data_2I9K # _model_server_result.job_id lV7wAUQs2TqlsTMwHWyocA _model_server_result.datetime_utc '2025-03-06 00:11:05' _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 2i9k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":328}' # _entry.id 2I9K # _exptl.entry_id 2I9K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _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 120 _cell.entry_id 2I9K _cell.length_a 97.51 _cell.length_b 97.51 _cell.length_c 319.7 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2I9K _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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 _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 3 _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 A N1 DG 2 C DG 402 1_555 B N3 DC 13 D DC 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 2 C DG 402 1_555 B O2 DC 13 D DC 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 2 C DG 402 1_555 B N4 DC 13 D DC 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DA 3 C DA 403 1_555 B N3 DT 12 D DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 DA 3 C DA 403 1_555 B O4 DT 12 D DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 DT 4 C DT 404 1_555 B N1 DA 11 D DA 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O4 DT 4 C DT 404 1_555 B N6 DA 11 D DA 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DA 5 C DA 405 1_555 B N3 DT 10 D DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N6 DA 5 C DA 405 1_555 B O4 DT 10 D DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 6 C DG 406 1_555 B N3 DC 9 D DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 6 C DG 406 1_555 B O2 DC 9 D DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 6 C DG 406 1_555 B N4 DC 9 D DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 7 C DC 407 1_555 B N1 DG 8 D DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 7 C DC 407 1_555 B O6 DG 8 D DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 7 C DC 407 1_555 B N2 DG 8 D DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 9 C DC 409 1_555 B N1 DG 6 D DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 9 C DC 409 1_555 B O6 DG 6 D DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 9 C DC 409 1_555 B N2 DG 6 D DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DT 10 C DT 410 1_555 B N1 DA 5 D DA 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O4 DT 10 C DT 410 1_555 B N6 DA 5 D DA 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 DA 11 C DA 411 1_555 B N3 DT 4 D DT 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N6 DA 11 C DA 411 1_555 B O4 DT 4 D DT 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N3 DT 12 C DT 412 1_555 B N1 DA 3 D DA 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O4 DT 12 C DT 412 1_555 B N6 DA 3 D DA 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N3 DC 13 C DC 413 1_555 B N1 DG 2 D DG 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N4 DC 13 C DC 413 1_555 B O6 DG 2 D DG 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O2 DC 13 C DC 413 1_555 B N2 DG 2 D DG 422 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 424 n n N HN1 SAH sing 425 n n N HN2 SAH sing 426 n n CA CB SAH sing 427 n n CA C SAH sing 428 n n CA HA SAH sing 429 n n CB CG SAH sing 430 n n CB HB1 SAH sing 431 n n CB HB2 SAH sing 432 n n CG SD SAH sing 433 n n CG HG1 SAH sing 434 n n CG HG2 SAH sing 435 n n SD C5' SAH sing 436 n n C O SAH doub 437 n n C OXT SAH sing 438 n n OXT HXT SAH sing 439 n n C5' C4' SAH sing 440 n n C5' "H5'1" SAH sing 441 n n C5' "H5'2" SAH sing 442 n n C4' O4' SAH sing 443 n n C4' C3' SAH sing 444 n n C4' H4' SAH sing 445 n n O4' C1' SAH sing 446 n n C3' O3' SAH sing 447 n n C3' C2' SAH sing 448 n n C3' H3' SAH sing 449 n n O3' HO3' SAH sing 450 n n C2' O2' SAH sing 451 n n C2' C1' SAH sing 452 n n C2' H2' SAH sing 453 n n O2' HO2' SAH sing 454 n n C1' N9 SAH sing 455 n n C1' H1' SAH sing 456 n n N9 C8 SAH sing 457 n y N9 C4 SAH sing 458 n y C8 N7 SAH doub 459 n y C8 H8 SAH sing 460 n n N7 C5 SAH sing 461 n y C5 C6 SAH sing 462 n y C5 C4 SAH doub 463 n y C6 N6 SAH sing 464 n n C6 N1 SAH doub 465 n y N6 HN61 SAH sing 466 n n N6 HN62 SAH sing 467 n n N1 C2 SAH sing 468 n y C2 N3 SAH doub 469 n y C2 H2 SAH sing 470 n n N3 C4 SAH sing 471 n y # _atom_sites.entry_id 2I9K _atom_sites.fract_transf_matrix[1][1] 0.010255 _atom_sites.fract_transf_matrix[1][2] 0.005921 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011842 _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] 0.003128 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id D _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id SAH _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 328 _pdbx_nonpoly_scheme.auth_seq_num 328 _pdbx_nonpoly_scheme.pdb_mon_id SAH _pdbx_nonpoly_scheme.auth_mon_id SAH _pdbx_nonpoly_scheme.pdb_ins_code . # 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 3 -18.285 30.595 79.609 1 29.08 ? N SAH 328 A 1 HETATM 2 C CA SAH . . . D 3 -18.944 30.037 80.872 1 29.84 ? CA SAH 328 A 1 HETATM 3 C CB SAH . . . D 3 -18.753 30.734 82.171 1 28.25 ? CB SAH 328 A 1 HETATM 4 C CG SAH . . . D 3 -17.344 30.991 82.636 1 29.76 ? CG SAH 328 A 1 HETATM 5 S SD SAH . . . D 3 -17.447 31.666 84.324 1 30.33 ? SD SAH 328 A 1 HETATM 6 C C SAH . . . D 3 -20.476 29.869 80.548 1 29.95 ? C SAH 328 A 1 HETATM 7 O O SAH . . . D 3 -20.895 30.172 79.429 1 31.9 ? O SAH 328 A 1 HETATM 8 O OXT SAH . . . D 3 -21.2 29.414 81.496 1 30.85 ? OXT SAH 328 A 1 HETATM 9 C C5' SAH . . . D 3 -15.984 31.075 85.018 1 30.52 ? C5' SAH 328 A 1 HETATM 10 C C4' SAH . . . D 3 -16.143 29.532 85.361 1 31.33 ? C4' SAH 328 A 1 HETATM 11 O O4' SAH . . . D 3 -14.888 29.242 85.92 1 33.51 ? O4' SAH 328 A 1 HETATM 12 C C3' SAH . . . D 3 -17.128 29.186 86.442 1 31.26 ? C3' SAH 328 A 1 HETATM 13 O O3' SAH . . . D 3 -18.099 28.29 85.944 1 31.63 ? O3' SAH 328 A 1 HETATM 14 C C2' SAH . . . D 3 -16.206 28.591 87.574 1 32.58 ? C2' SAH 328 A 1 HETATM 15 O O2' SAH . . . D 3 -16.879 27.623 88.363 1 32.08 ? O2' SAH 328 A 1 HETATM 16 C C1' SAH . . . D 3 -15.036 28.063 86.765 1 33.37 ? C1' SAH 328 A 1 HETATM 17 N N9 SAH . . . D 3 -13.86 27.883 87.374 1 34.43 ? N9 SAH 328 A 1 HETATM 18 C C8 SAH . . . D 3 -13.111 28.661 88.233 1 34.25 ? C8 SAH 328 A 1 HETATM 19 N N7 SAH . . . D 3 -11.993 28.144 88.613 1 34.92 ? N7 SAH 328 A 1 HETATM 20 C C5 SAH . . . D 3 -11.947 26.882 87.958 1 35.34 ? C5 SAH 328 A 1 HETATM 21 C C6 SAH . . . D 3 -10.947 25.836 87.97 1 36.37 ? C6 SAH 328 A 1 HETATM 22 N N6 SAH . . . D 3 -9.798 25.897 88.668 1 36.36 ? N6 SAH 328 A 1 HETATM 23 N N1 SAH . . . D 3 -11.258 24.741 87.198 1 36.57 ? N1 SAH 328 A 1 HETATM 24 C C2 SAH . . . D 3 -12.417 24.638 86.472 1 36.68 ? C2 SAH 328 A 1 HETATM 25 N N3 SAH . . . D 3 -13.388 25.614 86.434 1 34.25 ? N3 SAH 328 A 1 HETATM 26 C C4 SAH . . . D 3 -13.083 26.703 87.2 1 35.11 ? C4 SAH 328 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #