data_9EY1 # _model_server_result.job_id YiCH_iY6q-FjoSMDGpUC_g _model_server_result.datetime_utc '2025-03-31 02:45:42' _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 9ey1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 9EY1 # _exptl.entry_id 9EY1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 384.411 _entity.id 7 _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 9EY1 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9EY1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id J _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 covale ? covale1 F O3' U 7 T U 8 1_555 F P 1MA 8 T 1MA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale2 F O3' 1MA 8 T 1MA 9 1_555 F P G 9 T G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? metalc ? metalc1 A OD2 ASP 521 E ASP 550 1_555 H ZN ZN . E ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc2 A NE2 HIS 522 E HIS 551 1_555 H ZN ZN . E ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc3 A OD2 ASP 637 E ASP 666 1_555 H ZN ZN . E ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc4 A NE2 HIS 695 E HIS 724 1_555 H ZN ZN . E ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? hydrog WATSON-CRICK hydrog1 F N3 U 1 T U 2 1_555 F N1 A 66 T A 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 F O4 U 1 T U 2 1_555 F N6 A 66 T A 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 F N1 A 2 T A 3 1_555 F N3 U 65 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 F N6 A 2 T A 3 1_555 F O4 U 65 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 F N1 A 3 T A 4 1_555 F N3 U 64 T U 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 F N6 A 3 T A 4 1_555 F O4 U 64 T U 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 F N1 A 4 T A 5 1_555 F N3 U 63 T U 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 F N6 A 4 T A 5 1_555 F O4 U 63 T U 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 F N3 U 5 T U 6 1_555 F N1 A 62 T A 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 F O4 U 5 T U 6 1_555 F N6 A 62 T A 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 F N1 A 6 T A 7 1_555 F N3 U 61 T U 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 F N6 A 6 T A 7 1_555 F O4 U 61 T U 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog13 F N3 U 7 T U 8 1_555 F O4 U 12 T U 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 F N1 G 9 T G 10 1_555 F N3 C 21 T C 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 F N2 G 9 T G 10 1_555 F O2 C 21 T C 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 F O6 G 9 T G 10 1_555 F N4 C 21 T C 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 F N3 U 10 T U 11 1_555 F N1 A 20 T A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 F O4 U 10 T U 11 1_555 F N6 A 20 T A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 F N3 U 11 T U 12 1_555 F N1 A 19 T A 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 F O4 U 11 T U 12 1_555 F N6 A 19 T A 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog21 F N3 U 12 T U 13 1_555 F N1 A 18 T A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-C MISPAIR' hydrog22 F N1 A 13 T A 14 1_555 F N4 C 43 T C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 F N3 U 23 T U 24 1_555 F N1 A 39 T A 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 F O4 U 23 T U 24 1_555 F N6 A 39 T A 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 F N3 C 24 T C 25 1_555 F N1 G 38 T G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 F N4 C 24 T C 25 1_555 F O6 G 38 T G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 F O2 C 24 T C 25 1_555 F N2 G 38 T G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 F N1 A 25 T A 26 1_555 F N3 U 37 T U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 F N6 A 25 T A 26 1_555 F O4 U 37 T U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 F N1 G 26 T G 27 1_555 F N3 C 36 T C 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 F N2 G 26 T G 27 1_555 F O2 C 36 T C 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 F O6 G 26 T G 27 1_555 F N4 C 36 T C 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 F N1 A 27 T A 28 1_555 F N3 U 35 T U 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 F N6 A 27 T A 28 1_555 F O4 U 35 T U 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 F N1 A 44 T A 45 1_555 F N3 U 60 T U 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 F N6 A 44 T A 45 1_555 F O4 U 60 T U 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 F N1 G 45 T G 46 1_555 F N3 C 59 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 F N2 G 45 T G 46 1_555 F O2 C 59 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 F O6 G 45 T G 46 1_555 F N4 C 59 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-C MISPAIR' hydrog40 F N1 A 46 T A 47 1_555 F N4 C 58 T C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 F N1 G 47 T G 48 1_555 F N3 C 57 T C 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 F N2 G 47 T G 48 1_555 F O2 C 57 T C 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 F O6 G 47 T G 48 1_555 F N4 C 57 T C 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 F N1 G 48 T G 49 1_555 F N3 C 56 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 F N2 G 48 T G 49 1_555 F O2 C 56 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 F O6 G 48 T G 49 1_555 F N4 C 56 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog47 F N3 C 49 T C 50 1_555 F N6 A 55 T A 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-C MISPAIR' hydrog48 F O2 U 50 T U 51 1_555 F N4 C 53 T C 54 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 . _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 482 n n N HN1 SAH sing 483 n n N HN2 SAH sing 484 n n CA CB SAH sing 485 n n CA C SAH sing 486 n n CA HA SAH sing 487 n n CB CG SAH sing 488 n n CB HB1 SAH sing 489 n n CB HB2 SAH sing 490 n n CG SD SAH sing 491 n n CG HG1 SAH sing 492 n n CG HG2 SAH sing 493 n n SD C5' SAH sing 494 n n C O SAH doub 495 n n C OXT SAH sing 496 n n OXT HXT SAH sing 497 n n C5' C4' SAH sing 498 n n C5' "H5'1" SAH sing 499 n n C5' "H5'2" SAH sing 500 n n C4' O4' SAH sing 501 n n C4' C3' SAH sing 502 n n C4' H4' SAH sing 503 n n O4' C1' SAH sing 504 n n C3' O3' SAH sing 505 n n C3' C2' SAH sing 506 n n C3' H3' SAH sing 507 n n O3' HO3' SAH sing 508 n n C2' O2' SAH sing 509 n n C2' C1' SAH sing 510 n n C2' H2' SAH sing 511 n n O2' HO2' SAH sing 512 n n C1' N9 SAH sing 513 n n C1' H1' SAH sing 514 n n N9 C8 SAH sing 515 n y N9 C4 SAH sing 516 n y C8 N7 SAH doub 517 n y C8 H8 SAH sing 518 n n N7 C5 SAH sing 519 n y C5 C6 SAH sing 520 n y C5 C4 SAH doub 521 n y C6 N6 SAH sing 522 n n C6 N1 SAH doub 523 n y N6 HN61 SAH sing 524 n n N6 HN62 SAH sing 525 n n N1 C2 SAH sing 526 n y C2 N3 SAH doub 527 n y C2 H2 SAH sing 528 n n N3 C4 SAH sing 529 n y # _atom_sites.entry_id 9EY1 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 H 5 ZN E 1 1000 1000 ZN ZN . I 6 GTP T 1 201 1 GTP GTP . J 7 SAH F 1 501 401 SAH SAH . # 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 . . . J 7 218.163 216.78 249.614 1 87.76 ? N SAH 501 F 1 HETATM 2 C CA SAH . . . J 7 218.199 218.061 248.924 1 83.4 ? CA SAH 501 F 1 HETATM 3 C CB SAH . . . J 7 217.106 218.115 247.867 1 89.82 ? CB SAH 501 F 1 HETATM 4 C CG SAH . . . J 7 216.398 216.79 247.599 1 90.37 ? CG SAH 501 F 1 HETATM 5 S SD SAH . . . J 7 214.944 216.986 246.535 1 113 ? SD SAH 501 F 1 HETATM 6 C C SAH . . . J 7 218.057 219.229 249.891 1 89.51 ? C SAH 501 F 1 HETATM 7 O O SAH . . . J 7 218.252 220.385 249.517 1 88.92 ? O SAH 501 F 1 HETATM 8 O OXT SAH . . . J 7 217.744 219.045 251.065 1 93.8 ? OXT SAH 501 F 1 HETATM 9 C C5' SAH . . . J 7 215.774 216.233 245.11 1 78.3 ? C5' SAH 501 F 1 HETATM 10 C C4' SAH . . . J 7 216.031 217.218 243.972 1 81.16 ? C4' SAH 501 F 1 HETATM 11 O O4' SAH . . . J 7 214.817 217.802 243.536 1 81.29 ? O4' SAH 501 F 1 HETATM 12 C C3' SAH . . . J 7 216.95 218.343 244.415 1 83.65 ? C3' SAH 501 F 1 HETATM 13 O O3' SAH . . . J 7 218.156 218.308 243.699 1 90.16 ? O3' SAH 501 F 1 HETATM 14 C C2' SAH . . . J 7 216.225 219.628 244.107 1 84.81 ? C2' SAH 501 F 1 HETATM 15 O O2' SAH . . . J 7 216.997 220.393 243.217 1 90.75 ? O2' SAH 501 F 1 HETATM 16 C C1' SAH . . . J 7 214.938 219.208 243.431 1 80.51 ? C1' SAH 501 F 1 HETATM 17 N N9 SAH . . . J 7 213.799 219.86 244.096 1 78.84 ? N9 SAH 501 F 1 HETATM 18 C C8 SAH . . . J 7 213.025 219.317 245.084 1 78.51 ? C8 SAH 501 F 1 HETATM 19 N N7 SAH . . . J 7 212.088 220.221 245.441 1 82.02 ? N7 SAH 501 F 1 HETATM 20 C C5 SAH . . . J 7 212.259 221.335 244.703 1 77.78 ? C5 SAH 501 F 1 HETATM 21 C C6 SAH . . . J 7 211.581 222.543 244.672 1 79.04 ? C6 SAH 501 F 1 HETATM 22 N N6 SAH . . . J 7 210.551 222.752 245.484 1 83.89 ? N6 SAH 501 F 1 HETATM 23 N N1 SAH . . . J 7 211.985 223.524 243.797 1 84.21 ? N1 SAH 501 F 1 HETATM 24 C C2 SAH . . . J 7 213.056 223.297 242.959 1 85.09 ? C2 SAH 501 F 1 HETATM 25 N N3 SAH . . . J 7 213.724 222.092 242.994 1 81.91 ? N3 SAH 501 F 1 HETATM 26 C C4 SAH . . . J 7 213.33 221.123 243.851 1 78.05 ? C4 SAH 501 F 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 433 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #