data_8RDO # _model_server_result.job_id FG78JGgC4Qe98j6APzE47A _model_server_result.datetime_utc '2024-10-22 23:31:59' _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 8rdo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8RDO # _exptl.entry_id 8RDO _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 90 _cell.angle_gamma 90 _cell.entry_id 8RDO _cell.length_a 53.43 _cell.length_b 53.43 _cell.length_c 209.31 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RDO _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 8_665 -y+1,-x+1,-z+1/4 0 -1 0 -1 0 0 0 0 -1 53.43 53.43 52.3275 # _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 . _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 304 n n N HN1 SAH sing 305 n n N HN2 SAH sing 306 n n CA CB SAH sing 307 n n CA C SAH sing 308 n n CA HA SAH sing 309 n n CB CG SAH sing 310 n n CB HB1 SAH sing 311 n n CB HB2 SAH sing 312 n n CG SD SAH sing 313 n n CG HG1 SAH sing 314 n n CG HG2 SAH sing 315 n n SD C5' SAH sing 316 n n C O SAH doub 317 n n C OXT SAH sing 318 n n OXT HXT SAH sing 319 n n C5' C4' SAH sing 320 n n C5' "H5'1" SAH sing 321 n n C5' "H5'2" SAH sing 322 n n C4' O4' SAH sing 323 n n C4' C3' SAH sing 324 n n C4' H4' SAH sing 325 n n O4' C1' SAH sing 326 n n C3' O3' SAH sing 327 n n C3' C2' SAH sing 328 n n C3' H3' SAH sing 329 n n O3' HO3' SAH sing 330 n n C2' O2' SAH sing 331 n n C2' C1' SAH sing 332 n n C2' H2' SAH sing 333 n n O2' HO2' SAH sing 334 n n C1' N9 SAH sing 335 n n C1' H1' SAH sing 336 n n N9 C8 SAH sing 337 n y N9 C4 SAH sing 338 n y C8 N7 SAH doub 339 n y C8 H8 SAH sing 340 n n N7 C5 SAH sing 341 n y C5 C6 SAH sing 342 n y C5 C4 SAH doub 343 n y C6 N6 SAH sing 344 n n C6 N1 SAH doub 345 n y N6 HN61 SAH sing 346 n n N6 HN62 SAH sing 347 n n N1 C2 SAH sing 348 n y C2 N3 SAH doub 349 n y C2 H2 SAH sing 350 n n N3 C4 SAH sing 351 n y # _atom_sites.entry_id 8RDO _atom_sites.fract_transf_matrix[1][1] 0.018716 _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] 0.018716 _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] 0.004778 _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 1 401 998 SAH SAH . C 3 YRD A 1 402 999 YRD LIG . D 4 GOL A 1 403 1 GOL GOL . E 4 GOL A 1 404 2 GOL GOL . F 4 GOL A 1 405 3 GOL GOL . G 5 MLT A 1 406 4 MLT MLT . H 6 HOH A 1 501 41 HOH HOH . H 6 HOH A 2 502 8 HOH HOH . H 6 HOH A 3 503 128 HOH HOH . H 6 HOH A 4 504 56 HOH HOH . H 6 HOH A 5 505 7 HOH HOH . H 6 HOH A 6 506 109 HOH HOH . H 6 HOH A 7 507 25 HOH HOH . H 6 HOH A 8 508 85 HOH HOH . H 6 HOH A 9 509 116 HOH HOH . H 6 HOH A 10 510 124 HOH HOH . H 6 HOH A 11 511 115 HOH HOH . H 6 HOH A 12 512 37 HOH HOH . H 6 HOH A 13 513 9 HOH HOH . H 6 HOH A 14 514 38 HOH HOH . H 6 HOH A 15 515 24 HOH HOH . H 6 HOH A 16 516 80 HOH HOH . H 6 HOH A 17 517 26 HOH HOH . H 6 HOH A 18 518 32 HOH HOH . H 6 HOH A 19 519 16 HOH HOH . H 6 HOH A 20 520 122 HOH HOH . H 6 HOH A 21 521 121 HOH HOH . H 6 HOH A 22 522 94 HOH HOH . H 6 HOH A 23 523 81 HOH HOH . H 6 HOH A 24 524 52 HOH HOH . H 6 HOH A 25 525 10 HOH HOH . H 6 HOH A 26 526 123 HOH HOH . H 6 HOH A 27 527 43 HOH HOH . H 6 HOH A 28 528 17 HOH HOH . H 6 HOH A 29 529 113 HOH HOH . H 6 HOH A 30 530 103 HOH HOH . H 6 HOH A 31 531 79 HOH HOH . H 6 HOH A 32 532 6 HOH HOH . H 6 HOH A 33 533 35 HOH HOH . H 6 HOH A 34 534 66 HOH HOH . H 6 HOH A 35 535 83 HOH HOH . H 6 HOH A 36 536 31 HOH HOH . H 6 HOH A 37 537 48 HOH HOH . H 6 HOH A 38 538 98 HOH HOH . H 6 HOH A 39 539 50 HOH HOH . H 6 HOH A 40 540 47 HOH HOH . H 6 HOH A 41 541 29 HOH HOH . H 6 HOH A 42 542 20 HOH HOH . H 6 HOH A 43 543 75 HOH HOH . H 6 HOH A 44 544 5 HOH HOH . H 6 HOH A 45 545 104 HOH HOH . H 6 HOH A 46 546 74 HOH HOH . H 6 HOH A 47 547 36 HOH HOH . H 6 HOH A 48 548 112 HOH HOH . H 6 HOH A 49 549 49 HOH HOH . H 6 HOH A 50 550 126 HOH HOH . H 6 HOH A 51 551 23 HOH HOH . H 6 HOH A 52 552 55 HOH HOH . H 6 HOH A 53 553 102 HOH HOH . H 6 HOH A 54 554 108 HOH HOH . H 6 HOH A 55 555 130 HOH HOH . H 6 HOH A 56 556 84 HOH HOH . H 6 HOH A 57 557 77 HOH HOH . H 6 HOH A 58 558 129 HOH HOH . H 6 HOH A 59 559 100 HOH HOH . H 6 HOH A 60 560 54 HOH HOH . H 6 HOH A 61 561 127 HOH HOH . H 6 HOH A 62 562 125 HOH HOH . H 6 HOH A 63 563 11 HOH HOH . H 6 HOH A 64 564 114 HOH HOH . H 6 HOH A 65 565 120 HOH HOH . H 6 HOH A 66 566 105 HOH HOH . H 6 HOH A 67 567 131 HOH HOH . H 6 HOH A 68 568 117 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 14.771 66.989 43.03 1 22.51 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . B 2 13.463 66.36 43.396 1 22.4 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . B 2 12.282 67.192 42.889 1 22.91 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . B 2 12.372 67.568 41.423 1 23.75 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . B 2 10.853 68.348 40.821 1 24.56 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . B 2 13.386 64.951 42.796 1 22.05 ? C SAH 401 A 1 HETATM 7 O O SAH . . . B 2 14.144 64.628 41.89 1 22.33 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . B 2 12.571 64.119 43.201 1 22.12 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . B 2 11.365 70.076 40.662 1 24.59 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . B 2 11.235 70.866 41.943 1 24.53 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . B 2 11.525 72.255 41.664 1 25.19 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . B 2 9.838 70.846 42.582 1 24.26 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . B 2 9.849 70.157 43.83 1 23.68 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . B 2 9.454 72.33 42.702 1 24.63 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . B 2 8.796 72.639 43.911 1 24.29 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . B 2 10.805 73.025 42.593 1 25.13 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . B 2 10.753 74.401 42.108 1 26.14 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . B 2 10.055 74.87 41.024 1 26.72 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . B 2 10.212 76.154 40.816 1 27.57 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . B 2 11.078 76.559 41.822 1 27.39 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . B 2 11.641 77.812 42.139 1 28.02 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . B 2 11.411 78.917 41.439 1 28.63 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . B 2 12.481 77.87 43.202 1 27.47 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . B 2 12.716 76.747 43.895 1 26.95 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . B 2 12.244 75.518 43.689 1 26.39 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . B 2 11.423 75.487 42.624 1 26.66 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #