data_6SG9 # _model_server_result.job_id DbrJSSLTW_kUmlihh6HEGQ _model_server_result.datetime_utc '2025-03-01 13:49:18' _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 6sg9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"EB","auth_seq_id":1}' # _entry.id 6SG9 # _exptl.entry_id 6SG9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 384.411 _entity.id 57 _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 6SG9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SG9 _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 53-meric _pdbx_struct_assembly.oligomeric_count 53 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB _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 ? _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 ? 57 EB N N ? 57 FB 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 'A-A MISPAIR' hydrog1 G N1 A 391 CA A 391 1_555 G N6 A 522 CA A 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog2 G N3 U 392 CA U 392 1_555 G O6 G 521 CA G 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog3 G O2 U 392 CA U 392 1_555 G N1 G 521 CA G 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 G N3 U 392 CA U 392 1_555 G N1 A 522 CA A 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 G O4 U 392 CA U 392 1_555 G N6 A 522 CA A 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 G N3 U 393 CA U 393 1_555 G N1 A 520 CA A 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 G O4 U 393 CA U 393 1_555 G N6 A 520 CA A 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 G N1 A 394 CA A 394 1_555 G N3 U 519 CA U 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 G N6 A 394 CA A 394 1_555 G O4 U 519 CA U 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog10 G N3 U 395 CA U 395 1_555 G O6 G 518 CA G 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog11 G O2 U 395 CA U 395 1_555 G N1 G 518 CA G 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog12 G N3 U 397 CA U 397 1_555 G O6 G 516 CA G 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog13 G N1 G 449 CA G 449 1_555 G O2 U 477 CA U 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog14 G O6 G 449 CA G 449 1_555 G N3 U 477 CA U 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog15 G N6 A 450 CA A 450 1_555 G N1 A 476 CA A 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 G N3 U 451 CA U 451 1_555 G N1 A 475 CA A 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 G O4 U 451 CA U 451 1_555 G N6 A 475 CA A 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 G N1 A 452 CA A 452 1_555 G N3 U 474 CA U 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 G N6 A 452 CA A 452 1_555 G O4 U 474 CA U 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 G N1 A 453 CA A 453 1_555 G N3 U 473 CA U 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 G N6 A 453 CA A 453 1_555 G O4 U 473 CA U 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog22 G N7 G 454 CA G 454 1_555 G N2 G 472 CA G 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog23 G O6 G 454 CA G 454 1_555 G N1 G 472 CA G 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog24 G N1 G 455 CA G 455 1_555 G O2 U 471 CA U 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog25 G O6 G 455 CA G 455 1_555 G N3 U 471 CA U 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog26 G N1 A 456 CA A 456 1_555 G N1 G 470 CA G 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog27 G N6 A 456 CA A 456 1_555 G O6 G 470 CA G 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 G N3 U 457 CA U 457 1_555 G N1 A 469 CA A 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 G O4 U 457 CA U 457 1_555 G N6 A 469 CA A 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog30 G N3 U 457 CA U 457 1_555 G O6 G 470 CA G 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog31 G O2 U 457 CA U 457 1_555 G N1 G 470 CA G 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 G N3 U 458 CA U 458 1_555 G N1 A 469 CA A 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 G O4 U 458 CA U 458 1_555 G N6 A 469 CA A 469 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 442 n n N HN1 SAH sing 443 n n N HN2 SAH sing 444 n n CA CB SAH sing 445 n n CA C SAH sing 446 n n CA HA SAH sing 447 n n CB CG SAH sing 448 n n CB HB1 SAH sing 449 n n CB HB2 SAH sing 450 n n CG SD SAH sing 451 n n CG HG1 SAH sing 452 n n CG HG2 SAH sing 453 n n SD C5' SAH sing 454 n n C O SAH doub 455 n n C OXT SAH sing 456 n n OXT HXT SAH sing 457 n n C5' C4' SAH sing 458 n n C5' "H5'1" SAH sing 459 n n C5' "H5'2" SAH sing 460 n n C4' O4' SAH sing 461 n n C4' C3' SAH sing 462 n n C4' H4' SAH sing 463 n n O4' C1' SAH sing 464 n n C3' O3' SAH sing 465 n n C3' C2' SAH sing 466 n n C3' H3' SAH sing 467 n n O3' HO3' SAH sing 468 n n C2' O2' SAH sing 469 n n C2' C1' SAH sing 470 n n C2' H2' SAH sing 471 n n O2' HO2' SAH sing 472 n n C1' N9 SAH sing 473 n n C1' H1' SAH sing 474 n n N9 C8 SAH sing 475 n y N9 C4 SAH sing 476 n y C8 N7 SAH doub 477 n y C8 H8 SAH sing 478 n n N7 C5 SAH sing 479 n y C5 C6 SAH sing 480 n y C5 C4 SAH doub 481 n y C6 N6 SAH sing 482 n n C6 N1 SAH doub 483 n y N6 HN61 SAH sing 484 n n N6 HN62 SAH sing 485 n n N1 C2 SAH sing 486 n y C2 N3 SAH doub 487 n y C2 H2 SAH sing 488 n n N3 C4 SAH sing 489 n y # _atom_sites.entry_id 6SG9 _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 BB 54 GTP CgA 1 1 1 GTP GTP . CB 55 MG CgB 1 1 1 MG MG . DB 56 ZN F1A 1 1 1 ZN ZN . EB 57 SAH F1B 1 1 1 SAH SAH . FB 57 SAH FFA 1 1 1 SAH SAH . GB 56 ZN FGA 1 1 1 ZN ZN . HB 56 ZN FLA 1 1 1 ZN ZN . IB 56 ZN FLB 1 1 1 ZN ZN . JB 56 ZN FeA 1 1 1 ZN ZN . KB 58 HOH CgC 1 1 1 HOH HOH . KB 58 HOH CgC 2 2 2 HOH HOH . KB 58 HOH CgC 3 3 3 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 . . . EB 57 326.982 281.207 254.304 1 85.71 0 N SAH 1 F1B 1 HETATM 2 C CA SAH . . . EB 57 325.889 280.886 253.395 1 85.71 0 CA SAH 1 F1B 1 HETATM 3 C CB SAH . . . EB 57 324.568 280.829 254.153 1 85.71 0 CB SAH 1 F1B 1 HETATM 4 C CG SAH . . . EB 57 324.505 281.705 255.397 1 85.71 0 CG SAH 1 F1B 1 HETATM 5 S SD SAH . . . EB 57 323.101 281.271 256.453 1 85.71 0 SD SAH 1 F1B 1 HETATM 6 C C SAH . . . EB 57 325.8 281.888 252.253 1 85.71 0 C SAH 1 F1B 1 HETATM 7 O O SAH . . . EB 57 326.485 282.909 252.252 1 85.71 0 O SAH 1 F1B 1 HETATM 8 O OXT SAH . . . EB 57 325.045 281.696 251.301 1 85.71 -1 OXT SAH 1 F1B 1 HETATM 9 C C5' SAH . . . EB 57 324.232 280.702 257.747 1 85.71 0 C5' SAH 1 F1B 1 HETATM 10 C C4' SAH . . . EB 57 324.194 279.191 257.941 1 85.71 0 C4' SAH 1 F1B 1 HETATM 11 O O4' SAH . . . EB 57 325.113 278.791 258.94 1 85.71 0 O4' SAH 1 F1B 1 HETATM 12 C C3' SAH . . . EB 57 322.825 278.712 258.395 1 85.71 0 C3' SAH 1 F1B 1 HETATM 13 O O3' SAH . . . EB 57 322.187 278.016 257.353 1 85.71 0 O3' SAH 1 F1B 1 HETATM 14 C C2' SAH . . . EB 57 323.092 277.762 259.54 1 85.71 0 C2' SAH 1 F1B 1 HETATM 15 O O2' SAH . . . EB 57 322.535 276.501 259.262 1 85.71 0 O2' SAH 1 F1B 1 HETATM 16 C C1' SAH . . . EB 57 324.605 277.66 259.616 1 85.71 0 C1' SAH 1 F1B 1 HETATM 17 N N9 SAH . . . EB 57 325.022 277.613 261.028 1 85.71 0 N9 SAH 1 F1B 1 HETATM 18 C C8 SAH . . . EB 57 324.426 278.263 262.075 1 85.71 0 C8 SAH 1 F1B 1 HETATM 19 N N7 SAH . . . EB 57 325.094 277.955 263.209 1 85.71 0 N7 SAH 1 F1B 1 HETATM 20 C C5 SAH . . . EB 57 326.105 277.115 262.901 1 85.71 0 C5 SAH 1 F1B 1 HETATM 21 C C6 SAH . . . EB 57 327.081 276.502 263.673 1 85.71 0 C6 SAH 1 F1B 1 HETATM 22 N N6 SAH . . . EB 57 327.129 276.709 264.984 1 85.71 0 N6 SAH 1 F1B 1 HETATM 23 N N1 SAH . . . EB 57 328.005 275.674 263.072 1 85.71 0 N1 SAH 1 F1B 1 HETATM 24 C C2 SAH . . . EB 57 327.949 275.46 261.711 1 85.71 0 C2 SAH 1 F1B 1 HETATM 25 N N3 SAH . . . EB 57 326.98 276.079 260.951 1 85.71 0 N3 SAH 1 F1B 1 HETATM 26 C C4 SAH . . . EB 57 326.069 276.889 261.535 1 85.71 0 C4 SAH 1 F1B 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 137 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #