 SAH sing 352 n y C5 C6 SAH sing 353 n y C5 C4 SAH doub 354 n y C6 N6 SAH sing 355 n n C6 N1 SAH doub 356 n y N6 HN61 SAH sing 357 n n N6 HN62 SAH sing 358 n n N1 C2 SAH sing 359 n y C2 N3 SAH doub 360 n y C2 H2 SAH sing 361 n n N3 C4 SAH sing 362 n y # _atom_sites.entry_id 8KDZ _atom_sites.fract_transf_matrix[1][1] 0.019362 _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] 0.016468 _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] 0.005424 _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 C 2 SAH A 1 301 301 SAH SAH . D 3 QAP A 1 302 302 QAP LIG . E 3 QAP A 1 303 303 QAP LIG . F 2 SAH B 1 301 301 SAH SAH . G 4 HOH A 1 401 42 HOH HOH . G 4 HOH A 2 402 33 HOH HOH . G 4 HOH A 3 403 73 HOH HOH . G 4 HOH A 4 404 137 HOH HOH . G 4 HOH A 5 405 94 HOH HOH . G 4 HOH A 6 406 106 HOH HOH . G 4 HOH A 7 407 47 HOH HOH . G 4 HOH A 8 408 59 HOH HOH . G 4 HOH A 9 409 16 HOH HOH . G 4 HOH A 10 410 34 HOH HOH . G 4 HOH A 11 411 19 HOH HOH . G 4 HOH A 12 412 15 HOH HOH . G 4 HOH A 13 413 110 HOH HOH . G 4 HOH A 14 414 51 HOH HOH . G 4 HOH A 15 415 22 HOH HOH . G 4 HOH A 16 416 45 HOH HOH . G 4 HOH A 17 417 102 HOH HOH . G 4 HOH A 18 418 72 HOH HOH . G 4 HOH A 19 419 11 HOH HOH . G 4 HOH A 20 420 124 HOH HOH . G 4 HOH A 21 421 7 HOH HOH . G 4 HOH A 22 422 69 HOH HOH . G 4 HOH A 23 423 63 HOH HOH . G 4 HOH A 24 424 111 HOH HOH . G 4 HOH A 25 425 105 HOH HOH . G 4 HOH A 26 426 12 HOH HOH . G 4 HOH A 27 427 119 HOH HOH . G 4 HOH A 28 428 24 HOH HOH . G 4 HOH A 29 429 127 HOH HOH . G 4 HOH A 30 430 115 HOH HOH . G 4 HOH A 31 431 36 HOH HOH . G 4 HOH A 32 432 46 HOH HOH . G 4 HOH A 33 433 136 HOH HOH . G 4 HOH A 34 434 13 HOH HOH . G 4 HOH A 35 435 113 HOH HOH . G 4 HOH A 36 436 85 HOH HOH . G 4 HOH A 37 437 56 HOH HOH . G 4 HOH A 38 438 50 HOH HOH . G 4 HOH A 39 439 25 HOH HOH . G 4 HOH A 40 440 21 HOH HOH . G 4 HOH A 41 441 17 HOH HOH . G 4 HOH A 42 442 75 HOH HOH . G 4 HOH A 43 443 20 HOH HOH . G 4 HOH A 44 444 14 HOH HOH . G 4 HOH A 45 445 88 HOH HOH . G 4 HOH A 46 446 31 HOH HOH . G 4 HOH A 47 447 8 HOH HOH . G 4 HOH A 48 448 10 HOH HOH . G 4 HOH A 49 449 92 HOH HOH . G 4 HOH A 50 450 91 HOH HOH . G 4 HOH A 51 451 132 HOH HOH . G 4 HOH A 52 452 112 HOH HOH . G 4 HOH A 53 453 29 HOH HOH . G 4 HOH A 54 454 128 HOH HOH . G 4 HOH A 55 455 52 HOH HOH . G 4 HOH A 56 456 4 HOH HOH . G 4 HOH A 57 457 5 HOH HOH . G 4 HOH A 58 458 130 HOH HOH . G 4 HOH A 59 459 139 HOH HOH . G 4 HOH A 60 460 68 HOH HOH . G 4 HOH A 61 461 140 HOH HOH . G 4 HOH A 62 462 70 HOH HOH . G 4 HOH A 63 463 40 HOH HOH . G 4 HOH A 64 464 114 HOH HOH . G 4 HOH A 65 465 103 HOH HOH . G 4 HOH A 66 466 133 HOH HOH . G 4 HOH A 67 467 79 HOH HOH . G 4 HOH A 68 468 81 HOH HOH . H 4 HOH B 1 401 131 HOH HOH . H 4 HOH B 2 402 66 HOH HOH . H 4 HOH B 3 403 104 HOH HOH . H 4 HOH B 4 404 30 HOH HOH . H 4 HOH B 5 405 37 HOH HOH . H 4 HOH B 6 406 38 HOH HOH . H 4 HOH B 7 407 74 HOH HOH . H 4 HOH B 8 408 117 HOH HOH . H 4 HOH B 9 409 84 HOH HOH . H 4 HOH B 10 410 39 HOH HOH . H 4 HOH B 11 411 96 HOH HOH . H 4 HOH B 12 412 76 HOH HOH . H 4 HOH B 13 413 107 HOH HOH . H 4 HOH B 14 414 35 HOH HOH . H 4 HOH B 15 415 49 HOH HOH . H 4 HOH B 16 416 108 HOH HOH . H 4 HOH B 17 417 116 HOH HOH . H 4 HOH B 18 418 58 HOH HOH . H 4 HOH B 19 419 86 HOH HOH . H 4 HOH B 20 420 64 HOH HOH . H 4 HOH B 21 421 98 HOH HOH . H 4 HOH B 22 422 27 HOH HOH . H 4 HOH B 23 423 77 HOH HOH . H 4 HOH B 24 424 89 HOH HOH . H 4 HOH B 25 425 54 HOH HOH . H 4 HOH B 26 426 26 HOH HOH . H 4 HOH B 27 427 55 HOH HOH . H 4 HOH B 28 428 134 HOH HOH . H 4 HOH B 29 429 71 HOH HOH . H 4 HOH B 30 430 65 HOH HOH . H 4 HOH B 31 431 123 HOH HOH . H 4 HOH B 32 432 126 HOH HOH . H 4 HOH B 33 433 28 HOH HOH . H 4 HOH B 34 434 48 HOH HOH . H 4 HOH B 35 435 138 HOH HOH . H 4 HOH B 36 436 129 HOH HOH . H 4 HOH B 37 437 90 HOH HOH . H 4 HOH B 38 438 67 HOH HOH . H 4 HOH B 39 439 121 HOH HOH . H 4 HOH B 40 440 60 HOH HOH . H 4 HOH B 41 441 125 HOH HOH . H 4 HOH B 42 442 41 HOH HOH . H 4 HOH B 43 443 135 HOH HOH . H 4 HOH B 44 444 23 HOH HOH . H 4 HOH B 45 445 61 HOH HOH . H 4 HOH B 46 446 122 HOH HOH . H 4 HOH B 47 447 32 HOH HOH . H 4 HOH B 48 448 87 HOH HOH . H 4 HOH B 49 449 120 HOH HOH . H 4 HOH B 50 450 78 HOH HOH . H 4 HOH B 51 451 118 HOH HOH . H 4 HOH B 52 452 99 HOH HOH . H 4 HOH B 53 453 53 HOH HOH . H 4 HOH B 54 454 18 HOH HOH . H 4 HOH B 55 455 80 HOH HOH . H 4 HOH B 56 456 82 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 . . . F 2 15.84 50.233 10.008 1 52.95 0 N SAH 301 B 1 HETATM 2 C CA SAH . . . F 2 16.362 48.839 9.98 1 52.44 0 CA SAH 301 B 1 HETATM 3 C CB SAH . . . F 2 16.256 48.257 8.567 1 51.92 0 CB SAH 301 B 1 HETATM 4 C CG SAH . . . F 2 14.829 48.006 8.145 1 49.15 0 CG SAH 301 B 1 HETATM 5 S SD SAH . . . F 2 14.43 48.651 6.529 1 46 0 SD SAH 301 B 1 HETATM 6 C C SAH . . . F 2 17.829 48.87 10.406 1 53.22 0 C SAH 301 B 1 HETATM 7 O O SAH . . . F 2 18.435 47.882 10.844 1 51.51 0 O SAH 301 B 1 HETATM 8 O OXT SAH . . . F 2 18.394 49.95 10.295 1 48.14 0 OXT SAH 301 B 1 HETATM 9 C C5' SAH . . . F 2 14.247 47.103 5.621 1 45.22 0 C5' SAH 301 B 1 HETATM 10 C C4' SAH . . . F 2 15.435 46.889 4.709 1 42.29 0 C4' SAH 301 B 1 HETATM 11 O O4' SAH . . . F 2 15.429 45.518 4.256 1 37.69 0 O4' SAH 301 B 1 HETATM 12 C C3' SAH . . . F 2 15.431 47.771 3.448 1 38.83 0 C3' SAH 301 B 1 HETATM 13 O O3' SAH . . . F 2 16.528 48.676 3.418 1 38.32 0 O3' SAH 301 B 1 HETATM 14 C C2' SAH . . . F 2 15.492 46.79 2.271 1 38.18 0 C2' SAH 301 B 1 HETATM 15 O O2' SAH . . . F 2 16.453 47.155 1.304 1 43.71 0 O2' SAH 301 B 1 HETATM 16 C C1' SAH . . . F 2 15.909 45.482 2.935 1 36.87 0 C1' SAH 301 B 1 HETATM 17 N N9 SAH . . . F 2 15.359 44.303 2.284 1 33.3 0 N9 SAH 301 B 1 HETATM 18 C C8 SAH . . . F 2 14.087 44.137 1.799 1 31.91 0 C8 SAH 301 B 1 HETATM 19 N N7 SAH . . . F 2 13.884 42.95 1.284 1 32.38 0 N7 SAH 301 B 1 HETATM 20 C C5 SAH . . . F 2 15.1 42.301 1.422 1 32.48 0 C5 SAH 301 B 1 HETATM 21 C C6 SAH . . . F 2 15.54 41.013 1.06 1 33.52 0 C6 SAH 301 B 1 HETATM 22 N N6 SAH . . . F 2 14.775 40.117 0.448 1 35.99 0 N6 SAH 301 B 1 HETATM 23 N N1 SAH . . . F 2 16.821 40.679 1.335 1 31.05 0 N1 SAH 301 B 1 HETATM 24 C C2 SAH . . . F 2 17.589 41.584 1.945 1 32.18 0 C2 SAH 301 B 1 HETATM 25 N N3 SAH . . . F 2 17.29 42.818 2.338 1 33.58 0 N3 SAH 301 B 1 HETATM 26 C C4 SAH . . . F 2 16.017 43.125 2.039 1 32.79 0 C4 SAH 301 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 590 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #