data_3ID5 # _model_server_result.job_id xgOt01PrNpLi6VmSEfKKaw _model_server_result.datetime_utc '2025-07-01 15:13:47' _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 3id5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":301}' # _entry.id 3ID5 # _exptl.entry_id 3ID5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 3ID5 _cell.length_a 265.485 _cell.length_b 265.485 _cell.length_c 129.434 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ID5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,I,J _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 ? 5 I N N ? 5 J N 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 'G-C PAIR' hydrog1 D N1 G 4 D G 4 1_555 D N3 C 5 D C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N3 C 11 D C 11 1_555 D N1 G 31 D G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N4 C 11 D C 11 1_555 D O6 G 31 D G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D O2 C 11 D C 11 1_555 D N2 G 31 D G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog5 D N3 C 11 D C 11 1_555 D N6 A 32 D A 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog6 D N3 U 12 D U 12 1_555 D O4 U 30 D U 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog7 D O2 U 12 D U 12 1_555 D N3 U 30 D U 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog8 D N2 G 13 D G 13 1_555 D N7 A 29 D A 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog9 D N3 G 13 D G 13 1_555 D N6 A 29 D A 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog10 D N6 A 14 D A 14 1_555 D N3 G 28 D G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog11 D N7 A 14 D A 14 1_555 D N2 G 28 D G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog12 D N1 G 15 D G 15 1_555 D N3 C 24 D C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog13 D N1 G 15 D G 15 1_555 D O2 U 25 D U 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog14 D O6 G 15 D G 15 1_555 D N3 U 25 D U 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog15 D O2 C 16 D C 16 1_555 D N2 G 23 D G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog16 D N2 G 17 D G 17 1_555 D O2 C 22 D C 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog17 H O6 G 4 H G 4 1_555 H N4 C 5 H C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 H N3 C 11 H C 11 1_555 H N1 G 31 H G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 H N4 C 11 H C 11 1_555 H O6 G 31 H G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 H O2 C 11 H C 11 1_555 H N2 G 31 H G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog21 H N3 C 11 H C 11 1_555 H N6 A 32 H A 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog22 H N3 U 12 H U 12 1_555 H O4 U 30 H U 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog23 H O2 U 12 H U 12 1_555 H N3 U 30 H U 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog24 H N2 G 13 H G 13 1_555 H N7 A 29 H A 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog25 H N3 G 13 H G 13 1_555 H N6 A 29 H A 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog26 H N6 A 14 H A 14 1_555 H N3 G 28 H G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog27 H N7 A 14 H A 14 1_555 H N2 G 28 H G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog28 H N1 G 15 H G 15 1_555 H N3 C 24 H C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog29 H N1 G 15 H G 15 1_555 H O2 U 25 H U 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog30 H O6 G 15 H G 15 1_555 H N3 U 25 H U 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog31 H O2 C 16 H C 16 1_555 H N2 G 23 H G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog32 H N2 G 17 H G 17 1_555 H O2 C 22 H C 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 SAM sing 390 n n N HN1 SAM sing 391 n n N HN2 SAM sing 392 n n CA C SAM sing 393 n n CA CB SAM sing 394 n n CA HA SAM sing 395 n n C O SAM doub 396 n n C OXT SAM sing 397 n n CB CG SAM sing 398 n n CB HB1 SAM sing 399 n n CB HB2 SAM sing 400 n n CG SD SAM sing 401 n n CG HG1 SAM sing 402 n n CG HG2 SAM sing 403 n n SD CE SAM sing 404 n n SD C5' SAM sing 405 n n CE HE1 SAM sing 406 n n CE HE2 SAM sing 407 n n CE HE3 SAM sing 408 n n C5' C4' SAM sing 409 n n C5' "H5'1" SAM sing 410 n n C5' "H5'2" SAM sing 411 n n C4' O4' SAM sing 412 n n C4' C3' SAM sing 413 n n C4' H4' SAM sing 414 n n O4' C1' SAM sing 415 n n C3' O3' SAM sing 416 n n C3' C2' SAM sing 417 n n C3' H3' SAM sing 418 n n O3' HO3' SAM sing 419 n n C2' O2' SAM sing 420 n n C2' C1' SAM sing 421 n n C2' H2' SAM sing 422 n n O2' HO2' SAM sing 423 n n C1' N9 SAM sing 424 n n C1' H1' SAM sing 425 n n N9 C8 SAM sing 426 n y N9 C4 SAM sing 427 n y C8 N7 SAM doub 428 n y C8 H8 SAM sing 429 n n N7 C5 SAM sing 430 n y C5 C6 SAM sing 431 n y C5 C4 SAM doub 432 n y C6 N6 SAM sing 433 n n C6 N1 SAM doub 434 n y N6 HN61 SAM sing 435 n n N6 HN62 SAM sing 436 n n N1 C2 SAM sing 437 n y C2 N3 SAM doub 438 n y C2 H2 SAM sing 439 n n N3 C4 SAM sing 440 n y # _atom_sites.entry_id 3ID5 _atom_sites.fract_transf_matrix[1][1] 0.003767 _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] 0.003767 _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] 0.007726 _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 I 5 SAM B 1 301 301 SAM SAM . J 5 SAM F 1 301 401 SAM SAM . # 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 SAM . . . J 5 54.835 92.562 52.118 1 146.04 ? N SAM 301 F 1 HETATM 2 C CA SAM . . . J 5 54.792 91.182 51.637 1 146.1 ? CA SAM 301 F 1 HETATM 3 C C SAM . . . J 5 53.906 91.072 50.395 1 145.98 ? C SAM 301 F 1 HETATM 4 O O SAM . . . J 5 54.385 90.794 49.298 1 145.9 ? O SAM 301 F 1 HETATM 5 O OXT SAM . . . J 5 52.693 91.267 50.446 1 145.92 ? OXT SAM 301 F 1 HETATM 6 C CB SAM . . . J 5 54.328 90.221 52.739 1 146.22 ? CB SAM 301 F 1 HETATM 7 C CG SAM . . . J 5 55.364 89.884 53.821 1 146.61 ? CG SAM 301 F 1 HETATM 8 S SD SAM . . . J 5 54.992 88.384 54.786 1 147.06 ? SD SAM 301 F 1 HETATM 9 C CE SAM . . . J 5 53.982 89.032 56.145 1 147.05 ? CE SAM 301 F 1 HETATM 10 C C5' SAM . . . J 5 56.561 88.045 55.64 1 146.46 ? C5' SAM 301 F 1 HETATM 11 C C4' SAM . . . J 5 57.432 87.019 54.917 1 146.04 ? C4' SAM 301 F 1 HETATM 12 O O4' SAM . . . J 5 58.732 86.922 55.477 1 145.87 ? O4' SAM 301 F 1 HETATM 13 C C3' SAM . . . J 5 56.835 85.619 54.976 1 145.86 ? C3' SAM 301 F 1 HETATM 14 O O3' SAM . . . J 5 56.236 85.302 53.74 1 145.77 ? O3' SAM 301 F 1 HETATM 15 C C2' SAM . . . J 5 58.006 84.699 55.267 1 145.73 ? C2' SAM 301 F 1 HETATM 16 O O2' SAM . . . J 5 58.126 83.694 54.287 1 145.55 ? O2' SAM 301 F 1 HETATM 17 C C1' SAM . . . J 5 59.227 85.611 55.258 1 145.74 ? C1' SAM 301 F 1 HETATM 18 N N9 SAM . . . J 5 60.243 85.183 56.252 1 145.77 ? N9 SAM 301 F 1 HETATM 19 C C8 SAM . . . J 5 60.016 84.459 57.398 1 145.79 ? C8 SAM 301 F 1 HETATM 20 N N7 SAM . . . J 5 61.192 84.256 58.034 1 145.84 ? N7 SAM 301 F 1 HETATM 21 C C5 SAM . . . J 5 62.179 84.834 57.316 1 145.79 ? C5 SAM 301 F 1 HETATM 22 C C6 SAM . . . J 5 63.557 84.926 57.518 1 145.74 ? C6 SAM 301 F 1 HETATM 23 N N6 SAM . . . J 5 64.118 84.371 58.591 1 145.73 ? N6 SAM 301 F 1 HETATM 24 N N1 SAM . . . J 5 64.341 85.595 56.594 1 145.69 ? N1 SAM 301 F 1 HETATM 25 C C2 SAM . . . J 5 63.754 86.17 55.482 1 145.74 ? C2 SAM 301 F 1 HETATM 26 N N3 SAM . . . J 5 62.385 86.075 55.291 1 145.76 ? N3 SAM 301 F 1 HETATM 27 C C4 SAM . . . J 5 61.6 85.421 56.191 1 145.77 ? C4 SAM 301 F 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 49 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 519 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #